OpenMS
PercolatorFeatureSetHelper Class Reference

Percolator feature set and integration helper. More...

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

Classes

struct  lq_PeptideEvidence
 For accession dependent sorting of PeptideEvidences. More...
 
struct  lq_ProteinHit
 For accession dependent sorting of ProteinHits. More...
 

Static Public Member Functions

static void concatMULTISEPeptideIds (std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, const String &search_engine)
 concatMULTISEPeptideIds More...
 
static void mergeMULTISEPeptideIds (std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, const String &search_engine)
 mergeMULTISEPeptideIds More...
 
static void mergeMULTISEProteinIds (std::vector< ProteinIdentification > &all_protein_ids, std::vector< ProteinIdentification > &new_protein_ids)
 mergeMULTISEProteinIds More...
 
static void addMSGFFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
 addMSGFFeatures More...
 
static void addXTANDEMFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
 addXTANDEMFeatures More...
 
static void addCOMETFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
 addCOMETFeatures More...
 
static void addMASCOTFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set)
 addMASCOTFeatures More...
 
static void addMULTISEFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &search_engines_used, StringList &feature_set, bool complete_only=true, bool limits_imputation=false)
 addMULTISEFeatures More...
 
static void addCONCATSEFeatures (std::vector< PeptideIdentification > &peptide_id_list, StringList &search_engines_used, StringList &feature_set)
 addCONCATSEFeatures More...
 
static void checkExtraFeatures (const std::vector< PeptideHit > &psms, StringList &extra_features)
 checkExtraFeatures More...
 
static void addMSFRAGGERFeatures (StringList &extra_features)
 addMSFraggerFeatures More...
 

Static Protected Member Functions

static double rescaleFragmentFeature_ (double featureValue, int NumMatchedMainIons)
 Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator. More...
 
static void assignDeltaScore_ (std::vector< PeptideHit > &hits, const String &score_ref, const String &output_ref)
 helper function for assigning the frequently occurring feature delta score More...
 
static String getScanMergeKey_ (std::vector< PeptideIdentification >::iterator it, std::vector< PeptideIdentification >::iterator start)
 gets the scan identifier to merge by More...
 

Detailed Description

Percolator feature set and integration helper.

This class contains functions to handle (compute, aggregate, integrate) Percolator features. This includes the calculation or extraction of Percolator features depending on the search engine(s) for later use with PercolatorAdapter. It also includes handling the reintegration of the percolator result into the set of Identifications.

Member Function Documentation

◆ addCOMETFeatures()

static void addCOMETFeatures ( std::vector< PeptideIdentification > &  peptide_ids,
StringList feature_set 
)
static

addCOMETFeatures

Parameters
peptide_idsPeptideIdentification vector to create Percolator features in
feature_setregister of added features

Creates and adds Comet specific Percolator features and registers them in feature_set

◆ addCONCATSEFeatures()

static void addCONCATSEFeatures ( std::vector< PeptideIdentification > &  peptide_id_list,
StringList search_engines_used,
StringList feature_set 
)
static

addCONCATSEFeatures

Parameters
peptide_id_listPeptideIdentification vector to create Percolator features in
search_engines_usedthe list of search engines to be considered
feature_setregister of added features

Adds multiple search engine specific Percolator features and registers them in feature_set

◆ addMASCOTFeatures()

static void addMASCOTFeatures ( std::vector< PeptideIdentification > &  peptide_ids,
StringList feature_set 
)
static

addMASCOTFeatures

Parameters
peptide_idsPeptideIdentification vector to create Percolator features in
feature_setregister of added features

Creates and adds Mascot specific Percolator features and registers them in feature_set

◆ addMSFRAGGERFeatures()

static void addMSFRAGGERFeatures ( StringList extra_features)
static

addMSFraggerFeatures

Parameters
extra_featuresregister of added features

Registers the MSFragger specific Percolator features in extra_features.

◆ addMSGFFeatures()

static void addMSGFFeatures ( std::vector< PeptideIdentification > &  peptide_ids,
StringList feature_set 
)
static

addMSGFFeatures

Parameters
peptide_idsPeptideIdentification vector to create Percolator features in
feature_setregister of added features

Creates and adds MSGF+ specific Percolator features and registers them in feature_set. MSGF+ should be run with the addFeatures flag enabled.

◆ addMULTISEFeatures()

static void addMULTISEFeatures ( std::vector< PeptideIdentification > &  peptide_ids,
StringList search_engines_used,
StringList feature_set,
bool  complete_only = true,
bool  limits_imputation = false 
)
static

addMULTISEFeatures

Parameters
peptide_idsPeptideIdentification vector to create Percolator features in
search_engines_usedthe list of search engines to be considered
feature_setregister of added features
complete_onlywill only add features for PeptideIdentifications where all given search engines identified something
limits_imputationAdds multiple search engine specific Percolator features and registers them in feature_set

◆ addXTANDEMFeatures()

static void addXTANDEMFeatures ( std::vector< PeptideIdentification > &  peptide_ids,
StringList feature_set 
)
static

addXTANDEMFeatures

Parameters
peptide_idsPeptideIdentification vector to create Percolator features in
feature_setregister of added features

Creates and adds X!Tandem specific Percolator features and registers them in feature_set

◆ assignDeltaScore_()

static void assignDeltaScore_ ( std::vector< PeptideHit > &  hits,
const String score_ref,
const String output_ref 
)
staticprotected

helper function for assigning the frequently occurring feature delta score

◆ checkExtraFeatures()

static void checkExtraFeatures ( const std::vector< PeptideHit > &  psms,
StringList extra_features 
)
static

checkExtraFeatures

Parameters
psmsthe vector of PeptideHit to be checked
extra_featuresthe list of requested extra features

checks and removes requested extra Percolator features that are actually unavailable (to compute)

◆ concatMULTISEPeptideIds()

static void concatMULTISEPeptideIds ( std::vector< PeptideIdentification > &  all_peptide_ids,
std::vector< PeptideIdentification > &  new_peptide_ids,
const String search_engine 
)
static

concatMULTISEPeptideIds

Parameters
all_peptide_idsPeptideIdentification vector to append to
new_peptide_idsPeptideIdentification vector to be appended
search_enginesearch engine to depend on for feature creation

Appends a vector of PeptideIdentification to another and prepares Percolator features in MetaInfo (With the respective key "CONCAT:" + search_engine).

◆ getScanMergeKey_()

static String getScanMergeKey_ ( std::vector< PeptideIdentification >::iterator  it,
std::vector< PeptideIdentification >::iterator  start 
)
staticprotected

gets the scan identifier to merge by

◆ mergeMULTISEPeptideIds()

static void mergeMULTISEPeptideIds ( std::vector< PeptideIdentification > &  all_peptide_ids,
std::vector< PeptideIdentification > &  new_peptide_ids,
const String search_engine 
)
static

mergeMULTISEPeptideIds

Parameters
all_peptide_idsPeptideIdentification vector to be merged into
new_peptide_idsPeptideIdentification vector to merge
search_enginesearch engine to create features from their scores

Merges a vector of PeptideIdentification into another and prepares the merged MetaInfo and scores for collection in addMULTISEFeatures for feature registration.

◆ mergeMULTISEProteinIds()

static void mergeMULTISEProteinIds ( std::vector< ProteinIdentification > &  all_protein_ids,
std::vector< ProteinIdentification > &  new_protein_ids 
)
static

mergeMULTISEProteinIds

Parameters
all_protein_idsProteinIdentification vector to be merged into
new_protein_idsProteinIdentification vector to merge

Concatenates SearchParameter of multiple search engine runs and merges PeptideEvidences, collects used search engines in MetaInfo for collection in addMULTISEFeatures for feature registration.

◆ rescaleFragmentFeature_()

static double rescaleFragmentFeature_ ( double  featureValue,
int  NumMatchedMainIons 
)
staticprotected

Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator.