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template<class IdentificationType > |
static bool | getBestHit (const std::vector< IdentificationType > identifications, bool assume_sorted, PeptideHit &best_hit) |
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template<class IdentificationType > |
static void | filterIdentificationsByThreshold (const IdentificationType &identification, double threshold_fraction, IdentificationType &filtered_identification) |
| filters a ProteinIdentification or PeptideIdentification by only allowing peptides/proteins which reach a score above threshold_fraction * SignificanceThreshold More...
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template<class IdentificationType > |
static void | filterIdentificationsByScore (const IdentificationType &identification, double threshold_score, IdentificationType &filtered_identification) |
| filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_score More...
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template<class IdentificationType > |
static void | filterIdentificationsByBestNHits (const IdentificationType &identification, Size n, IdentificationType &filtered_identification) |
| filters a ProteinIdentification or PeptideIdentification corresponding to the score. More...
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template<class IdentificationType > |
static void | filterIdentificationsByBestNToMHits (const IdentificationType &identification, Size n, Size m, IdentificationType &filtered_identification) |
| filters a ProteinIdentification or PeptideIdentification corresponding to the score. More...
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template<class IdentificationType > |
static void | filterIdentificationsByDecoy (const IdentificationType &identification, IdentificationType &filtered_identification) |
| filters a ProteinIdentification or PeptideIdentification corresponding to their decoy information. More...
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static void | filterIdentificationsByBestHits (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, bool strict=false) |
| filters a PeptideIdentification keeping only the best scoring hits (if strict is set, keeping only the best hit only if it is the only hit with that score) More...
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static bool | filterIdentificationsByMetaValueRange (const PeptideIdentification &identification, const String &key, double low, double high, bool missing=false) |
| Checks whether a meta value of the peptide identification is within a given range. More...
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static void | filterIdentificationsByProteins (const PeptideIdentification &identification, const std::vector< FASTAFile::FASTAEntry > &proteins, PeptideIdentification &filtered_identification, bool no_protein_identifiers=false) |
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static void | filterIdentificationsByProteins (const ProteinIdentification &identification, const std::vector< FASTAFile::FASTAEntry > &proteins, ProteinIdentification &filtered_identification) |
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static void | filterIdentificationsByExclusionPeptides (const PeptideIdentification &identification, const std::set< String > &peptides, bool ignore_modifications, PeptideIdentification &filtered_identification) |
| removes all peptide hits having a sequence equal to a String in peptides . If ignore_modifications is set, the unmodified versions are generated and compared to the set of Strings. More...
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static void | filterIdentificationsByLength (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, Size min_length, Size max_length=UINT_MAX) |
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static void | filterIdentificationsByCharge (const PeptideIdentification &identification, Int charge, PeptideIdentification &filtered_identification) |
| only peptides that have a charge equal to or greater than charge will be kept More...
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static void | filterIdentificationsByVariableModifications (const PeptideIdentification &identification, const std::vector< String > &fixed_modifications, PeptideIdentification &filtered_identification) |
| only peptides having a variable modification will be kept More...
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static void | removeUnreferencedProteinHits (const ProteinIdentification &identification, const std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &filtered_identification) |
| only protein hits in identification which are referenced by a peptide in peptide_identifications are kept More...
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static void | removeUnreferencedPeptideHits (const ProteinIdentification &identification, std::vector< PeptideIdentification > &peptide_identifications, bool delete_unreferenced_peptide_hits=false) |
| only peptide hits in peptide_identifications which are referenced by a protein in identification are kept More...
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static void | filterIdentificationsUnique (const PeptideIdentification &identification, PeptideIdentification &filtered_identification) |
| if a peptide hit occurs more than once per PSM, only one instance is kept More...
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static void | filterIdentificationsByMzError (const PeptideIdentification &identification, double mass_error, bool unit_ppm, PeptideIdentification &filtered_identification) |
| filter identifications by deviation to the theoretical mass More...
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static void | filterIdentificationsByRT (const std::vector< PeptideIdentification > &identifications, double min_rt, double max_rt, std::vector< PeptideIdentification > &filtered_identifications) |
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static void | filterIdentificationsByMZ (const std::vector< PeptideIdentification > &identifications, double min_mz, double max_mz, std::vector< PeptideIdentification > &filtered_identifications) |
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static void | filterIdentificationsByRTPValues (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, double p_value=0.05) |
| Filters the peptide hits according to their predicted RT p-values. More...
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static void | filterIdentificationsByRTFirstDimPValues (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, double p_value=0.05) |
| Filters the peptide hits according to their predicted RT p-values of the first dimension. More...
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template<class PeakT > |
static void | filterIdentificationsByThresholds (MSExperiment< PeakT > &experiment, double peptide_threshold_fraction, double protein_threshold_fraction) |
| filters an MS/MS experiment corresponding to the threshold fractions More...
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template<class PeakT > |
static void | filterIdentificationsByScores (MSExperiment< PeakT > &experiment, double peptide_threshold_score, double protein_threshold_score) |
| filters an MS/MS experiment corresponding to the threshold scores More...
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template<class PeakT > |
static void | filterIdentificationsByBestNHits (MSExperiment< PeakT > &experiment, Size n) |
| filters an MS/MS experiment corresponding to the best n hits for every spectrum More...
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template<class PeakT > |
static void | filterIdentificationsByProteins (MSExperiment< PeakT > &experiment, const std::vector< FASTAFile::FASTAEntry > &proteins) |
| filters an MS/MS experiment corresponding to the given proteins More...
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static bool | updateProteinGroups (const std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits, std::vector< ProteinIdentification::ProteinGroup > &filtered_groups) |
| Update protein groups after protein hits were filtered. More...
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Used to filter identifications by different criteria.
The identifications are filtered by significance thresholds and by sequences. The filtering by significance thresholds looks for the best ProteinIdentification that fulfills the significance threshold criterion. score > significance-threshold * significance_fraction. The filtering by sequences looks for the best ProteinIdentification that is contained in one of the protein sequences.
TODO: fix design of filter functions. There will be an error e.g. if input and output points to the same PeptideIdentification.