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

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.
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
static String	getScanMergeKey_ (PeptideIdentificationList::iterator it, PeptideIdentificationList::iterator start)
	gets the scan identifier to merge by

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 ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addCOMETFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register of added features

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

addCONCATSEFeatures()

static void addCONCATSEFeatures ( PeptideIdentificationList &  peptide_id_list, StringList &  search_engines_used, StringList &  feature_set  )

static

addCONCATSEFeatures

Parameters

[in]	peptide_id_list	PeptideIdentification vector to create Percolator features in
[in]	search_engines_used	the list of search engines to be considered
[in]	feature_set	register of added features

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

addMASCOTFeatures()

static void addMASCOTFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addMASCOTFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register 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

[in]

extra_features

register of added features

Registers the MSFragger specific Percolator features in extra_features.

addMSGFFeatures()

static void addMSGFFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addMSGFFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register 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 ( PeptideIdentificationList &  peptide_ids, StringList &  search_engines_used, StringList &  feature_set, bool  complete_only = true, bool  limits_imputation = false  )

static

addMULTISEFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	search_engines_used	the list of search engines to be considered
[in]	feature_set	register of added features
[in]	complete_only	will only add features for PeptideIdentifications where all given search engines identified something
[in]	limits_imputation

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

addXTANDEMFeatures()

static void addXTANDEMFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addXTANDEMFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register 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

[in]	psms	the vector of PeptideHit to be checked
[in]	extra_features	the list of requested extra features

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

concatMULTISEPeptideIds()

static void concatMULTISEPeptideIds ( PeptideIdentificationList &  all_peptide_ids, PeptideIdentificationList &  new_peptide_ids, const String &  search_engine  )

static

concatMULTISEPeptideIds

Parameters

[in]	all_peptide_ids	PeptideIdentification vector to append to
[in]	new_peptide_ids	PeptideIdentification vector to be appended
[in]	search_engine	search 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_ ( PeptideIdentificationList::iterator  it, PeptideIdentificationList::iterator  start  )

staticprotected

gets the scan identifier to merge by

mergeMULTISEPeptideIds()

static void mergeMULTISEPeptideIds ( PeptideIdentificationList &  all_peptide_ids, PeptideIdentificationList &  new_peptide_ids, const String &  search_engine  )

static

mergeMULTISEPeptideIds

Parameters

[in]	all_peptide_ids	PeptideIdentification vector to be merged into
[in]	new_peptide_ids	PeptideIdentification vector to merge
[in]	search_engine	search 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

[in]	all_protein_ids	ProteinIdentification vector to be merged into
[in]	new_protein_ids	ProteinIdentification 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.