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NCBI C++ ToolKit: Seq-id Management

Definition at line 317 of file Seq_id.hpp.

Compare return values.

some problem

different SeqId types-can't compare

SeqIds compared, but are different.

SeqIds compared, are equivalent

Definition at line 579 of file Seq_id.hpp.

For IdentifyAccession (below)

Definition at line 220 of file Seq_id.hpp.

Definition at line 736 of file Seq_id.hpp.

Flags specifying special treatment for certain types of Seq-ids in ComposeOSLT().

See also

ComposeOSLT

Add "ACC.VER(=1)" for a 2ndary id.

Definition at line 821 of file Seq_id.hpp.

Definition at line 108 of file seq_id_mapper.hpp.

Error types that CSeq_id can generate.

Unrecognized Seq-id type.

Contents not parsable as expected.

Definition at line 1006 of file Seq_id.hpp.

Definition at line 107 of file Seq_id.hpp.

Tag for method variants that would otherwise be ambiguous.

Definition at line 116 of file Seq_id.hpp.

Allow prefixes to contain underscores.

Definition at line 898 of file Seq_id.hpp.

Show the version.

For type general, use the database name as the tag and the (text or numeric) key as the content.

Trim trailing FASTA delimeters.

Upper case label, with special encoding for PDB chain-ids.

default options - always show the version

Definition at line 614 of file Seq_id.hpp.

return the label for a given string

FASTA-style type, or database in GeneralDbIsContent mode.

Untagged human-readable accession or the like.

Type and content, delimited by a vertical bar.

Tagged ID in NCBI's traditional FASTA style.

Like eFasta, but without any tag.

default is to show type + content

Definition at line 603 of file Seq_id.hpp.

Numerical quality ranking; lower is better.

(Text)Score, aka WorstRank, corresponds to the C Toolkit's SeqIdFindWorst, which favors textual accessions, whereas BestRank corresponds to the C Toolkit's SeqIdFindBest and favors GIs. In addition, there is a pair of methods corresponding to the C Toolkit's GetOrderBySeqId, used when generating FASTA deflines.

All rankings give a slight bonus to accessions that carry versions.

Definition at line 732 of file Seq_id.hpp.

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions, either from unsupported syntax or because it is only possible to accept a single ID anyway (in the string-based constructor and corresponding Set() variant).

Try to ID raw non-numeric accessions.

Treat raw numbers as GIs, not local IDs.

Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validation.

Also, accept PDB accessions with chains but no delimiters.

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style IDs (or ID sets).

Don't bother checking for a tag.

For IdentifyAccession, don't warn about falling back to a different specific type because broad identification is sufficient.

(Automatically on when calling IdentifyAccession internally.)

By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local accessions.

(The string-based constructor and Set method have a stricter default: fParse_AnyRaw.)

Definition at line 75 of file Seq_id.hpp.

SNP annotation scale limits.

Definition at line 849 of file Seq_id.hpp.

Get a string representation of the sequence IDs of a given bioseq.

This function produces strings in a number of possible formats.

Definition at line 661 of file Seq_id.hpp.

Definition at line 862 of file Seq_id.hpp.

Definition at line 3196 of file Seq_id.cpp.

References flags, CSeq_id::fRequireAccessions, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::IsGeneral(), and kMax_Int.

Referenced by CSeq_id::BestRankScore(), CSeq_id::BlastScore(), CSeq_id::FastaAAScore(), CSeq_id::FastaNAScore(), PSGRank(), CSeq_id::StrictAdjustScore(), and CSeq_id::TextScore().

Definition at line 2266 of file Seq_id.cpp.

References str(), and CSeq_id::WriteAsFasta().

Referenced by CGapAnalysis::AddBioseqGaps(), AddChromosomeNoLocation(), CGBProjectHelper::AddProjectItemsFromRID(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CTaxIdSet::AddTaxId(), BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::BuildUserUrl(), CAlnMapPrinter::CAlnMapPrinter(), CAlnMix::ChooseSeqId(), CBlastBioseqMaker::CreateBioseqFromId(), CSeq_align::CreateDensegFromDisc(), CSeq_align::CreateDensegFromStdseg(), CVcfTrackDataFactory::CreateTrackData(), CAlignResultsSet::DropQuery(), CRawWiggleRecord::Dump(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractSeqId(), CFtableFormatter::FormatFeatHeader(), CScore_FrameShifts::Get(), CScore_SequenceLength::Get(), CScore_SymmetricOverlap::Get(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), CScore_GeneID::Get(), CScore_RibosomalSlippage::Get(), CScore_SegPct::Get(), CScore_Entropy::Get(), CObjFingerprint::GetAlignSignature(), CAlnVec::GetBioseqHandle(), GetBlastSeqIdString(), CObjFingerprint::GetComponentSignature(), CObjFingerprint::GetFeatSignature(), CObjFingerprint::GetGraphSignature(), CObjFingerprint::GetHistogramSignature(), GetIdStartStopStrandStr(), CSeq_id::GetLabel(), CGuiObjectInfoSeq_align::GetLinks(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CObjFingerprint::GetRsiteSignature(), CShowBlastDefline::GetSeqIdListString(), IRepeatRegion::GetSeqIdString(), CObjFingerprint::GetSeqLocSignature(), CAlnMixSeq::GetSeqString(), CWriteUtil::GetStringId(), CObjFingerprint::GetVcfVariantSignature(), CAlignFormatUtil::HspListToHitMap(), IdRefLess(), CBlastBioseqMaker::IsProtein(), CSeqUtils::isTopLevel(), CMergeTreeThread::Main(), MakeEmptyResults(), MakeKey(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CAnnotObjectType_Less::operator()(), CAlignSort::SAlignExtractor::operator()(), hash_seqid::operator()(), CSeqIdBioseqHandleComp< TSeqIdPtr >::operator()(), CFastaReader::ParseDefLine(), CFastaReader::PostWarning(), CTabularFormatter_Indels::Print(), CTabularFormatter_StartCodonChanges::Print(), PrintBestSeqId(), CReadBlastApp::processFeature(), CAlignResultsSet::QueryExists(), CFeature_table_reader::ReadSequinFeatureTables(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), RemasterWithStructure(), CSeedTopApp::Run(), CVectorScreen::Run(), CWalkAsnCacheApplication::Run(), CBlastDemoApplication::Run(), CTestBlastp_All::RunTest(), s_BlastXMLAddIteration(), s_CompareProtProdToTrans(), s_DeflineCompare(), s_GetBestIDForURL(), s_GetCountIdentityMismatch(), s_GetLabel(), s_GetSequenceId(), s_GetSplicedSegIdentityMismatch(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), s_SeqAlignToXMLHit(), s_SetBlastXMLSearch(), s_TestFastaRoundTrip(), s_ValidateExon(), SeqDB_SimplifySeqid(), CSeqDBImpl::SeqidToOids(), CSeqDBVol::SeqidToOids(), CIgBlastTabularInfo::SetAirrFormatData(), CPhyTreeCalc::SetQuery(), CHookBioseq__Seq_id::SkipClassMember(), CUnorderedSplitter::SplitId(), CSeqDBIsam::StringToOids(), SeqSwapper::swapSequences(), sx_MakeUniqueId(), TestOneOtherAcc(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CValidError_bioseq::ValidateIDSetAgainstDb(), CVdbFastaExtractor::Write(), WriteBlastSeqidlistFile(), CAlnWriter::WriteSparseAlign(), CWriteDB_IsamIndex::x_AddLocal(), CWriteDB_IsamIndex::x_AddPatent(), CWriteDB_IsamIndex::x_AddPdb(), CWriteDB_IsamIndex::x_AddStringIds(), CHugeFileDemoApp::x_AddUserObjects(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), CSourceModParser::CBadModError::x_CalculateErrorString(), CSourceModParser::CUnkModError::x_CalculateErrorString(), CFeatureGenerator::SImplementation::x_CheckInconsistentDbxrefs(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CDeflineProcess::x_FastaSeqIdWrite(), CShowBlastDefline::x_FillDeflineAndId(), CIgBlast::x_FillJDomain(), CUnorderedSplitter::x_FixAlignment(), CSeqVectorProcess::x_FsaSeqIdWrite(), CSeqMap_CI::x_GetBioseq(), CBlastDbDataLoader::x_GetOid(), CColumnarVCFLoaderManager::x_GetRefSeqs(), CPsiBlastInputData::x_GetSubjectSequence(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CWriteDB_LMDB::x_InsertEntry(), CAlignGlyph::x_IsSRA(), CAppHitFilter::x_LoadConstraints(), CSplign::x_LoadSequence(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CRNAValidator::x_ReportRNATranslationProblems(), CBuildDatabase::x_ResolveFromSource(), CBlastFormat::x_ReverseQuery(), CFeatureItem::x_SeqIdWriteForTable(), CBlastDBExtractor::x_SetGi2SeqIdMap(), CBlastTabularInfo::x_SetQueryCovSubject(), CBlastTabularInfo::x_SetQueryCovUniqSubject(), CVariationNormalization_base< T >::x_Shift(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CSequenceDataTester::x_TestSingleSequence_Remote(), CTitleProcess::x_TitleSeqIdWrite(), CValidError_bioseq::x_TranscriptIDsMatch(), CVectorTrimPanel::x_TrimSelected(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().

Optimized implementation of CSerialObject::Assign, which is not so efficient.

Reimplemented from CSerialObject.

Definition at line 318 of file Seq_id.cpp.

References CSerialObject::Assign(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSerialObject::GetThisTypeInfo(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), CSeq_id_Base::Reset(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGibbmt(), CSeq_id_Base::SetGibbsq(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetLocal(), CSeq_id_Base::SetNamed_annot_track(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), CSeq_id_Base::SetTpg(), CSeq_id_Base::Which(), and x_Assign().

Referenced by CAlnMixSequences::Add(), CBioseq_Info::AddId(), CCleanup::AddProtein(), AddSentinelRNASeq(), AddSpanningSentinelFeat(), CVDBBlastUtil::AddSubjectsToScope(), AdjustMappedStop(), CTable2AsnContext::ApplyAccession(), CNWFormatter::AsDenseSeg(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CSeq_loc::Assign(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CContigAssembly::BandedGlobalAlignment(), Blast_FindWindowMaskerLoc(), BOOST_AUTO_TEST_CASE(), CSeqAnnotFromFasta::BuildMasterSlaveSeqAlign(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CCompareSeqRegions::CCompareSeqRegions(), CGtfLocationRecord::CGtfLocationRecord(), CLocMapper_Default::CLocMapper_Default(), CFixForTransSplicing::CombineFeatures(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CopyGiSeqId(), CopyPdbSeqId(), CpSeqId(), CBlastBioseqMaker::CreateBioseqFromId(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CreateSparseAlign(), CRemoveSeqId::CRemoveSeqId(), CValidError_feat::DoesCDSHaveShortIntrons(), CCmdAddCDS::Execute(), CDense_seg::ExtractRows(), SeqTreeAsnizer::fillAsnSeqTreeNode(), CdBlaster::FillOutSeqLoc(), CSimpleB2SWrapper::FillOutSeqLoc(), sequpd::FixCollidingIDs_Bioseq(), FixMixLoc(), fta_get_acc_minmax_strand(), CFlatFileGenerator::Generate(), get_bioseq(), GetAccAndVersion(), CCDDClientPool::GetBlobBySeq_id(), CCDDClientPool::GetBlobBySeq_ids(), CSeqUtils::GetCdsMappingInfoFromRna(), CApplyRNAITSDlg::GetCommand(), CFarPointerSeq::GetCommand(), CFuseFeaturesDlg::GetCommand(), CLocationListCtrl::GetIdFromForm(), CBioseq::GetLabel(), GetLastCodonLoc(), CFeatureGenePanel::GetLocationForGene(), GetLowHighFromSeqLoc(), CSeqUtils::GetMappingInfoFromLocation(), CTableDataBioTreeContainer::GetObjectValue(), CCleanup::GetProteinLocationFromNucleotideLocation(), CSelectionEvent::GetRangeSelectionAsLocs(), CProjectTreeView::GetSearchLoc(), GetSeqLocFromString(), CSeq_align::GetSeqRange(), CFeatGlyph::GetTooltip(), GetWGSMasterSeq_id(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CNSeq::Init(), CAlignCollapser::InitContig(), InitSplicedsegFromPairwiseAln(), IsInScope(), CFastaObjectLoader::LoadFromStream(), MakeCompartment(), MakeEmptyResults(), MakeMaskingBioseq(), CAliToSeq_align::MakeSeq_align(), CAlignModel::MakeSeqAlign(), CGtfLocationMerger::MergeLocationForGene(), CBioseqEditor::OnCreateBiosourceFeat(), CBioseqEditor::OnCreateFeature(), SCigarAlignment::operator()(), CGtfLocationRecord::operator=(), PatchTargetSequence(), CBlastFormat::PrintPhiResult(), CHgvsReader::ReadSeqAnnot(), RenameGeneratedBioseqs(), CTableDataVcfJob::Run(), CLocalFinderApp::Run(), CXcompareAnnotsApplication::Run(), CTestBMApp::Run(), s_AddCDS(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_AssignSeq_id(), s_CodonVariation(), s_ConvertWholeToInt(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_CreateMappingInfo(), s_DoNWalign(), s_FixCollidingIDs_Annot(), s_GetCDSLoc(), s_GetQuerySequence(), s_Load_Seq_point(), s_MakeSliceMapper(), s_RemapFeatureSeqIds(), s_ReplaceGIs(), s_ReplaceLocalId(), CWeightedIdentityScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CProSplign::CImplementation::SeekStartStop(), CSeqDBImpl::SeqidToOids(), CAutoDefExonListClause::SeqLocIntersect(), CSeq_loc::SetId(), CCDSTranslationPanel::SetProtein(), SimpleSeqLocFromBioseq(), SModelData::SModelData(), CFeatGapInfo::Split(), CFeatureGenerator::SImplementation::StitchSmallHoles(), BlockModel::toSeqAlign(), MarkupTrustedGenes::transform_align(), ProjectCDS::transform_align(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), TranslateCDSCommand(), CFeatGapInfo::Trim(), CScore_Overlap::UpdateState(), CValidError_bioseq::ValidateIDSetAgainstDb(), CAlnWriter::WriteAlignSplicedSeg(), CGC_Assembly_Parser::x_AddBioseq(), CIdMapperGCAssembly::x_AddUnversionedMapping(), CSeq_loc_Mapper::x_AddVirtualBioseq(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CProSplignJob::x_CreateProjectItems(), CBamLoadingJob::x_CreateProjectItems(), CVcfLoadingJob::x_CreateSeqIdProjectItem(), CVcfFeatureJob::x_Execute(), CSequenceUpdater::x_FixIDInNewEntry(), CCommonComponentScorer::x_GetCompList(), CCommonComponentScorer::x_GetDeltaExtCompList(), CAutoDef::x_GetFeatureClauses(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), CEditingBtnsPanel::x_GetSelectedLocations(), CCommonComponentScorer::x_GetSeqHistCompList(), CCdregionValidator::x_GetShortIntrons(), CCommonComponentScorer::x_GetUserCompList(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CBioseqIndex::x_InitFeats(), CSplign::x_LoadSequence(), CTreeAlignMerger::x_MakeSeqAlign(), CSequenceUpdater::x_PrepareNewEntry(), CGenBankLoadOptionPanel::x_ProccessText(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CGencollIdMapper::x_RecursiveSeqFix(), CGencollIdMapper::x_RemoveHiddenAccessions(), CSequenceUpdater::x_RemoveNewIDInFeature(), CGFFReader::x_ResolveNewID(), CSplign::x_RunOnCompartment(), CSequenceSearchJob::x_SearchSequence(), CFeatureGenerator::SImplementation::x_SetComment(), CBioseqContext::x_SetId(), CCDSTranslationPanel::x_SetLocationForProtein(), CGencollIdMapper::x_StripPseudoSeq(), CFeatTrim::x_TrimLocation(), CVectorTrimPanel::x_TrimSelected(), CAdjustForConsensusSpliceSite::x_UpdateMixLocations(), CRNAValidator::x_ValidateTrnaType(), CFeatureTableReader::xAddProteinToSeqEntry(), and xgbint_ver().

Definition at line 220 of file seq_id_handle.cpp.

References CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, and CSeq_id::WriteAsFasta().

Referenced by CAlnSeqId::AsString(), BOOST_AUTO_TEST_CASE(), CCSRAFileInfo::CCSRAFileInfo(), CAlignCompare::SAlignment::CompareGroup(), CBlobSplitterImpl::CopySkeleton(), CFeatureGenerator::CreateMicroIntrons(), CLDS2_ObjectParser::EndBlob(), CFeatTableEdit::GenerateLocusTags(), GetAccVer(), CLDS2_Database::GetAnnotBlobs(), CSplitCacheApp::GetBioseqHandle(), CLDS2_Database::GetBioseqId(), CAsnCache_DataLoader::GetBlobById(), CHugeAsnDataLoader::GetBlobId(), CAgpFastaComparator::CTmpSeqVecStorage::GetFileName(), CFeatGlyph::GetHTMLActiveAreas(), GetLabel(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), CGBDataLoader_Native::GetNamedAnnotAccessions(), CPSGDataLoader_Impl::GetRecordsOnce(), CWGSDataLoader_Impl::GetRecordsOnce(), CIdMapperApp::GetTargetString(), idAlpha(), CPubseqReader::LoadSeq_idInfo(), CReadDispatcher::LogStat(), CIdMapper::MapErrorString(), CTreeAlignMerger::Merge_Dist(), SBlobInserter::operator()(), PConvertToString< CSeq_id_Handle >::operator()(), CFastaReader::ParseDefLine(), PatchTargetSequence(), CSplitCacheApp::ProcessBlob(), CSplitCacheApp::ProcessSeqId(), ReplaceWellknownSeqs(), CGBDataLoader_Native::ResolveConflict(), CAgpFastaComparator::Run(), CPrimeCacheApplication::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), s_IdxGetBestIdString(), CCacheWriter::SaveSeq_idAccVer(), CBAMBlobId::ToString(), CScope_Impl::x_AddSynonym(), CSeq_id_Resolver__LRG::x_Create(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CAsnSubCacheCreateApplication::x_FetchMissingBlobs(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CScore_BlastRatio::x_GetPerfectScore(), CGBDataLoader_Native::x_GetRecords(), variation::CHgvsParser::x_header(), CBioseqIndex::x_InitFeats(), CLDS2_Database::x_InitGetBioseqsSql(), CSeq_loc_Mapper_Base::x_MapNextRange(), CPrimeCacheApplication::x_Process_Fasta(), CPrimeCacheApplication::x_Process_Ids(), CAlignFilter::x_Query_Op(), CScope_Impl::x_ReportNewDataConflict(), CHugeFileDemoApp::x_TestRW1848(), and CFeatTableEdit::xGenerateMissingGeneForFeats().

Definition at line 3081 of file Seq_id.cpp.

References CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id::kMaxScore, CSeq_id::PreferAccessionOverGi(), and CSeq_id_Base::Which().

Referenced by CSeq_id::BestRankScore(), CDiscrepancyContext::BuildSeqSummary(), pub_report::GetBestId(), and CSeq_id::StrictBestRankScore().

Definition at line 3158 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id::kMaxScore, CSeq_id::PreferAccessionOverGi(), and CSeq_id_Base::Which().

Referenced by CSeq_id::BlastScore(), and CSeq_id::StrictBlastScore().

Definition at line 3127 of file Seq_id.cpp.

References CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id::kMaxScore, CSeq_id::PreferAccessionOverGi(), and CSeq_id_Base::Which().

Referenced by CSeq_id::FastaAAScore(), and CSeq_id::StrictFastaAAScore().

Definition at line 3097 of file Seq_id.cpp.

References CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id::kMaxScore, CSeq_id::PreferAccessionOverGi(), and CSeq_id_Base::Which().

Referenced by CSeq_id::FastaNAScore(), and CSeq_id::StrictFastaNAScore().

Definition at line 3040 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::kMaxScore, CSeq_id::PreferAccessionOverGi(), and CSeq_id_Base::Which().

Referenced by CSeq_id::BaseWorstRankScore(), CSeq_id::StrictTextScore(), and CSeq_id::TextScore().

Definition at line 776 of file Seq_id.hpp.

References kMax_Int.

Referenced by CSourceModParser::ApplyAllMods(), BestRank_SeqIdHandle(), BOOST_AUTO_TEST_CASE(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), ChangeSeqId(), CAlnMix::ChooseSeqId(), Convert_Bioseq_Seq_id(), Convert_Seq_entry_Seq_id(), Convert_Seq_entry_Seq_loc(), Convert_SeqSubmit_Seq_id(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMembershipInteger(), CSeqFastaReader::GenerateID(), CAlnReader::GenerateID(), CTextAlnReader::GenerateID(), GetBestBioseqLabel(), CSequenceUpdater::GetRevCompReport(), GetSequenceLengthAndId(), CFastaReader::ParseDefLine(), CFastaReader::PostProcessIDs(), CSeqFastaReader::PostProcessIDs(), s_ConvertBioseqs2TSeqLocVector(), s_ConvertSubjects2TSeqLocVector(), s_ExtractQueryIdsFromBioseqSet(), s_FixBioseqDeltas(), s_UseFastaReaderDeflines(), SeqDB_SimplifyAccession(), CBlastDB_FastaFormatter::Write(), CBlastFormat::x_CreateSubjectBioseq(), CImportFeatTable::x_DoImportCDS(), CRemoteBlast::x_ExtractQueryIds(), CBlastFastaInputSource::x_FastaToSeqLoc(), CAutoDef::x_GetFeatureClauses(), CFeatModApply::x_GetWholeSeqLoc(), CBlastKmerResults::x_InitScoreVec(), CCompareWithBiosample::x_LoadData(), and CSequenceUpdater::x_RemoveNewIDInFeature().

Perform rudimentary validation on potential local IDs, whose contents should not exceed fifty characters and are limited to ASCII characters excluding >[]|"".

Definition at line 2584 of file Seq_id.cpp.

References CTempString::begin(), CTempString::end(), CSeq_id::fEmptyId, CSeq_id::fExceedsMaxLength, CSeq_id::fInvalidChar, CSeq_id::fNoError, NStr::IsBlank(), CSeq_id::kMaxLocalIDLength, and CTempString::length().

Referenced by CSeq_id::IsValidLocalID(), CFastaIdValidate::IsValidLocalString(), and CSeqIdValidate::operator()().

Compare() - more general.

Definition at line 411 of file Seq_id.cpp.

References CanCmpAcc(), NStr::CompareNocase(), CSeq_id_Base::e_Ddbj, CSeq_id::e_DIFF, CSeq_id_Base::e_Embl, CSeq_id::e_error, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id::e_NO, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::e_YES, CDbtag_Base::GetDb(), CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CGiimport_id_Base::GetId(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSeq_id::GetTextseq_Id(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), CObject_id::Match(), CPatent_seq_id::Match(), CPDB_seq_id::Match(), CSeq_id::Match(), CTextseq_id::Match(), and CSeq_id_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdregionFeatBC(), CheckForeignLoc(), fta_seqid_same(), GetAlignColl(), GetLocalGeneByLocus(), GetLowHighFromSeqLoc(), CRemoteBlast::GetMasks(), CRemoteBlast::GetSeqAlignSets(), CSeq_align::GetSeqRange(), CPacked_seqint::GetStrand(), CSeq_loc_mix::GetStrand(), CSeq_id::Match(), OkToAdjustLoc(), CNewCleanup_imp::RnaFeatBC(), s_IdsMatch(), s_MatchSeqIds(), s_SplitAlignVectorBySubjects(), s_TestFastaRoundTrip(), CStructuredCommentsReader::SeqIdMatchesCommentId(), and CBlastDbDataLoader::x_GetOid().

Definition at line 486 of file Seq_id.cpp.

References CDbtag::Compare(), CObject_id::Compare(), CPatent_seq_id::Compare(), CPDB_seq_id::Compare(), CTextseq_id::Compare(), CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CGiimport_id_Base::GetId(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id::GetTextseq_Id(), and CSeq_id_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), Compare(), seqsubmit_split::SIdCompare::compare_seq(), CSeq_id_Info::CompareOrdered(), SAlignSortByQueryId::operator()(), SCompareOrdered< TSeqIdPtr >::operator()(), CSeq_id::operator<(), CSourceModParser::SMod::operator<(), s_LocSortCompare(), s_SeqIdCompare(), s_SeqIdMatch(), CSeq_loc::x_CompareSingleId(), and CMultiAligner::x_SetDomainHits().

JIRA ID-5188 : Compose OSLT string for the primary id, as well as OSLT strings for the secondary ids, if any.

NB: given a single Seq-id, it is not always possible to determine whether it should be treated as primary or secondary if it were part of a list of Seq-ids in a Bioseq. In that case, this function returns it as primary, and the final judgement needs to be made by the caller.

Parameters

secondary_ids OSLT strings for the secondary ids parse_flags Flags specifying special treatment for certain types of Seq-ids.

Returns

OSLT string for the primary id

Definition at line 3417 of file Seq_id.cpp.

References CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::CanGetName(), CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id::fAllowLocalId, CSeq_id::fGpipeAddSecondary, CAliasBase< TPrim >::Get(), CTextseq_id_Base::GetAccession(), CId_pat_Base::C_Id::GetApp_number(), CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CPatent_seq_id_Base::GetCit(), CId_pat_Base::GetCountry(), CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), GetId(), CId_pat_Base::GetId(), CObject_id_Base::GetId(), CSeq_id_Base::GetLocal(), CPDB_seq_id_Base::GetMol(), CTextseq_id_Base::GetName(), CId_pat_Base::C_Id::GetNumber(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CPatent_seq_id_Base::GetSeqid(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CObject_id_Base::IsId(), CId_pat_Base::C_Id::IsNumber(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CTextseq_id_Base::IsSetVersion(), CObject_id_Base::IsStr(), NStr::NumericToString(), string, NStr::ToUpper(), and CSeq_id_Base::Which().

Referenced by CSeq_id::GetLabel(), and CPSGS_ResolveBase::x_ComposeOSLT().

Construct a seq-id from a dbtag.

Parameters

tag Input dbtag. set_as_general Whether to store tags from unrecognized databases as is in Seq-ids of type general rather than rejecting them altogether.

Definition at line 2379 of file Seq_id.cpp.

References CSeq_id::Set().

Construct a Seq-id from a flat string.

Parameters

the_id Input ID, preferably FASTA-style. flags How to interpret anything other than a single FASTA-style ID.

Definition at line 2452 of file Seq_id.cpp.

References flags, and CSeq_id::Set().

Construct a Seq-id from a flat representation.

Parameters

the_type Type of Seq_id to construct acc_in Primary string value – normally accession, overridden as country for patents, database for "general" IDs, molecule ID for PDB IDs. name_in Additional string value – normally name/locus, overridden as (application) number for patents, tag for "general" IDs, chain ID for PDB. version Numeric value – normally version number, overriden as sequence number for patents. release_in Historically used to convey release identifiers; for patents, may be set to "pgp" (case-insensitive) to indicate a Pre-Grant Patent [application].

Definition at line 2888 of file Seq_id.cpp.

References CSeq_id::Set(), and dtl::version.

Construct a numeric Seq-id.

Parameters

the_type Type of Seq-id (normally e_Gi) int_seq_id Numeric value.

Definition at line 2839 of file Seq_id.cpp.

References CSeq_id::Set().

Construct a Seq-id from a FASTA string with the leading (type) component already parsed out.

Parameters

the_type Type of Seq_id to construct the_content FASTA-style content, with embedded vertical bars as appropriate.

Definition at line 2555 of file Seq_id.cpp.

References f, and CSeq_id::Set().

Check if the handle is a valid or an empty one.

template<class container >

Return gi from id list if exists, return 0 otherwise.

Definition at line 1043 of file Seq_id.hpp.

References CSeq_id_Base::e_Gi, GetSeq_idByType(), and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::BuildUserUrl(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CAlignFormatUtil::GetDbType(), CAlignFormatUtil::GetLinkoutUrl(), CAlignFormatUtil::GetSeqLinkoutInfo(), s_GetFullLinkoutUrl(), s_GetSeqIdListString(), s_ModifySeqAlnWithFilteredSeqIDs(), CAsn2FlatApp::x_AddSNPAnnots(), CDisplaySeqalign::x_DisplayBl2SeqLink(), CShowBlastDefline::x_FillDeflineAndId(), CAlnGraphic::x_GetAlnInfo(), CDisplaySeqalign::x_GetFeatureInfo(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), and CDisplaySeqalign::x_PrepareRowData().

template<class container >

Return best label for a sequence from single Seq-id, or set of Seq-ids.

Return empty string if the label cannot be determined. GetDirectLabel() will return non-empty string only if the Seq-id is very likely enough to get good label without loading full set of sequence Seq-ids.

Definition at line 253 of file seq_id_handle.cpp.

References CTextseq_id_Base::GetAccession(), CDbtag_Base::GetDb(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), and CObject_id_Base::IsStr().

Referenced by GetDirectLabel(), CScope_Impl::GetLabel(), and CScope_Impl::GetLabels().

Definition at line 283 of file seq_id_handle.hpp.

References CSeq_id_Handle::IsGi(), CSeq_id_Handle::m_Packed, and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_id_Handle::CompareOrdered(), CRemoveFeatChecker::Do(), CAddFeatChecker::Do(), CSeqUtils::GetAccessionPlacementsMsec(), CLDS2_Database::GetAnnotBlobs(), CGenbankIdResolve::GetBestId(), CDefaultSynonymMapper::GetBestSynonym(), CLDS2_Database::GetBioseqId(), CBlobSplitterImpl::GetChunkData(), CWGSDataLoader_Impl::GetFileInfo(), CBAMDataLoader_Impl::GetGi(), GetGiForAccession(), GetGiForId(), CTestMapperSeqInfo::GetSequenceLength(), CTestMapperSeqInfo::GetSequenceType(), CLocalBlastDbAdapter::GetTaxId(), CId1Reader::LoadGiBlob_ids(), CPubseqReader::LoadGiHash(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CGICacheReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idInfo(), CHgvsReader::ReadSeqAnnot(), CGiCache::RecordKnown(), ReplaceWellknownSeqs(), s_GetBestSynonym(), s_GetFeatureKeyLinkLocation(), s_GetGi(), sx_MakeUniqueId(), CTreeBuilderJob::x_CreateProjectItems(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CAlignGroup::x_GetTaxId(), CNAUtils::x_Init(), CSFTranslationJob::x_InitGeneticCode(), CLDS2_Database::x_InitGetBioseqsSql(), x_LocalCDDEntryIdToBioId(), x_MakeLocalCDDEntryId(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), and CAssemblyListPanel::x_UpdateSearchTerm().

Faster way to create a handle for a gi.

Definition at line 188 of file seq_id_handle.hpp.

References CSeq_id_Handle::GetHandle().

Referenced by CSeqFetchQueue::Add(), BOOST_AUTO_TEST_CASE(), GetId(), CSeqTableLocColumns::GetIdHandle(), CIdMapperApp::GetSourceHandle(), CSplitParser::Load(), CId1Reader::LoadSeq_idBlob_ids(), CId1Reader::LoadSeq_idSeq_ids(), CPubseqReader::LoadSeq_idSeq_ids(), CCacheReader::LoadSequenceHash(), CPubseqReader::LoadSequenceHash(), CProcessor::OffsetId(), CSeqTableLocColumns::ParseDefaults(), CProcessor_ExtAnnot::Process(), CSeq_entry::ReassignConflictingIds(), CEditBioseqSampleApp::Run(), s_GetModelEvidance(), sx_MakeUniqueId(), CSplitParser::x_AddGiInterval(), CSplitParser::x_AddGiWhole(), and x_ParseLocalCDDEntryId().

Normal way of getting a handle, works for any seq-id.

Definition at line 113 of file seq_id_handle.cpp.

References CSeq_id_Mapper::GetHandle(), and CSeq_id_Mapper::GetInstance().

Referenced by CSeqsRange::Add(), CCDDBlobCache::Add(), CHandleRangeMap::AddLocation(), CHandleRangeMap::AddRange(), CSAM_CIGAR_Formatter::AddRow(), SAlignment_Segment::AddRow(), CMasterSeqSegments::AddSegmentIds(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CBAMDataLoader_Impl::AddSrzDef(), CSeq_id_Descr::Assign(), CBedFeatureRecord::AssignLocation(), CNewCleanup_imp::BasicCleanupSeqIds(), BioseqHandleFromLocation(), BOOST_AUTO_TEST_CASE(), CGencollIdMapper::CanMeetSpec(), CBAMBlobId::CBAMBlobId(), CBamFileInfo::CBamFileInfo(), CBioseq_SplitInfo::CBioseq_SplitInfo(), CCachedSequence::CCachedSequence(), CCmdChangeBioseqId::CCmdChangeBioseqId(), CCmdRemoveBioseqId::CCmdRemoveBioseqId(), CCSraDb_Impl::CCSraDb_Impl(), CCSraRefSeqIterator::CCSraRefSeqIterator(), CIdMapperScope::CIdMapperScope(), CIdRangeMap::CIdRangeMap(), IProjectViewFactory::CombineInputObjects(), IProjectViewFactory::CombineObjects(), CTableViewWithTextViewNav::CombineObjects(), CBioseq_Handle::ContainsSegment(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), Convert_Seq_align_Seq_id(), Convert_Seq_annot_Seq_id(), Convert_Seq_annot_Seq_loc_All(), Convert_Seq_annot_Seq_loc_TotalRange(), Convert_Seq_entry_Seq_id(), CSeq_loc_Conversion_Set::ConvertBond(), CSeq_loc_Conversion_Set::ConvertInterval(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPoint(), CBlobSplitterImpl::CopySkeleton(), CSparseGraph::CreateCompoundID(), CGC_Assembly::CreateIndex(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSNPDb_Impl::CSNPDb_Impl(), CVDBGraphBlobId::CVDBGraphBlobId(), CVDBGraphDb_Impl::CVDBGraphDb_Impl(), CAdvancedAlignCleanup::DivideByQuerySubjectPairs(), DoImportFTable(), CMAViewManager::DoTransition(), CScope::Exists(), ExtractExtraIds(), FindCompartments(), FindLatestSequence(), sequpd::FindMatches(), CCSRABlobId::FromString(), CSNPBlobId::FromString(), fta_add_hist(), g_DoesNotReferencePrimary(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CFastaIdHandler::GenerateID(), CScore_OverlapBoth::Get(), CScore_OrdinalPos::Get(), CScore_BlastRatio::Get(), CIdResolver::GetAccessionVersion(), CCSRADataLoader_Impl::GetAccVerOnce(), CWGSDataLoader_Impl::GetAccVerOnce(), GetAlignmentForRna(), CLDS2_Database::GetAnnots(), GetBestCdsForMrna(), CMacroBioData_BioSourceIter::GetBestDescr(), CMacroBioData_PubdescIter::GetBestDescr(), CAlnWriter::GetBestId(), CGenbankIdResolve::GetBestId(), GetBestMrnaForCds(), CTotalRangeSynonymMapper::GetBestSynonym(), CDummySynonymMapper::GetBestSynonym(), CDefaultSynonymMapper::GetBestSynonym(), CTSE_Handle::GetBioseqHandle(), CScope::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CScoreBuilder::GetBlastScoreProtToNucl(), CScoreBuilder::GetBlastScoreStd(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CSeqUtils::GetChrGI(), variation::GetFocusLocusIDs(), CGffIdGenerator::GetGffSourceId(), GetGIForSeqId(), CSeq_id_Handle::GetGiHandle(), GetId(), GetIdHandle(), CSeqTableLocColumns::GetIdHandle(), CScope::GetIds(), CHugeAsnDataLoader::GetIds(), CCSRADataLoader_Impl::GetIdsOnce(), CWGSDataLoader_Impl::GetIdsOnce(), CScope::GetLabel(), CMappedFeat::GetLocationId(), CSeq_feat_Handle::GetLocationId(), CSeq_id::GetMatchingIds(), CSeq_id::GetMatchingTextseqIds(), CTableDataBioTreeContainer::GetObjectValue(), CBioseqContext::GetPreferredSynonym(), CWGSResolver_DL::GetPrefixes(), CRemoveFeaturesDlg::GetProductId(), CMappedFeat::GetProductId(), CSeq_feat_Handle::GetProductId(), CAdvancedAlignCleanup::GetProsplignCompartments(), CMTTestThread::GetRandomId(), CSeqUtils::GetRangeCollection(), CMaskedRangeSet::GetRanges(), CSeqMap_CI::GetRefSeqid(), CGBDataLoader::GetSatSatkey(), CViewGraphic::GetSelection(), CAsnCacheStore::GetSeqIds(), CVDBGraphDb_Impl::GetSeqInfoAtRow(), GetSeqsStatus(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CScope::GetSequenceHash(), CSeq_loc_Mapper_Base::GetSequenceLength(), CScope::GetSequenceLength(), CScope::GetSequenceState(), CScope::GetSequenceType(), CIdMapperApp::GetSourceHandle(), CAdvancedAlignCleanup::GetSplignCompartments(), CScope::GetSynonyms(), CLDS2_Database::GetSynonyms(), CGencollIdMapper::GetSynonyms(), CScope::GetTaxId(), TaxClient::GetTaxIDForSeqId(), CGuiObjectInfoSeq_align::GetToolTip(), variation::GetUniquePrimaryTranscriptId(), GetWGSMasterSeq_id(), CSeq_loc_Mapper_Base::GetWidthById(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CGencollIdMapper::Guess(), CAsn2FastaApp::HandleSeqEntry(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), CSNPClient::HaveValidSeq_id(), CIdMapperConfig::Initialize(), CMPCrossAlignView::InitView(), CWinMaskUtil::CIdSet_SeqId::insert(), CMaskedRangeSet::Insert(), CSeq_loc_I::InsertEmpty(), CSeq_loc_I::InsertInterval(), CSeq_loc_I::InsertPoint(), CSeq_loc_I::InsertWhole(), IsSameBioseq(), IsSequenceFetchable(), CBioseq_Handle::IsSynonym(), CSplitParser::Load(), CBamRefSeqInfo::LoadAlignChunk(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CCacheReader::LoadSeq_idAccVer(), CGICacheReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idAccVer(), CBamRefSeqInfo::LoadSeqChunk(), CBlobSplitterImpl::MakeID2Chunk(), MakeSubjectScores(), CMakeBadSpecificHostTable::MakeTable(), CIdMapper::Map(), CGencollIdMapperAdapter::Map(), CGencollIdMapper::Map(), CIdMapper::MapObject(), CAlignFilter::Match(), CSelectionEvent::MatchLocWithId(), CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), CCdsToMatPeptide::MergeConvert(), CMAViewManager::NeedAnchorPanel(), CProcessor::OffsetId(), SrcEditDialog::OneRowOk(), CAlignSort::SAlignExtractor::operator()(), CPsiBlastAlignmentProcessor::operator()(), variation::SFastLocSubtract::operator()(), CWinMaskUtil::CInputBioseq_CI::operator++(), operator<<(), CSeqTableLocColumns::ParseDefaults(), CFastaReader::ParseDefLine(), CTabularFormatter_AllSeqIds::Print(), CTabularFormatter_SeqId::Print(), CTabularFormatter_Defline::Print(), CTabularFormatter_ProtRef::Print(), CTabularFormatter_AssemblyInfo::Print(), CTabularFormatter_PatchType::Print(), CProcessor_ExtAnnot::Process(), CSplitCacheApp::ProcessSeqId(), PsgIdToHandle(), CGlimmerReader::Read(), CSeqIdChunkFile::Read(), CCacheReader::ReadSeq_ids(), CSeq_entry::ReassignConflictingIds(), CCachedSequence::RegisterIds(), CScope::RemoveFromHistory(), CBioseq_Info::RemoveId(), CGBDocument::ReplaceGiSeqIds(), ReplaceWellknownSeqs(), CFastaIdsResolver::ResolveSeqId(), CMergeyApp::Run(), CFeatCompareJob_Align::Run(), CAgpFastaComparator::Run(), CTestCompartApplication::Run(), CAsnCacheTestApplication::Run(), CPrimeCacheApplication::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), CTestBMApp::Run(), RunNIterationsWithoutConverging(), s_CollectSeqIds(), s_Convert(), s_DumpSequences_wRange(), s_ExtractSeqidsAndRanges(), s_FindGaps(), s_FixIntervalProtToCds(), s_GetAlignmentContent(), s_GetAlignmentTooltip(), s_GetAlignTitle(), s_GetSequenceRegionId(), s_IsVirtualLocation(), s_IsVirtualSeqInt(), s_Match_id(), s_ParseId< CSeq_id_Handle >(), s_ReadIdsFromFile(), s_Render_SeqAlign(), s_Seq_align_Seq_loc(), s_SeqAlignToXMLHit(), s_TestForOverlapEx(), CAlignCompare::SAlignment::SAlignment(), CConversionResultPanel::SetObjects(), CPhyTreeCalc::SetQuery(), CSeq_loc_I::SetSeq_id(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CGridTableSeqIds::SetValue(), sGenerateFields(), CLDS2_Seq_id_Hook::SkipObject(), CLDS2_AnnotType_Hook::SkipObject(), SortAndFetchSeqData(), CIdMapperConfig::SourceHandle(), StrippedAccVer(), sx_CollectProductIds(), sx_MakeUniqueId(), sx_ProcessId(), CIdMapperConfig::TargetHandle(), CMacroFunction_UpdateProteinSeqs::TheFunction(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_ApplyRNA::TheFunction(), CMacroFunction_ApplyGene::TheFunction(), CMacroFunction_ApplyOtherFeature::TheFunction(), UpdateOrgInformation(), CScore_OverlapBoth::UpdateState(), CAsnvalThreadState::ValidateAsync(), CFlatSeqLoc::x_Add(), CIdMapperGCAssembly::x_AddAccessionMapping(), CIdMapperGCAssembly::x_AddAliasMappings(), CSeq_loc_Mapper_Base::x_AddConversion(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddQualProteinId(), CFeatureItem::x_AddQualsRna(), CGencollIdMapper::x_AddSeqToMap(), CDBSourceItem::x_AddSPBlock(), CIdMapperGCAssembly::x_AddUnversionedMapping(), x_ApplyCmd(), CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly(), CBioseq_Info::x_CalcBioseqLength(), CAlignCleanup::x_Cleanup_AlignVec(), CAlignCleanup::x_Cleanup_AnchoredAln(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CSeq_id_Resolver::x_Create(), CSeq_id_Resolver__CCDS::x_Create(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CImportFeatTable::x_CreateCommand(), CBLASTSeqToolJob::x_CreateProjectItems(), CMergeAlignmentsJob::x_CreateProjectItems(), CComponentSearchJob::x_DoSearch(), CSGSegmentsSeqIDJob::x_Execute(), CPrimeCacheApplication::x_ExtractAndIndex(), CPrimeCacheApplication::x_ExtractDelta(), CGencollIdMapper::x_FindChromosomeSequence(), x_FindLatestSequence(), CImportFeatTable::x_FindLocalBioseq_Handle(), CGencollIdMapper::x_FindParentSequence(), CAlignFilter::x_FuncCall(), CDBSourceItem::x_GatherInfo(), CReportEntry::x_GetAdjustment(), CSeqMap::x_GetBioseqInfo(), x_GetCDDIds(), CCreateGeneModelTask::x_GetCommand(), CImportFeatTable::x_GetFixedId(), CAlnTableDS::x_GetNumSeqs(), CAlignFilter::x_GetRegionMap(), CCommonComponentScorer::x_GetSeqHistCompList(), CMacroBioData_SeqdescIter::x_GetSeqId(), CScope_Impl::x_GetSynonyms(), variation::CVariationUtil::CCdregionIndex::x_Index(), CSeq_align_Mapper_Base::x_Init(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CIdMapperNumAssembly::x_InitializeMapping(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CWGSFileInfo::x_InitMasterDescr(), CGencollIdMapper::x_IsExactIdInAssembly(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CSeq_loc_Mapper_Base::x_IsSynonym(), CSeq_loc_Mapper::x_IsUCSCRandomChr(), CSplign::x_LoadSequence(), CTreeAlignMerger::x_MakeMergeableGroups(), CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CPhyTreeFormatter::x_MarkLeavesBySeqId(), CPSGS_SNPProcessor::x_OnSeqIdResolveFinished(), CLDS2_Manager::x_ParseFile(), CGC_Assembly_Parser::x_ParseGCSequence(), x_ParseLocalCDDEntryId(), CSplitParser::x_ParseLocation(), CNgAlignApp::x_PrintNoHitList(), CGenBankLoadOptionPanel::x_ProccessText(), CPSGS_SNPProcessor::x_ProcessAnnotationRequest(), CProSplignJob::x_ProcessCompartment(), CId2ReaderBase::x_ProcessEmptyReply(), CId2ReaderBase::x_ProcessGetBlobId(), CId2ReaderBase::x_ProcessGetSeqId(), CId2ReaderBase::x_ProcessGetSeqIdSeqId(), CSplignApp::x_ProcessPair(), CPSGS_CDDProcessor::x_ProcessResolveRequest(), CAlignFilter::x_Query_Op(), CAltValidator::x_QueryAccessions(), CPrimeCacheApplication::x_Read_Ids(), CPSGDataLoader_Impl::x_ReadCDDChunk(), CSeqMap_CI::x_RefTSEMatch(), CID2SNPProcessor_Impl::x_ResolveBlobId(), CSeqMap::x_ResolveSegmentLength(), CAnnot_Collector::x_SearchRange(), CSequenceSearchJob::x_SearchSequence(), CAlignGroup::x_SeparateByTaxId(), CSeq_loc_CI_Impl::x_SetId(), CBioseqContext::x_SetLocation(), CMasterContext::x_SetNumParts(), CBioseq_Info::x_SetObject(), CMappingObjectLoader::x_ShowMappingDlg(), CSplitDataLoader::x_SplitAligns(), CSplitDataLoader::x_SplitSeq(), CBlastFormat::x_SplitSeqAlign(), CFeaturePanel::x_StartAssemblyJob(), CAlignTabExportPage2::x_StartNAAlignNamesJob(), CAlnMultiDSBuilder::x_TestAlignments(), CSeq_annot_SNP_Info::x_UnmapAnnotObjects(), CSNPDb_Impl::x_Update(), CSeq_annot_SNP_Info::x_UpdateAnnotIndexContents(), CMappingObjectLoader::x_UpdateMap(), CProjectFileWriter::x_WriteGtf(), CFastaOstream::x_WriteSeqIds(), CGff3FlybaseWriter::xAssignAlignmentScores(), CGff3Writer::xAssignSourceSeqId(), CEditObjectFeaturePropagate::xInit(), CBsDiffApp::xLoadSeqEntry(), CWiggleWriter::xTableGetChromName(), CSrcChkApp::xTryProcessIdFile(), CAnnotWriterApp::xTryProcessInputId(), CWiggleWriter::xWriteSingleGraphFixedStep(), CWiggleWriter::xWriteTableBedStyle(), CWiggleWriter::xWriteTableFixedStep(), and CWiggleWriter::xWriteTableVariableStep().

Definition at line 3646 of file Seq_id.cpp.

References SSeqIdRange::acc_info, SSeqIdRange::digits, CSeq_id_Base::e_not_set, CSeq_id::eAcc_unknown, CSeq_id::eAcc_unreserved_nuc, CSeq_id::eAcc_unreserved_prot, flags, CSeq_id::fParse_AnyRaw, CSeq_id::fParse_FallbackOK, CSeq_id::GetAccType(), CSeq_id::IdentifyAccession(), SSeqIdRange::const_iterator::m_Range, SSeqIdRange::prefix, and SSeqIdRange::size().

Definition at line 288 of file seq_id_handle.cpp.

References CTextseq_id_Base::GetAccession(), CDbtag_Base::GetDb(), CTextseq_id_Base::GetName(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetVersion(), CObject_id_Base::IsStr(), and NStr::ToUpper().

Referenced by CheckOneFeatureType(), CProjectTreeViewFactory::CreateInstanceByFingerprint(), CwxGLTestViewFactory::CreateInstanceByFingerprint(), CClockViewFactory::CreateInstanceByFingerprint(), CDiagConsoleViewFactory::CreateInstanceByFingerprint(), CEventViewFactory::CreateInstanceByFingerprint(), CTaskViewFactory::CreateInstanceByFingerprint(), CSelectionViewFactory::CreateInstanceByFingerprint(), CFeatTableDS::SFeatureRow::FillIn(), CFixedSeq_ids::FindLabel(), CHTMLFormatterEx::FormatLocation(), CDiscrepancyContext::GetAminoacidName(), CDesktopFeatItem::GetDescription(), CValidErrorFormat::GetFeatureContentLabel(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CGroupMapWidget::CGroupItem::GetFullDescr(), CSeq_featHandler::GetLabel(), CUserFeatHandler::GetLabel(), CDataLoader::GetLabel(), CDataSource::GetLabel(), CBAMDataLoader_Impl::GetLabel(), GetLabel(), CScope_Impl::GetLabel(), CCSRADataLoader_Impl::GetLabelOnce(), CDataSource::GetLabels(), CScope_Impl::GetLabels(), CPSGDataLoader_Impl::GetLabelsOnce(), GetRNAProductString(), GetSeqFeatLabel(), CTableDataFTable::GetStringValue(), GetTitle(), CAlignSmearGlyph::GetTooltip(), CGuiObjectInfoImpFeature::GetToolTip(), CGuiObjectInfoRegionFeature::GetToolTip(), CGuiObjectInfoSiteFeature::GetToolTip(), CGuiObjectInfoVariation::GetToolTip(), CCompareSeqRegions::NextComparisonGroup(), CMacroAddConstraint::OnAccept(), CMacroEditor::OnAcceptClick(), CDiscrepancyDlg::OnRefresh(), SFeats_OpLess::operator()(), SCompareFeats_OpLess::operator()(), SFeatureByName::operator()(), CDemoApp::Run(), s_AreFeatureLabelsSame(), s_GetFeatDesc(), CCompareFeats::s_GetFeatLabel(), NSearchFeatPanel::s_GetFeatureLabel(), s_GetProductFlagFromCDSProductNames(), s_ReportDuplicateIds(), CCompareSeqRegions::SelectMatches(), SeqLocToBioseq(), CwxLabelEditDlg::SetParams(), CReportEditingDialog::Show(), CMiscFeatValidator::Validate(), CValidError_bioseq::ValidateCollidingGenes(), CLinkUtils::x_AddDbxrefFeatureLinks(), CFeatureItem::x_AddFTableRnaQuals(), CGeneModelFeatJob::x_CreateGeneModels(), CSortedProteins::x_GatherProteinNames(), CDisplaySeqalign::x_GetFeatureInfo(), CGuiObjectInfoSeq_feat::x_GetFeatureToolTip(), CGuiObjectInfoSeq_feat::x_GetGroupToolTip(), CAutoDefFeatureClause::x_GetProductName(), CCompareSeqRegions::x_GetPutativeMatches(), x_GetSegSeqInfoViaCDS(), CAlignedFeatureGraph::x_GetTooltip(), CXcompareAnnotsApplication::x_ProcessComparison(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CEditingBtnsPanel::x_ResetRemovedTab(), CDeflineGenerator::x_SetTitleFromNM(), CDeflineGenerator::x_SetTitleFromNR(), CHugeAsnReader::x_ThrowDuplicateId(), CIdentifiersPanel::x_UpdateXrefDescriptions(), CGeneValidator::x_ValidateOperon(), and CVcfWriter::x_WriteFeatureGenotypeData().

Definition at line 332 of file seq_id_handle.cpp.

References ERR_POST, CTextseq_id_Base::GetAccession(), GetLabel(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetTextseq_Id(), CSeq_id_Handle::IsGi(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), ITERATE, CSeq_id::kMaxScore, and ZERO_GI.

Append a label for this Seq-id to the supplied string.

Parameters

label String to append to. type Type of label (human-readable type-tagged content, by default). flags Flags fine-tuning behavior for human-readable output (ignored in eFasta and eFastaContent mode).

See also

ELabelType, ELabelFlags

Definition at line 2040 of file Seq_id.cpp.

References CSeq_id::AsFastaString(), CSeq_id::ComposeOSLT(), CSeq_id::eBoth, CSeq_id::eContent, CSeq_id::eFasta, CSeq_id::eFastaContent, CSeq_id::eType, CSeq_id::fAllowLocalId, CSeq_id::fLabel_Trimmed, CSeq_id::fLabel_UpperCase, CSeq_id::fLabel_Version, flags, CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CTextseq_id_Base::IsSetVersion(), label, NULL, NStr::ToUpper(), x_GetLabel_Content(), x_GetLabel_Type(), and CSeq_id::x_WriteContentAsFasta().

Referenced by CExportTableDlg::AddCdsGeneMrnaTable(), CExportTableDlg::AddDblinkToTable(), CExportTableDlg::AddDeflinesToTable(), CExportTableDlg::AddFeaturesToTable(), CGBProjectHelper::AddProjectItemsFromRID(), CExportTableDlg::AddPubsToTable(), CExportTableDlg::AddRnaToTable(), CExportTableDlg::AddSourceToTable(), CTrimN::apply(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), BOOST_AUTO_TEST_CASE(), CDiscrepancyContext::BuildSeqSummary(), CheckDuplicates(), CBarcodeTool::ClickLink(), CPSG_BioId::CPSG_BioId(), CRevCompSequencesDlg::CreateControls(), CCDSTranslationPanel::CreateControls(), CBlastDBExtractor::ExtractAccession(), CSelectTargetDlg::FindBioseq(), CFlatSeqIdQVal::Format(), fta_check_feat_overlap(), GetBarcodeId(), CAddFluComments::GetBestLabel(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CWGSClient::GetBioseqInfo(), CBulkCDSAddPanel::GetCommand(), CMixedStrands::GetCommand(), CRemoveSequencesDlg::GetCommand(), CObjectCoords::GetCoordinates(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CDesktopBioseqItem::GetDescription(), CDesktopBioseqsetItem::GetDescription(), GetGeneralOrLocal(), CSeq_featHandler::GetLabel(), CAlignFormatUtil::GetLinkoutUrl(), CLocationListCtrl::GetListIdStrForSeqId(), CBamAlignIterator::GetMatchAlign(), GetNewProtId(), CSequenceUpdater::GetNotImportedFeatsReport(), CSequenceUpdater::GetRevCompReport(), CShowBlastDefline::GetSeqIdListString(), CSeq_id::GetSeqIdString(), CSeq_id::GetStringDescr(), CTableDataGCAssembly::GetStringValue(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), CGuiObjectInfoSeq_align::GetToolTip(), CGuiObjectInfoClone::GetToolTip(), CSeqIdField::GetVal(), CLocalIDField::GetVals(), CEditingActionDescLocalId::GetValue(), CEditingActionSeqid::GetValue(), CEditingActionFileId::GetValue(), CAlignGroup::GroupBySequenceType(), CSeqTextPanel::InitObject(), CVcfTableView::InitView(), CTextPanel::InitWidget(), CLocalIDField::IsEmpty(), CAttribTableColumnIdPanel::IsInputValid(), CNGAlignParams::LogDump(), CAssemblyTrackingPanel::OnPopulateBtnClick(), CRevCompSequencesDlg::OnSelect(), CSeqVectorCache::PrefetchSequence(), CTabularFormatter_SeqId::Print(), CBlastFormat::PrintReport(), CFeaturePropagator::Propagate(), RelaxedMatch(), ReportMailReportLine(), s_AddOtherRelatedInfoLinks(), s_AgpWrite(), s_CompareSeqAlignByEvalue(), s_CompareSeqAlignByScoreAndName(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_DescribeSegment(), s_ExtendEntriesFromAlignments(), s_GetAccession(), s_GetAlignmentTooltip(), s_GetDescription(), CCompareSeqRegions::s_GetGeneId(), s_GetIdBase(), s_GetSeqIdListString(), NSearchFeatPanel::s_GetSeqLabel(), s_GetSeqLabel(), s_GetSequenceRegionId(), s_IdLabel(), s_MatchSeqIds(), s_Render_SeqAlign(), s_SetCloneInfo(), SeqDB_SimplifySeqid(), CAgpwriteProcess::SeqEntryProcess(), CIgBlastTabularInfo::SetAirrFormatData(), sGenerateFields(), pub_report::CSkipSeqIdHook::SkipClassMember(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), CCreateSeqHistForTpa::ValidateAlignments(), CValidError_bioseq::ValidateSegRef(), CConversionApp::Write(), CUCSCRegionWriter::WriteAnnot(), CVcfWriter::WriteAnnot(), CFeatureItem::x_AddQualsRna(), CMixedStrands::x_AddSequenceIds(), CAsn2FlatApp::x_AddSNPAnnots(), CFeaturePropagator::x_CdsMapCodeBreaks(), CImportFeatTable::x_DoImportCDS(), CShowBlastDefline::x_FillDeflineAndId(), CAlnGraphic::x_GetAlnInfo(), CSGSegmentSmearJob::x_GetCacheKey(), CCreateGeneModelTask::x_GetCommand(), CVecscreenRun::CFormatter::x_GetIdsAndTitlesForSeqAlign(), CGridTableSeqIds::x_GetLabel(), CUpdateSeqPanel::x_GetNameAndLength(), CEditObjectSeq_feat::x_HandleCdsProduct(), CDisplaySeqalign::x_InitAlignParams(), CDisplaySeqalign::x_InitDefLinesHeader(), CFeatureTableReader_Imp::x_InitId(), CReportEntry::x_NewCoordinate(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CFeaturePropagator::x_PropagatetRNA(), CCdregionValidator::x_ReportTranslationProblems(), CBlastDBExtractor::x_SetGi2AccMap(), CBioseqContext::x_SetId(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphValues(), CVcfWriter::x_WriteFeature(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentSplicedSeqId(), CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CFeatTableEdit::xConvertToGeneralIds(), CSrcWriter::xGatherLocalId(), CWiggleWriter::xTableGetChromName(), CBedGraphWriter::xWriteAnnotSeqTable(), CBedGraphWriter::xWriteSingleFeature(), and CWiggleWriter::xWriteSingleGraphFixedStep().

Append a label for this Seq-id to the supplied string, splitting out the version to a separate output parameter.

Note

In eFasta and eFastaContent mode, this method includes the version (if any) in the label and does not touch *version.

Parameters

label String to append to. version Pointer to hold the returned version. type Type of label (human-readable type-tagged content, by default).

See also

ELabelType

Definition at line 2106 of file Seq_id.cpp.

References CSeq_id::AsFastaString(), CSeq_id::eBoth, CSeq_id::eContent, CSeq_id::eFasta, CSeq_id::eFastaContent, CSeq_id::eType, label, dtl::version, x_GetLabel_Content(), x_GetLabel_Type(), and CSeq_id::x_WriteContentAsFasta().

Collect partially matching seq-ids: no-version, no-name etc.

The original id is not added to the set.

Definition at line 3336 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id_Base::GetGeneral(), CSeq_id_Handle::GetHandle(), CSeq_id_Base::GetLocal(), CSeq_id::GetMatchingTextseqIds(), CSeq_id_Base::GetPdb(), set< Key, Compare >::insert(), match(), and CSeq_id_Base::Which().

Referenced by CSeq_loc_Mapper_Base::CollectSynonyms().

Collect partially matching textseq-ids.

See also

GetMatchingIds

Definition at line 3269 of file Seq_id.cpp.

References A, CSeq_id_Handle::GetHandle(), CSeq_id::GetTextseq_Id(), set< Key, Compare >::insert(), kEmptyStr, match(), N, orig, r(), CTextseq_id_Base::Reset(), CTextseq_id_Base::ResetRelease(), CTextseq_id_Base::ResetVersion(), s_GetTextseq_id(), CTextseq_id_Base::SetAccession(), CTextseq_id_Base::SetName(), CTextseq_id_Base::SetRelease(), CTextseq_id_Base::SetVersion(), and CSeq_id_Base::Which().

Referenced by CSeq_id::GetMatchingIds().

template<class container >

Definition at line 304 of file seq_id_handle.hpp.

References CSeq_id_Info::GetPackedSeqId(), CSeq_id_Info::GetSeqId(), CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, and CSeq_id_Handle::m_Variant.

Referenced by CLinkUtils::AddBlastProductLink(), CExplicit_Mapper_Sequence_Info::AddSeq(), CLinkUtils::AddSequenceLinks(), CSAM_CIGAR_Formatter::AdjustSeqIdType(), CSeq_id_Handle::AsString(), BestRank_SeqIdHandle(), BOOST_AUTO_TEST_CASE(), CReadDispatcher::CannotProcess(), CannotProcess(), variation::ChangeIdsInPlace(), CVisibleRange::Clamp(), CBarcodeTool::ClickLink(), CSeq_id_Info::CompareOrdered(), Convert_Seq_annot_Seq_id(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), CSparseGraph::CreateCompoundID(), CRevCompSequencesDlg::CreateControls(), CTextItemSeq_loc::CreateObject(), CGuiObjectInfoSeq_id::CreateObject(), CHgvsNaIrepReader::CreateSeqfeat(), CHgvsProtIrepReader::CreateSeqfeat(), CSixFramesTransTrackFactory::CreateTracks(), CSegmentGlyph::CSegmentGlyph(), CMAViewManager::DoTransition(), CAnnotCompareDS::DumpTextReport(), CSequenceEditingEventHandler::ExportStructuredCommentsTable(), FastaAARank_SeqIdHandle(), FastaNARank_SeqIdHandle(), FindLatestSequence(), CSNPDb_Impl::FindSeq(), Get_ConstRef_Seq_id(), GetAccession(), GetAccessionForGi(), GetAccessionForId(), GetAccVer(), CBAMDataLoader_Impl::GetAccVer(), CObjFingerprint::GetAlignSignature(), CFindRSites::GetAnnot(), CGenbankIdResolve::GetBestId(), CDefaultSynonymMapper::GetBestSynonym(), CCDDClientPool::GetBlobBySeq_id(), CHugeAsnDataLoader::GetBlobId(), CCDDClientPool::GetBlobIdBySeq_id(), CRemoteBlastDbDataLoader::GetBlobs(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CBlobSplitterImpl::GetChunkData(), CBulkCDSAddPanel::GetCommand(), CFarPointerSeq::GetCommand(), CMixedStrands::GetCommand(), CRemoveSequencesDlg::GetCommand(), CObjFingerprint::GetComponentSignature(), CObjectCoords::GetCoordinates(), GetDeleteFeatureCommand(), CDesktopBioseqItem::GetDescription(), CDesktopBioseqsetItem::GetDescription(), GetDirectLabel(), CMappingRange::GetDstId(), CObjFingerprint::GetFeatSignature(), CWGSDataLoader_Impl::GetFileInfo(), CCSRABlobId::GetGeneralIdType(), GetGeneralOrLocal(), CCSRABlobId::GetGeneralSRAAccLabel(), CCSRABlobId::GetGeneralSRAAccReadId(), CObjFingerprint::GetGraphSignature(), CObjFingerprint::GetHistogramSignature(), GetId(), SGeneCdsmRnaFeats::GetID(), CHugeAsnDataLoader::GetIds(), CWriteUtil::GetIdType(), CSeq_featHandler::GetLabel(), GetLabel(), GetLocalGeneByLocus(), CBulkLocationPanel::GetLocForBioseq(), GetMiscTableFromSeqEntry(), CSequenceUpdater::GetNotImportedFeatsReport(), CTableDataBioTreeContainer::GetObjectValue(), CRemoveFeaturesDlg::GetProductId(), GetProductToCDSMap(), CBioseq_Handle::GetRangeSeq_loc(), CObjFingerprint::GetRsiteSignature(), CSeq_id_Mapper::GetSeq_id(), CBioseq_Handle::GetSeqId(), CSeq_id_Handle_Wrapper::GetSeqId(), CSeq_id_Handle::GetSeqIdOrNull(), CVDBGraphDb_Impl::GetSeqInfo(), CObjFingerprint::GetSeqLocSignature(), CBlastDbDataLoader::GetSequenceLength(), CHugeAsnDataLoader::GetSequenceLength(), GetSequenceType(), CHugeAsnDataLoader::GetSequenceType(), CHugeAsnDataLoader::GetSequenceTypeFound(), CCommentItem::GetStringForTPA(), CTableDataGCAssembly::GetStringValue(), CLocalBlastDbAdapter::GetTaxId(), CHugeAsnDataLoader::GetTaxId(), CScope_Impl::GetTaxId(), CFeatGlyph::GetTooltip(), CGuiObjectInfoSeq_align::GetToolTip(), CGuiObjectInfoClone::GetToolTip(), CObjFingerprint::GetVcfVariantSignature(), GetWGSMasterSeq_id(), CAlignGroup::GroupBySequenceType(), HasNameAndAccession(), CSeq_id_Handle::IdentifyAccession(), CViewGraphic::InitView(), CVcfTableView::InitView(), CSeq_id_Handle::IsAccVer(), CSeq_id_Handle::IsAllowedSNPScaleLimit(), CSGUtils::IsChromosome(), CSGUtils::IsmRNA(), CGuiObjectInfoSeq_align::IsPolyA(), CSGUtils::IsRefSeq(), CSGUtils::IsSegSet(), CValidError_bioseq::IsWp(), CId2ReaderBase::LoadBlobs(), CId1Reader::LoadGiBlob_ids(), CId1Reader::LoadGiSeq_ids(), CId2ReaderBase::LoadSeq_idAccVer(), CId1Reader::LoadSeq_idBlob_ids(), CId2ReaderBase::LoadSeq_idBlob_ids(), CId1Reader::LoadSeq_idGi(), CId2ReaderBase::LoadSeq_idGi(), CPubseqReader::LoadSeq_idInfo(), CId2ReaderBase::LoadSeq_idLabel(), CId1Reader::LoadSeq_idSeq_ids(), CId2ReaderBase::LoadSeq_idSeq_ids(), CId2ReaderBase::LoadSeq_idTaxId(), CId2ReaderBase::LoadSequenceHash(), CId2ReaderBase::LoadSequenceLength(), CId2ReaderBase::LoadSequenceType(), CIdMapper::Map(), CIdMapper::MapObject(), CRevCompSequencesDlg::OnSelect(), CAlignSort::SAlignExtractor::operator()(), operator<<(), CTabularFormatter_SeqId::Print(), PrintBestSeqId(), CResolveRequest::Process(), CFeaturePropagator::Propagate(), CGlimmerReader::Read(), variation::CVariationUtil::RemapToAnnotatedTarget(), ReplaceWellknownSeqs(), ReportMailReportLine(), CFeatCompareJob_Align::Run(), CTestBMApp::Run(), s_AgpWrite(), s_ConvertId(), s_Fingerprint_Seq_id(), s_GetAccession(), s_GetAlignmentContent(), s_GetAlignmentTooltip(), s_GetAlignTitle(), s_GetAnnotContent(), s_GetBestSynonym(), s_GetDescription(), s_GetIdBase(), CUpdateMultiSeq_Dlg::s_GetSeqIDLabel(), s_GetSeqLabel(), s_IdxSeqIdHandle(), s_IsIpgAccession(), s_Match_id(), s_RecordSeqId(), s_Render_SeqAlign(), s_ScoreForDBSource(), s_ScoreSeqIdHandle(), s_SeqAlignToXMLHit(), s_SeqMapForHandle(), Score_SeqIdHandle(), SeqLocMapperToPairwiseAligns(), CConversionResultPanel::SetObjects(), CSeqMap::SetSegmentRef(), sGenerateFields(), StrippedAccVer(), sx_GetReadId(), sx_MakeUniqueId(), sx_ProcessId(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CIdHandler::ToCanonical(), UpdateOrgInformation(), WorstRank_SeqIdHandle(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualsRna(), CMixedStrands::x_AddSequenceIds(), CDBSourceItem::x_AddSPBlock(), CFastaExportJob::x_CheckForDuplicates(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CImportFeatTable::x_CreateCommand(), CHgvsNaIrepReader::x_CreateConversionVarref(), CTreeBuilderJob::x_CreateProjectItems(), CHgvsNaIrepReader::x_CreateSimpleVariantFeat(), CHgvsProtIrepReader::x_CreateSimpleVariantFeat(), CComponentSearchJob::x_DoSearch(), CGenbankGatherer::x_DoSingleSection(), CDBSourceItem::x_FormatDBSourceID(), CDBSourceItem::x_GatherInfo(), CTableDataAlnSummary::x_GetAlnSummary(), CSGSegmentSmearJob::x_GetCacheKey(), x_GetCDDIds(), CCreateGeneModelTask::x_GetCommand(), CCommonComponentScorer::x_GetDeltaExtCompList(), CGridTableSeqIds::x_GetDescriptionLabel(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstSparse(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CProjectFileWriter::x_GetGi(), x_GetId(), CGridTableSeqIds::x_GetLabel(), CUpdateSeqPanel::x_GetNameAndLength(), CBlastDbDataLoader::x_GetOid(), CScore_BlastRatio::x_GetPerfectScore(), CCommonComponentScorer::x_GetSeqHistCompList(), CPhyTreeFormatter::x_GetSeqIDString(), CPrimaryItem::x_GetStrForPrimary(), CCommonComponentScorer::x_GetUserCompList(), CFastaExportJob::x_GetWholeLoc(), variation::CHgvsParser::x_header(), CAnnot_Collector::x_Initialize(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CPhyTreeFormatter::x_InitTreeFeatures(), CAlignGlyph::x_IsSRA(), CBuffer_DataLoader::x_LoadData(), CTreeAlignMerger::x_MakeSeqAlign(), CReportEntry::x_NewCoordinate(), CGenBankLoadOptionPanel::x_ProccessText(), CProSplignJob::x_ProcessCompartment(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CAlignFilter::x_Query_Op(), CSeq_loc_Mapper_Base::x_RangeToSeq_loc(), CSequenceSearchJob::x_SearchSequence(), CDeflineGenerator::x_SetFlags(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CAlnMultiDSBuilder::x_TestAlignments(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegType(), CGff3Writer::xAssignAlignmentSplicedMethod(), CGff3Writer::xAssignAlignmentSplicedSeqId(), CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedType(), CGff3Writer::xAssignFeatureMethod(), CEditObjectFeaturePropagate::xInit(), and CGff3Writer::xSplicedSegHasProteinProd().

Definition at line 315 of file seq_id_handle.hpp.

References CSeq_id_Handle::GetSeqId(), and CSeq_id_Handle::m_Info.

Referenced by CBioseq_Handle::GetInitialSeqIdOrNull(), CGuiObjectInfoSeq_align::GetToolTip(), CRepeatMaskerReader::ParseRecord(), s_FindGi(), s_FindLocalId(), s_GetAlignmentTooltip(), s_GetAlignTitle(), s_GetModelEvidance(), s_ReplaceGIs(), sGenerateFields(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CVectorScreen::x_FindAccession(), CVectorScreen::x_FindLocalId(), CVectorScreen::x_FindTypeGeneral(), and CFeaturePanel::x_StartAssemblyJob().

Return seqid string with optional version for text seqid type.

Definition at line 2145 of file Seq_id.cpp.

References CSeq_id::eContent, CSeq_id::fLabel_Version, flags, CSeq_id::GetLabel(), and label.

Referenced by CContigAssembly::Align(), CBedFeatureRecord::AssignLocation(), BOOST_AUTO_TEST_CASE(), CSparseGraph::CreateCompoundID(), variation::CVariationUtil::CreateFlankLocs(), CGBObjectLoader::Execute(), CFlatSeqIdQVal::Format(), CGBSeqFormatter::FormatFeature(), fta_seqid_same(), g_DoesNotReferencePrimary(), CSeqFastaReader::GenerateID(), CTextAlnReader::GenerateID(), GetAccessionForGi(), GetAccessionForId(), CWholeFileAnnotation::GetAndUseAnnot(), GetBlastSeqIdString(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CDesktopAlignItem::GetDescription(), CSNPTableModel::GetExtraValueAt(), CBioseq_set::GetLabel(), CVDBBlastUtil::GetOIDFromVDBSeqId(), CVDBBlastUtil::GetOidsFromSeqIds_WGS(), CAlignFormatUtil::GetSeqLinkoutInfo(), CCommentItem::GetStringForTPA(), CGencollIdMapper::Guess(), Make_SeqID_String(), CBamRefSequencesPanel::OnIdle(), CVcfRefSequencesPanel::OnIdle(), CProSplignText::Output(), CSeqFastaReader::PostProcessIDs(), CResolveRequest::Process(), CDemoContigAssemblyApp::Run(), CSeqDescrRetrievalJob::Run(), CAnnotMetaDataJob::Run(), CLocalFinderApp::Run(), CTestProtProd_EntrezNeighbors::RunTest(), s_AddTopLevelGenomicLinks(), s_CompareIdList(), s_CreateQueryMap(), s_DupIdsBioseq(), s_GenerateAccsList(), s_GetAlignTitle(), s_GetAnnotContent(), s_GetClipLoc(), s_GetQueryBioseq(), s_GetSeqLabel(), s_GetUngapLoc(), s_MakeFastaSubIds(), s_PreProcessAccessionsForDBv5(), s_ProcessSeqIDsForV5(), CClippedScorer::ScoreAlignments(), CAliToSeq_align::Seq_idToString(), CSeqDBImpl::SeqidToOids(), CBedImportData::Serialize(), CGtfImportData::Serialize(), CMultAlign::SetGenomic(), CConversionResultPanel::SetObjects(), CVDBBlastUtil::VDBIdType(), WriteBlastSeqidlistFile(), CFlatSeqLoc::x_AddID(), CFeatureItem::x_AddQualProteinId(), CDBSourceItem::x_AddSPBlock(), CDescPlacementPanel::x_AddToStrings(), CGencollIdMapper::x_ApplyPatternToId(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CImportFeatTable::x_CheckCollidingIds(), CBlastInputReader::x_CreateBioseq(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CTreeBuilderJob::x_CreateProjectItems(), CElementaryMatching::x_CreateRemapData(), CGencollIdMapper::x_FindChromosomeSequence(), CBamUILoadManager::x_GetBamRefSeqs(), CGencollIdMapper::x_GetIdFromSeqAndSpec(), CPrimaryItem::x_GetStrForPrimary(), CClonePlacementGlyph::x_GetSupportTypeForNonPrototypeEnds(), CGencollIdMapper::x_Init(), CWriteDB_LMDB::x_InsertEntry(), CSplign::x_LoadSequence(), CGenbankFormatter::x_LocusHtmlPrefix(), CGencollIdMapper::x_MakeSpecForSeq(), CGencollIdMapper::x_NCBI34_Guess(), CGencollIdMapper::x_NCBI34_Map_IdFix(), CVcfLoadingJob::x_OnVCFVariantListReady(), CMultiAlnPrinter::x_PrintNexus(), CFastaDeflineReader::x_ProcessIDs(), CASN1InputSourceOMF::x_ReadOneSeq(), CFeatureGenerator::SImplementation::x_SetQualForGapFilledModel(), CAlignTabExportPage2::x_StartAlignNamesJob(), CFeaturePanel::x_StartAssemblyJob(), CAlignTabExportPage2::x_StartNAAlignNamesJob(), CGff2Writer::xAssignFeatureAttributeProteinId(), and CEditObjectFeaturePropagate::xInit().

Definition at line 2292 of file Seq_id.cpp.

References CSeq_id::eDefault, CSeq_id::eFormat_BestWithoutVersion, CSeq_id::eFormat_BestWithVersion, CSeq_id::eFormat_FastA, CSeq_id::eFormat_ForceGI, CSeq_inst_Base::eMol_aa, CSeq_id::FastaAARank(), CSeq_id::FastaNARank(), FindBestChoice(), CSeq_id::fLabel_Version, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_id::GetLabel(), CSeq_inst_Base::GetMol(), ITERATE, label, CRef< C, Locker >::NotEmpty(), and CSeq_id::WriteAsFasta().

Referenced by BOOST_AUTO_TEST_CASE(), CSGSequenceDS::GetAcc_All(), GetStringDescr(), CReadBlastApp::hasProblems(), Sequence::IdentifierString(), CMaskWriter::IdToString(), CReadBlastApp::ProcessCDD(), CReadBlastApp::ReadBlast(), CReadBlastApp::reportProblems(), and CReadBlastApp::StoreBlast().

Return embedded CTextseq_id, if any.

Definition at line 169 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGpipe(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), and CSeq_id_Base::Which().

Referenced by CSeq_id::AdjustScore(), AllowOrphanedProtein(), CSeq_id_Descr::Assign(), BOOST_AUTO_TEST_CASE(), CAlnMix::ChooseSeqId(), CSeq_id::Compare(), CSeq_id::CompareOrdered(), CSeq_id::ComposeOSLT(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CSeq_id_Textseq_Tree::Dump(), CSeq_id_Textseq_Tree::FindMatch(), CSNPDb_Impl::FindSeq(), FindTextseq_id(), FTASeqLocCheck(), GetAccession(), GetAccessionAndDatabaseSource(), GetAccVer(), CBAMDataLoader_Impl::GetAccVer(), CWholeFileAnnotation::GetAndUseAnnot(), CDefaultSynonymMapper::GetBestSynonym(), GetGiForAccession(), GetLabel(), CBioseq::GetLabel(), CSeq_id::GetLabel(), CSeq_id::GetMatchingTextseqIds(), CSeq_id_Textseq_PlainInfo::GetPackedSeqId(), CSeq_id_Textseq_Info::GetPackedSeqId(), GetWGSMasterSeq_id(), HasNameAndAccession(), CSeq_id::IdentifyAccession(), IsAccessionNoVersion(), CSeq_id::IsAllowedSNPScaleLimit(), CSNPClient::IsValidSeqId(), CSeq_id_Textseq_PlainInfo::ParseCaseVariant(), s_CheckQuals_cdregion(), s_GetBestSynonym(), s_GetModelEvidance(), s_GetNameForBioseq(), s_IsIpgAccession(), s_Match_id(), s_Matches(), s_PSGRank(), s_ValidateAcc(), SeqDB_SimplifySeqid(), CStructuredCommentsReader::SeqIdMatchesCommentId(), CValidError_imp::Setup(), StrippedAccVer(), CValidError_imp::ValidateBioSource(), CWriteDB_IsamIndex::x_AddStringIds(), CGencollIdMapper::x_ApplyPatternToId(), CFeatureGenerator::SImplementation::x_CheckMatch(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CComponentSearchJob::x_DoSearch(), CGencollIdMapper::x_FixImperfectId(), x_GetId(), CScope_Impl::x_GetSynonyms(), CSeq_id_Textseq_Tree::x_GetVersion(), CWriteDB_LMDB::x_InsertEntry(), CFlatSeqLoc::x_IsAccessionVersion(), CFlatGatherer::x_MergeEqualBioSources(), CPSGS_ResolveBase::x_OptimizedResolutionInCache(), CBuildDatabase::x_ResolveRemoteId(), CPSGS_ResolveBase::x_ResolveSeqId(), CPSGS_ResolveBase::x_ResolveViaComposeOSLTInCache(), CSingleFeatValidator::x_ValidateSeqFeatProduct(), and CFastaOstream::x_WriteAsFasta().

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on properties.

Definition at line 1634 of file Seq_id.cpp.

References CTempString::data(), CSeq_id::eAcc_unknown, CTempString::find(), CTempString::find_first_not_of(), flags, i, kDigits, NPOS, CTempString::size(), NStr::ToUpper(), toupper(), and CSeq_id::x_IdentifyAccession().

Referenced by CLinkUtils::AddSequenceLinks(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), CSixFramesTransTrackFactory::CreateTracks(), CAutoColValidatoraccession::DoValidate(), fta_fix_seq_id(), CWGSDataLoader_Impl::GetFileInfoByAcc(), SSeqIdRange::const_iterator::GetID(), GetNameCategory(), GetNucAccOwner(), GetProtAccOwner(), GetSequenceType(), GetTitle(), CVDBBlastUtil::GetVDBSeqIdFromOID(), GetWGSMasterSeq_id(), CAlignGroup::GroupBySequenceType(), CSeq_id::IdentifyAccession(), CSeq_id_Handle::IdentifyAccession(), IdentifyLocalId(), CSeq_id::IsAllowedSNPScaleLimit(), CSGUtils::IsChromosome(), CGuiSeqInfoSeq_id::IsDNA(), CGencollSvc::isGenCollSequence(), CSGUtils::IsmRNA(), CGuiObjectInfoSeq_align::IsPolyA(), CGuiSeqInfoSeq_id::IsProtein(), CSeqUtils::isQuasiLocal(), CSeqUtils::isTopLevel(), CValidError_bioseq::IsTSAAccession(), IsValidAccession(), CSNPClient::IsValidSeqId(), CValidError_bioseq::IsWGSAccession(), IsWGSAccession(), CValidError_bioseq::IsWp(), CAgpValidateReader::OnGapOrComponent(), CAgpValidateReader::OnObjectChange(), OverrideLenIfAccession(), CWGSResolver_Ids::ParseWGSPrefix(), CReadBlastApp::processFeature(), CAlignFormatUtil::RemoveSeqsOfAccessionTypeFromSeqInUse(), CWGSClient::ResolveAcc(), s_GetDescription(), s_GetSeqLabel(), s_ModifySeqAlnWithFilteredSeqIDs(), s_RenderAccList(), CSeq_id::Set(), CGffAlignmentRecord::SetMatchType(), ValidateAccessionFormat(), CValidError_bioseq::ValidateSeqId(), ValidSeqType(), CVDBBlastUtil::VDBIdType(), CGencollIdMapper::x_FindChromosomeSequence(), CGencollIdMapper::x_FixImperfectId(), x_GetCDDIds(), CTableColumnTypeGuesser::x_GuessType(), x_IsWgsSecondary(), CGenBankLoadOptionPanel::x_ProccessText(), COligoSpecificityCheck::x_SavePrimerInfo(), CDeflineGenerator::x_SetFlags(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CUCSCRegionReader::xParseFeatureUCSCFormat(), and CGff3Writer::xSplicedSegHasProteinProd().

Definition at line 1833 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_flag_mask, CSeq_id::eAcc_general, CSeq_id::eAcc_other, CSeq_id::eAcc_type_mask, CSeq_id::eAcc_wgs, CSeq_id::fAcc_prot, flags, CTextseq_id_Base::GetAccession(), CSeq_id::GetAccType(), CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id::GetTextseq_Id(), CSeq_id::IdentifyAccession(), CTextseq_id_Base::IsSetAccession(), NStr::ToUpper(), type, and CSeq_id_Base::Which().

Definition at line 3576 of file Seq_id.cpp.

References CSeq_id_Base::e_Other, CSeq_id::eAcc_chromosome, CSeq_id::eAcc_con, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_wgs_intermed, CSeq_id::eSNPScaleLimit_Chromosome, CSeq_id::eSNPScaleLimit_Contig, CSeq_id::eSNPScaleLimit_Default, CSeq_id::eSNPScaleLimit_Supercontig, CSeq_id::eSNPScaleLimit_Unit, CSeq_id::GetAccType(), CSeq_id::GetTextseq_Id(), CSeq_id::IdentifyAccession(), and CSeq_id_Base::IsGi().

Definition at line 279 of file seq_id_handle.hpp.

References CSeq_id_Base::e_Gi, CSeq_id_Info::GetType(), CSeq_id_Handle::m_Info, and CSeq_id_Handle::m_Packed.

Referenced by CSeq_id_Handle::AsString(), CSeq_id_Handle::CompareOrdered(), CBlobSplitterImpl::CopySkeleton(), CBAMDataLoader_Impl::GetAccVer(), CLDS2_Database::GetAnnotBlobs(), CGenbankIdResolve::GetBestId(), CDefaultSynonymMapper::GetBestSynonym(), CLDS2_Database::GetBioseqId(), CBlobSplitterImpl::GetChunkData(), GetDirectLabel(), CWGSDataLoader_Impl::GetFileInfo(), CBAMDataLoader_Impl::GetGi(), CSeq_id_Handle::GetGi(), GetGiForAccession(), GetGiForId(), sequpd::GetGoodSeqIdHandle(), GetId(), GetLabel(), CTestMapperSeqInfo::GetSequenceLength(), CTestMapperSeqInfo::GetSequenceType(), CLocalBlastDbAdapter::GetTaxId(), CSeq_id_Handle::IsAccVer(), CId1Reader::LoadGiBlob_ids(), CId1Reader::LoadGiSeq_ids(), CGICacheReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idAccVer(), CPubseqReader::LoadSeq_idInfo(), CCacheReader::LoadSequenceHash(), operator<<(), CSeq_id_Handle::operator==(), ReplaceWellknownSeqs(), s_GetBestSynonym(), s_GetFeatureKeyLinkLocation(), sx_ProcessId(), CSeq_id_Resolver__ChrNamesFromGC::x_Create(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CPhyTreeFormatter::x_GetSeqIDString(), CSeq_id_Mapper::x_GetTree(), CLDS2_Database::x_InitGetBioseqsSql(), x_MakeLocalCDDEntryId(), and CFeaturePanel::x_StartAssemblyJob().

Match() - TRUE if SeqIds are equivalent.

Definition at line 1067 of file Seq_id.hpp.

References CSeq_id::Compare(), and CSeq_id::e_YES.

Referenced by CAlnGraphic::AlnGraphicDisplay(), BadMultipleSequenceLocation(), BOOST_AUTO_TEST_CASE(), CBuildAlnVecJob::Build(), CSeq_id::Compare(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CCdCore::CopyBioseqForSeqId(), CCreateProteinId::create_protein_ids(), CDisplaySeqalign::DisplaySeqalign(), CMAViewManager::DoTransition(), CAlignFormatUtil::ExtractQuerySeqAlign(), CSeqAlignFilter::FilterByAccessionType(), CSeqAlignFilter::FilterByTaxonomy(), CAlignFormatUtil::FilterSeqalignBySeqList(), FormatAsAsn(), CScore_Overlap::Get(), CCdCore::GetAllRowIndicesForSeqId(), GetBestMrnaForCds(), CCdCore::GetBioseqWithSeqid(), CSeqUtils::GetCdsMappingInfoFromRna(), CShowBlastDefline::GetFormattingInfo(), IBISInteraction::GetGi(), SGeneCdsmRnaFeats::GetID(), CClusterDBSource::GetNext(), CBioseq::GetNonLocalId(), CTableDataGCAssembly::GetObjectValue(), CCdCore::GetSeqEntryForRow(), CTableDataGCAssembly::GetStringValue(), CAlignFormatUtil::GetSubjectsNumber(), CAlignFormatUtil::GetTaxidForSeqid(), CAlignFormatUtil::HspListToHitList(), CAlignFormatUtil::HspListToHitMap(), CAlnGraphic::Init(), IsSameBioseq(), CAlignFormatUtil::LimitSeqalignByHsps(), MakeSubjectScores(), Sequence::MatchesSeqId(), operator<<(), PrintSAM(), PrintTabular(), CAlignFormatUtil::PruneSeqalign(), CAlignFormatUtil::PruneSeqalignAll(), remasterAlignannot(), RestoreModelReadingFrame(), s_AddSeqDataToPssm(), s_CanAdd(), s_CompareSeqId(), s_GetLabel(), s_GetRnaMappingLocs(), s_GetSeq_intervalLabel(), s_LocationSpansMultipleSeqs(), s_MergeAlignSet(), s_RestoreHspPos(), s_SeqAlignSetToXMLHits(), s_SetBlastXMlHitList(), s_TestFastaRoundTrip(), s_UpdateSubjectInSeqalign(), testResultAlignments(), CSearchResults::TrimSeqAlign(), CScore_Overlap::UpdateState(), CValidError_bioseq::ValidateIDSetAgainstDb(), CValidError_imp::ValidateSeqLocIds(), CAlnGraphic::x_BuildHtmlTable(), CFeatureGenerator::SImplementation::x_CheckMatch(), CIgBlast::x_ConvertResultType(), CImportFeatTable::x_DoImportCDS(), CPsiBlastInputData::x_ExtractAlignmentData(), CDisplaySeqalign::x_FillLocList(), CUpdateAlign::x_FindNotPresentIDs(), CSequenceEditingEventHandler::x_FindRelevantAlignRow(), CAlnGraphic::x_FormatGraphOverview(), CAlignmentTrack::x_GetAlignGlyphType(), CClonePlacementGlyph::x_GetCloneEnds(), CShowBlastDefline::x_InitDefline(), CDisplaySeqalign::x_InitDefLinesHeader(), CShowBlastDefline::x_InitDeflineTable(), CTaxFormat::x_InitTaxInfoMap(), CBatchFeatJob::x_LoadFeatProducts(), CBlastFormat::x_PrintStructuredReport(), CBlastFormat::x_PrintXML2Report(), COligoSpecificityTemplate::x_SortHit(), and COligoSpecificityCheck::x_SortPrimerHit().

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

Parameters

ids Destination ID set. Existing contents will be preserved and appended to. s Input string to parse. allow_partial_failure If s contains invalid IDs, warn about them and try to process the remainder of the string, rather than throwing any exceptions.

Returns

The number of IDs successfully parsed.

Definition at line 2604 of file Seq_id.cpp.

References flags, CSeq_id::fParse_AnyLocal, CSeq_id::fParse_PartialOK, CSeq_id::fParse_RawText, and CSeq_id::ParseIDs().

Referenced by BOOST_AUTO_TEST_CASE(), ExtractAccession(), CVDBBlastUtil::GetVDBSeqIdFromOID(), CAgpValidateReader::OnObjectChange(), CGlimmerReader::Read(), CFastaIdsResolver::ResolveSeqId(), CSplignApp::Run(), s_MakeDefline(), s_TestFastaRoundTrip(), SeqDB_SimplifyAccession(), CAliToSeq_align::StringToSeq_id(), CIdMapperConfig::TargetHandle(), CImportFeatTable::x_CheckConsistentProteinIds(), CImportFeatTable::x_DoImportCDS(), CWriteDB_Impl::x_GetFastaReaderDeflines(), and CAgpConverter::x_InitializeCopyOfTemplate().

Parse a string representing one or more Seq-ids, appending the results to IDS.

Multiple IDs must appear in FASTA style.

Parameters

ids Destination ID set. Existing contents will be preserved and appended to. s Input string to parse. flags How to interpret anything other than well-formed FASTA IDs.

Returns

The number of IDs successfully parsed.

Definition at line 2614 of file Seq_id.cpp.

References _ASSERT, count, CSeq_id::CSeq_id(), CSeq_id_Base::e_General, CSeq_id_Base::e_not_set, CTempString::empty(), ERR_POST_X, NStr::eTrunc_Both, CSeq_id::eTV_plain, flags, CSeq_id::fParse_NoFASTA, CSeq_id::fParse_PartialOK, l(), NCBI_THROW, s_HasFastaTag(), NStr::Split(), NStr::TruncateSpaces_Unsafe(), Warning(), CSeq_id::WhichInverseSeqId(), and CSeq_id::x_IdentifyTypeVariant().

Referenced by BOOST_AUTO_TEST_CASE(), CFast5colReader::FindAnnots(), GetProtRefSeqId(), CSeqUtils::MapStringId(), CSeq_id::ParseFastaIds(), s_ConfigureDeflineTitle(), s_GetRefSeq_id(), s_RejoinDeflineTitle(), sx_GetRefSeq_id(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CAsn2FlatApp::x_GenerateHugeMode(), CFast5colReader::x_IndexFile(), CFeatureTableReader_Imp::x_InitId(), CCSraDb_Impl::x_MakeRefSeq_ids(), CAlnReader::x_ParseAndValidateSeqIds(), CFastaDeflineReader::x_ProcessIDs(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

Reset the handle (remove seq-id reference)

Definition at line 227 of file seq_id_handle.hpp.

References CSeq_id_Handle::m_Info, CSeq_id_Handle::m_Packed, CSeq_id_Handle::m_Variant, and CConstRef< C, Locker >::Reset().

Referenced by CIdMapper::AddMapping(), CSNPBlobId::FromSatString(), CCSRABlobId::FromString(), CSNPBlobId::FromString(), GetId(), SAnnotObject_Key::Reset(), CBioseq_Handle::Reset(), SAnnotObject_Key::SetMultiple(), CTSE_Info::SetSeq_entry(), and x_GetCDDIds().

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

Definition at line 772 of file Seq_id.hpp.

References kMax_Int.

Referenced by CFeatGapInfo::AdjustForRelevantGapIntervals(), CHTMLFormatterEx::FormatLocation(), CShowBlastDefline::GetSeqIdListString(), CVDBBlastUtil::GetVDBSeqIdFromOID(), CGlimmerReader::Read(), CFastaIdsResolver::ResolveSeqId(), s_ConfigureDeflineTitle(), s_GetIdLabel(), s_GetSeqIdListString(), s_IdxSeqIdHandle(), s_ScoreSeqIdHandle(), s_SeqAlignToXMLHit(), Score_SeqIdHandle(), CSearch< LEGACY, NHITS >::SetResult(), CAliToSeq_align::StringToSeq_id(), CSeq_id::WorstRank(), CId1FetchApp::WriteQualityScores(), CAsn2FlatApp::x_AddSNPAnnots(), and CVecscreenRun::CFormatter::x_GetIdsAndTitlesForSeqAlign().

Definition at line 2384 of file Seq_id.cpp.

References CSerialObject::Assign(), CSeq_id_Base::e_Gi, CObject_id_Base::e_Id, CObject_id_Base::e_Str, CDbtag::eDbtagType_bad, CDbtag::eDbtagType_DDBJ, CDbtag::eDbtagType_EMBL, CDbtag::eDbtagType_GI, CDbtag_Base::GetDb(), CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CDbtag::GetType(), GI_FROM, NStr::IntToString(), CObject_id_Base::IsStr(), NCBI_THROW, s_SplitVersion(), CObject_id_Base::SelectionName(), CTextseq_id::Set(), CSeq_id::Set(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), dtl::version, and CObject_id_Base::Which().

Reassign based on flat specifications; arguments interpreted as with constructors.

(Returns a reference to self.)

Definition at line 2457 of file Seq_id.cpp.

References CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Prf, CTempString::empty(), CTempString::erase(), ERR_POST_X, NStr::eTrunc_Both, CTempString::find(), CTempString::find_last_not_of(), flags, CSeq_id::fParse_AnyLocal, CSeq_id::fParse_AnyRaw, CSeq_id::fParse_FallbackOK, CSeq_id::fParse_NoFASTA, CSeq_id::fParse_PartialOK, CSeq_id::fParse_ValidLocal, CSeq_id::GetAccType(), CSeq_id::IdentifyAccession(), CSeq_id::IsValidLocalID(), ITERATE, kEmptyStr, NCBI_THROW, NPOS, s_CheckForFastaTag(), s_SplitVersion(), CTempString::size(), NStr::Split(), CTempString::substr(), NStr::ToUpper(), NStr::TruncateSpaces_Unsafe(), Warning(), CSeq_id::x_IdentifyTypeVariant(), and CSeq_id::x_Init().

Referenced by CSeq_id::CSeq_id(), CLocationListCtrl::GetIdFromForm(), CIdMapperConfig::Initialize(), IPSGS_Processor::ParseInputSeqId(), PrintFastaUnaligned(), PrintSAMUnaligned(), PrintTabularUnaligned(), s_MakeFastaSubIds(), CHangScorer::ScoreAlignments(), CSeq_id::Set(), CIdMapperGCAssembly::x_AddAliasMappings(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CURLTooltipHandler::x_DisplayUnalignedRegion(), CGencollIdMapper::x_FixImperfectId(), CShortReadFastaInputSource::x_GetNextSeqId(), CSeq_id::x_Init(), CPSGS_GetProcessor::x_OnSeqIdResolveFinished(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CAltValidator::x_QueryAccessions(), CUpdateSeq_Input::x_ReadAccession(), and CAssemblyListPanel::x_UpdateSearchTerm().

Definition at line 2899 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CTempString::empty(), NStr::EqualNocase(), ERR_POST_X, NStr::eTrunc_Both, Info(), NCBI_THROW, CPDB_seq_id_Base::ResetChain(), CPDB_seq_id_Base::ResetChain_id(), CId_pat_Base::ResetDoc_type(), CPDB_seq_id_Base::ResetRel(), CSeq_id_Base::SelectionName(), CTextseq_id::Set(), CSeq_id::Set(), CId_pat_Base::C_Id::SetApp_number(), CPDB_seq_id_Base::SetChain(), CPDB_seq_id_Base::SetChain_id(), CPatent_seq_id_Base::SetCit(), CId_pat_Base::SetCountry(), CDbtag_Base::SetDb(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGpipe(), CId_pat_Base::SetId(), CSeq_id_Base::SetLocal(), CPDB_seq_id_Base::SetMol(), CSeq_id_Base::SetNamed_annot_track(), CId_pat_Base::C_Id::SetNumber(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CPatent_seq_id_Base::SetSeqid(), CObject_id::SetStrOrId(), CSeq_id_Base::SetSwissprot(), CDbtag_Base::SetTag(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), CSeq_id_Base::SetTpg(), CTempString::size(), NStr::StringToNonNegativeInt(), NStr::TruncateSpaces_Unsafe(), dtl::version, and ZERO_GI.

Definition at line 2851 of file Seq_id.cpp.

References CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, GI_FROM, INT_ID_TO, NCBI_THROW, NStr::NumericToString(), CGiimport_id_Base::ResetDb(), CGiimport_id_Base::ResetRelease(), CSeq_id_Base::SelectionName(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGibbmt(), CSeq_id_Base::SetGibbsq(), CSeq_id_Base::SetGiim(), CGiimport_id_Base::SetId(), CObject_id_Base::SetId(), and CSeq_id_Base::SetLocal().

Definition at line 3603 of file Seq_id.cpp.

References SSeqIdRange::digits, SSeqIdRange::fAllowUnderscores, flags, isalpha(), isdigit(), n, NCBI_THROW, SSeqIdRange::prefix, CTempString::size(), SSeqIdRange::start, and SSeqIdRange::stop.

Definition at line 259 of file seq_id_handle.hpp.

References CSeq_id_Info::GetType(), and CSeq_id_Handle::m_Info.

Referenced by CLinkUtils::AddBlastProductLink(), CReadDispatcher::CannotProcess(), CannotProcess(), CSeq_id_Handle::CompareOrdered(), GetDescrType(), CWGSDataLoader_Impl::GetFileInfo(), CCSRABlobId::GetGeneralIdType(), GetId(), CCSRADataLoader_Impl::GetRecordsOnce(), CScope_Impl::GetTaxId(), GetWGSMasterSeq_id(), CValidError_bioseq::IsWp(), CId1Reader::LoadGiBlob_ids(), CPubseqReader::LoadGiHash(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CPubseqReader::LoadSeq_idAccVer(), CId1Reader::LoadSeq_idBlob_ids(), CId1Reader::LoadSeq_idSeq_ids(), CPubseqReader::LoadSeq_idSeq_ids(), CPubseqReader::LoadSequenceHash(), CSortableSeq_id::operator<(), s_LocIdType(), s_Match_id(), sx_GetReadId(), CSequenceUpdater::x_ChangeIDInFeature(), CGenbankGatherer::x_DoSingleSection(), CDBSourceItem::x_GatherInfo(), CUpdateSeq_Input::x_ReadAccession(), and CDeflineGenerator::x_SetFlags().

Definition at line 778 of file Seq_id.hpp.

References CSeq_id::Score().

Referenced by BOOST_AUTO_TEST_CASE(), ChangeSeqId(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CBlastDBExtractor::ExtractAccession(), CBlastDBExtractor::ExtractSeqId(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CBioseq::GetLabel(), CAlignFormatUtil::GetLinkoutUrl(), CAlignFormatUtil::GetSeqLinkoutInfo(), s_AddOtherRelatedInfoLinks(), s_GetBestIDForURL(), s_GetFullLinkoutUrl(), s_ModifySeqAlnWithFilteredSeqIDs(), s_SetCloneInfo(), CIgBlastTabularInfo::SetAirrFormatData(), WorstRank_SeqIdHandle(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CShowBlastDefline::x_FillDeflineAndId(), CDisplaySeqalign::x_FillSeqid(), CAlnGraphic::x_GetAlnInfo(), CDisplaySeqalign::x_GetDumpgnlLink(), CDisplaySeqalign::x_InitAlignParams(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CDisplaySeqalign::x_PrintDefLine(), COligoSpecificityCheck::x_SavePrimerInfo(), CBlastDBExtractor::x_SetGi2AccMap(), and CBlastDBExtractor::x_SetGi2SeqIdMap().

Write a bioseq's IDs in FASTA format.

Parameters

ostr Stream to write to bioseq Bioseq to get IDs from

Returns

The stream that was passed in, after all writes occurred

Definition at line 2347 of file Seq_id.cpp.

References CSeq_inst_Base::eMol_aa, CSeq_id::FastaAARank(), CSeq_id::FastaNARank(), FindBestChoice(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), CSeq_id_Base::IsGi(), ITERATE, CRef< C, Locker >::NotEmpty(), and CSeq_id::WriteAsFasta().

Implement serializable interface.

Definition at line 2164 of file Seq_id.cpp.

References CSeq_id_Base::e_MaxChoice, CSeq_id_Base::e_not_set, GetId(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetSwissprot(), CSeq_id_Base::IsPatent(), CSeq_id_Base::IsSwissprot(), out(), s_TextId, CSeq_id_Base::Which(), and CSeq_id::x_WriteContentAsFasta().

Referenced by CSeq_id::AsFastaString(), CSeq_id_Handle::AsString(), CSeq_id::GetStringDescr(), operator<<(), s_WriteGnlAndAcc(), CSeq_id::WriteAsFasta(), CDeflineProcess::x_FastaSeqIdWrite(), CSeqVectorProcess::x_FsaSeqIdWrite(), CTitleProcess::x_TitleSeqIdWrite(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), and CFastaOstream::x_WriteAsFasta().

Definition at line 163 of file seq_id_mapper.hpp.

References _ASSERT, CSeq_id_Mapper::m_Trees, and type.

Referenced by CSeq_id_Mapper::GetHandle(), CSeq_id_Mapper::GetMatchingHandles(), CSeq_id_Mapper::GetReverseMatchingHandles(), CSeq_id_Info::GetTree(), CSeq_id_Mapper::HaveMatchingHandles(), CSeq_id_Mapper::HaveReverseMatch(), CSeq_id_Mapper::x_GetTree(), CSeq_id_Mapper::x_IsBetter(), and CSeq_id_Mapper::x_Match().

Definition at line 1666 of file Seq_id.cpp.

References CTempString::data(), CSeq_id::eAcc_division_mask, CSeq_id::eAcc_gi, CSeq_id::eAcc_pdb, CSeq_id::eAcc_prf, CSeq_id::eAcc_swissprot, CSeq_id::eAcc_targeted, CSeq_id::eAcc_tsa, CSeq_id::eAcc_type_mask, CSeq_id::eAcc_unknown, CSeq_id::eAcc_wgs, CSeq_id::eAcc_wgs_intermed, ERR_POST_X, CSeq_id::fAcc_fallback, CSeq_id::fAcc_master, CSeq_id::fAcc_prot, CSeq_id::fAcc_specials, CTempString::find_first_not_of(), CTempString::find_first_of(), flags, CSeq_id::fParse_FallbackOK, CSeq_id::fParse_RawGI, CSeq_id::fParse_RawText, isalnum(), isalpha(), isdigit(), kDigits, NPOS, s_Guide, SAccGuide::s_Key(), CTempString::size(), NStr::UIntToString(), and Warning().

Referenced by CSeq_id::IdentifyAccession().

Definition at line 2699 of file Seq_id.cpp.

References _ASSERT, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Swissprot, ctll::empty(), NStr::EqualNocase(), CSeq_id::eTV_tr, i, NStr::Join(), NCBI_THROW, NPOS, NULL, s_TextId, CSeq_id::Set(), ncbi::grid::netcache::search::fields::size, string, NStr::StringToNonNegativeInt(), and CSeq_id::WhichInverseSeqId().

Referenced by CSeq_id::Set().

Definition at line 2186 of file Seq_id.cpp.

References CPatent_seq_id::AsFastaString(), CPDB_seq_id::AsFastaString(), CTextseq_id::AsFastaString(), CObject_id::AsString(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_MaxChoice, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CDbtag_Base::GetDb(), CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetEmbl(), CSeq_id_Base::GetGenbank(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbmt(), CSeq_id_Base::GetGibbsq(), CSeq_id_Base::GetGiim(), CSeq_id_Base::GetGpipe(), CGiimport_id_Base::GetId(), CSeq_id_Base::GetLocal(), CSeq_id_Base::GetNamed_annot_track(), CSeq_id_Base::GetOther(), CSeq_id_Base::GetPatent(), CSeq_id_Base::GetPdb(), CSeq_id_Base::GetPir(), CSeq_id_Base::GetPrf(), CSeq_id_Base::GetSwissprot(), CDbtag_Base::GetTag(), CSeq_id_Base::GetTpd(), CSeq_id_Base::GetTpe(), CSeq_id_Base::GetTpg(), out(), and CSeq_id_Base::Which().

Referenced by CSeq_id::GetLabel(), and CSeq_id::WriteAsFasta().

Definition at line 846 of file Seq_id.hpp.

Definition at line 347 of file seq_id_handle.hpp.

Referenced by CSeq_id_Handle::AsString(), CSeq_id_Handle::CompareOrdered(), CSeq_id_Handle::GetHash(), CSeq_id_Handle::GetMapper(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::GetSeqIdOrNull(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::operator!=(), CSeq_id_Handle::operator<(), CSeq_id_Handle::operator==(), CSeq_id_Handle::Reset(), CSeq_id_Handle::Swap(), CSeq_id_Handle::Which(), CSeq_id_Handle::x_GetInfo(), and CSeq_id_Mapper::x_GetTree().

Definition at line 975 of file Seq_id.hpp.

Referenced by SSeqIdRange::const_iterator::operator!=(), SSeqIdRange::const_iterator::operator+(), SSeqIdRange::const_iterator::operator++(), SSeqIdRange::const_iterator::operator+=(), SSeqIdRange::const_iterator::operator-(), SSeqIdRange::const_iterator::operator--(), SSeqIdRange::const_iterator::operator-=(), SSeqIdRange::const_iterator::operator<(), SSeqIdRange::const_iterator::operator<=(), SSeqIdRange::const_iterator::operator=(), SSeqIdRange::const_iterator::operator==(), SSeqIdRange::const_iterator::operator>(), and SSeqIdRange::const_iterator::operator>=().

Definition at line 348 of file seq_id_handle.hpp.

Referenced by CSeq_id_Handle::AsString(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::GetHash(), CSeq_id_Handle::GetPacked(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), CSeq_id_Handle::IsPacked(), CSeq_id_Handle::operator!=(), CSeq_id_Handle::operator<(), CSeq_id_Handle::operator==(), CSeq_id_Handle::Reset(), and CSeq_id_Handle::Swap().

Definition at line 121 of file seq_id_handle.hpp.

Referenced by CSeq_id_General_PlainInfo::CSeq_id_General_PlainInfo(), CSeq_id_Local_Info::CSeq_id_Local_Info(), CSeq_id_Textseq_PlainInfo::GetPackedSeqId(), CSeq_id_Textseq_Info::GetPackedSeqId(), CSeq_id_Local_Info::GetPackedSeqId(), CSeq_id_General_Id_Info::GetPackedSeqId(), CSeq_id_General_Str_Info::GetPackedSeqId(), CSeq_id_General_PlainInfo::GetPackedSeqId(), CSeq_id_PDB_Info::GetPackedSeqId(), CSeq_id_Gi_Info::GetPackedSeqId(), CSeq_id_Info::GetSeqId(), CSeq_id_General_PlainInfo::ParseCaseVariant(), CSeq_id_Textseq_PlainInfo::ParseCaseVariant(), and CSeq_id_Local_Info::ParseCaseVariant().

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