NuXLProteinReport Struct Reference

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#include <OpenNuXL/include/NuXLReport.h>

Static Public Member Functions
static void	annotateProteinModificationForTopHits (std::vector< ProteinIdentification > &prot_ids, const PeptideIdentificationList &peps, TextFile &tsv_file)
static std::map< char, double >	getCrossLinkEfficiency (const PeptideIdentificationList &peps)
static std::map< std::string, size_t >	countAdducts (const PeptideIdentificationList &peps)
static void	mapAccessionToTDProteins (ProteinIdentification &prot_id, std::map< std::string, ProteinHit * > &acc2protein_targets, std::map< std::string, ProteinHit * > &acc2protein_decoys)

Detailed Description

protein report

Member Function Documentation

annotateProteinModificationForTopHits()

void annotateProteinModificationForTopHits ( std::vector< ProteinIdentification > &  prot_ids, const PeptideIdentificationList &  peps, TextFile &  tsv_file  )

static

References ProteinIdentification::ProteinGroup::accessions, TextFile::addLine(), ListUtils::concatenate(), NuXLProteinReport::countAdducts(), NuXLProteinReport::getCrossLinkEfficiency(), ProteinIdentification::getHits(), ProteinIdentification::getIndistinguishableProteins(), PeptideHit::getPeptideEvidences(), OpenMS::getProteinReportEntries(), PeptideHit::getSequence(), NuXLProteinReport::mapAccessionToTDProteins(), OpenMS::printXLRegionDetails(), OpenMS::printXLSiteDetails(), OpenMS::StringUtils::toStr(), and AASequence::toUnmodifiedString().

Referenced by NuXLFDR::calculatePeptideAndXLQValueAndFilterAtPSMLevel().

countAdducts()

map< std::string, size_t > countAdducts ( const PeptideIdentificationList &  peps )

static

References MetaInfoInterface::getMetaValue().

Referenced by NuXLProteinReport::annotateProteinModificationForTopHits().

getCrossLinkEfficiency()

map< char, double > getCrossLinkEfficiency ( const PeptideIdentificationList &  peps )

static

References MetaInfoInterface::getMetaValue(), PeptideHit::getSequence(), PeptideHit::isDecoy(), and AASequence::toUnmodifiedString().

Referenced by NuXLProteinReport::annotateProteinModificationForTopHits().

mapAccessionToTDProteins()

void mapAccessionToTDProteins ( ProteinIdentification &  prot_id, std::map< std::string, ProteinHit * > &  acc2protein_targets, std::map< std::string, ProteinHit * > &  acc2protein_decoys  )

static

References ProteinIdentification::getHits().

Referenced by NuXLProteinReport::annotateProteinModificationForTopHits().