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NCBI C++ ToolKit: Iterators

Set bit filter for annotations that support it (SNP) If filter is set then collect only annotations that have masked (filter_mask) bits equal to the filter_bits.

Definition at line 790 of file annot_selector.hpp.

Search features with specified id.

Definition at line 142 of file feat_ci.hpp.

Definition at line 334 of file annot_selector.hpp.

Class of bioseqs to iterate.

Any bioseq.

Main bioseq only.

Parts only.

Search for bioseqs in any bioseq-set regardless of types and classes.

Definition at line 72 of file bioseq_ci.hpp.

Definition at line 66 of file seq_vector_ci.hpp.

Definition at line 75 of file seq_annot_ci.hpp.

Flags that affect iteration.

Flags that are irrelevant are ignored. For example, passing fIncludeGivenEntry into the constructor that takes a CBioseq_set_Handle is ignored because there is no "given entry" because only a CBioseq_set_Handle has been given.

Iterate recursively.

Include the top (given) entry.

Deprecated.

Deprecated:

No need to use.

Deprecated.

Deprecated:

Use fRecursive instead.

Definition at line 74 of file seq_entry_ci.hpp.

Definition at line 851 of file annot_selector.hpp.

Definition at line 477 of file annot_selector.hpp.

Flag to indicate location overlapping method.

default - overlapping of individual intervals

overlapping of total ranges only

Definition at line 92 of file annot_selector.hpp.

Flag to indicate references resolution method.

Do not search annotations on segments.

default - search only on segments in the same TSE

Search annotations for all referenced sequences.

Definition at line 97 of file annot_selector.hpp.

Flag to indicate sorting method.

do not sort annotations for faster retrieval

default - increasing start, decreasing length

decresing end, decreasing length

Definition at line 103 of file annot_selector.hpp.

Flag to indicate handling of unresolved seq-ids.

Ignore unresolved ids (default)

Search annotations for unresolvable IDs.

Throw exception for unresolved ids.

Definition at line 109 of file annot_selector.hpp.

Add named annot to set of annots names to look for.

Definition at line 476 of file annot_selector.cpp.

References SAnnotSelector::HasWildcardInAnnotsNames(), SAnnotSelector::m_ExcludeAnnotsNames, SAnnotSelector::m_HasWildcardInAnnotsNames, and SAnnotSelector::m_IncludeAnnotsNames.

Referenced by SAnnotSelector::AddNamedAnnots(), SAnnotSelector::AddUnnamedAnnots(), CGraphUtils::CalcGraphLevels(), CGBObjectLoader::Execute(), NSearchFeatPanel::GatherFeatures(), CSeqUtils::GetAnnotSelector(), NSnpBins::GetBinSelector(), CDataLoader::GetCDDAnnots(), NSnpAnnot::GetFeat_CI(), NSnpAnnot::GetGraph_CI(), CNAUtils::GetNATrackInfo(), NSnp::IsSnpKnown(), CDemoApp::Run(), CTestBMApp::Run(), s_GetAnnotSelector(), s_GetRnaMappingLocs(), SAnnotSelector::SetDataSource(), CSnpJob::x_FetchFtable(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CMacroBioData::x_GetAnnotSelector(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CLDBlockJob::x_Load(), CSGAnnotJob::x_LoadCoverageGraph(), CFeatureGenerator::x_SetAnnotName(), and CFeatureGraph::x_StartJob().

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

Definition at line 47 of file align_ci.cpp.

Create an iterator that enumerates CSeq_align objects related to the given bioseq.

Definition at line 56 of file align_ci.cpp.

Create an iterator that enumerates CSeq_align objects from the annotation regardless of their location.

Definition at line 118 of file align_ci.cpp.

Create an iterator that enumerates CSeq_align objects from the seq-entry regardless of their location.

Definition at line 151 of file align_ci.cpp.

Iterate all alignments from the seq-annot that annotate the location.

Definition at line 131 of file align_ci.cpp.

Create an iterator that enumerates CSeq_align objects related to the given seq-loc.

Definition at line 103 of file align_ci.cpp.

Check if the sequence can be obtained for the interval [start, stop)

Definition at line 206 of file seq_vector_ci.cpp.

References CSeqMap::CanResolveRange(), CSeqMap::fDefaultFlags, CHeapScope::GetScopeOrNull(), kMax_UInt, CSeqVector_CI::m_ScannedEnd, CSeqVector_CI::m_ScannedStart, CSeqVector_CI::m_Scope, CSeqVector_CI::m_SeqMap, CSeqVector_CI::m_Strand, CSeqVector_CI::m_TSE, CSeqVector_CI::m_UsedTSEs, max(), min(), SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetRange(), and SSeqMapSelector::SetStrand().

Referenced by CSeqVector::CanGetRange(), CSeqVector_CI::GetSeqData(), CSeqVector_CI::x_CheckBackward(), and CSeqVector_CI::x_CheckForward().

Create an iterator that enumerates bioseqs from the entry taken from the scope.

Use optional filter to iterate over selected bioseq types only. Filter value eMol_na may be used to include both dna and rna bioseqs.

Definition at line 234 of file bioseq_ci.cpp.

References CBioseq_CI::x_Initialize().

Create an iterator that enumerates CSeq_descr objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited).

Definition at line 72 of file seq_descr_ci.cpp.

References _ASSERT, CSeq_entry_Handle::GetSeq(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSeq(), CBioseq_Base_Info::IsSetDescr(), CSeq_descr_CI::m_CurrentBase, CSeq_descr_CI::m_CurrentSeq, CSeq_descr_CI::m_CurrentSet, CBioseq_Handle::x_GetInfo(), CBioseq_set_Handle::x_GetInfo(), and CSeq_descr_CI::x_Settle().

Create an iterator that enumerates Seq-entries inside the given Seq-entry.

Definition at line 52 of file seq_entry_ci.cpp.

Create an iterator that enumerates seq-entries related to the given seq-set.

Definition at line 239 of file seq_entry_ci.cpp.

Create an iterator that enumerates seq-entries related to the given seq-entry.

Definition at line 231 of file seq_entry_ci.cpp.

Iterate all Seq-tables from the seq-annot regardless of their location.

Definition at line 113 of file seq_table_ci.cpp.

Iterate all Seq-tables from the seq-entry regardless of their location.

Definition at line 126 of file seq_table_ci.cpp.

Create an iterator that enumerates CSeqdesc objects from a bioseq with limit number of seq-entries to "search_depth" (0 = unlimited) for set of types.

Create an iterator that enumerates CSeqdesc objects from a seq-entry, limit number of seq-entries to "search_depth" (0 = unlimited) for set of types.

Definition at line 501 of file seq_map_ci.hpp.

Check if iterator points to an object.

Check if iterator points to an object.

Check if iterator points to an object.

Check if iterator points to an object.

Check if iterator points to an object.

Check if iterator points to an object.

Check if iterator points to an object.

Check if iterator points to an object.

Exclude feature subtype from the search.

Definition at line 828 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetSubtypeIndex(), SAnnotSelector::IncludedFeatSubtype(), SAnnotSelector::m_AnnotTypesBitset, and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by CFeatTableEdit::GenerateLocusIds(), CFeatTableEdit::GenerateLocusTags(), CDemoApp::Run(), s_SetSelection(), CFeatureGenerator::SImplementation::x_CopyAdditionalFeatures(), CBioseqIndex::x_DefaultSelector(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), and CFeatTableEdit::xGenerateLocusIdsUseExisting().

Exclude feature type from the search.

Definition at line 798 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetFeatTypeRange(), i, SAnnotSelector::IncludedFeatType(), SAnnotSelector::m_AnnotTypesBitset, and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by CDemoApp::Run(), s_SetSelection(), and CBioseqIndex::x_DefaultSelector().

Add named annot to set of annots names to exclude.

Definition at line 499 of file annot_selector.cpp.

References SAnnotSelector::HasWildcardInAnnotsNames(), SAnnotSelector::m_ExcludeAnnotsNames, SAnnotSelector::m_HasWildcardInAnnotsNames, and SAnnotSelector::m_IncludeAnnotsNames.

Referenced by CGraphTrackFactory::CreateTracks(), CSeqTableGraphTrackFactory::CreateTracks(), SAnnotSelector::ExcludeNamedAnnots(), SAnnotSelector::ExcludeUnnamedAnnots(), ExtractExtraIds(), CSeqUtils::GetAnnotSelector(), GetBestCdsForMrna(), GetBestMrnaForCds(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeqUtils::GetMrnaForCds(), CAsn2FastaApp::HandleSeqEntry(), CId1FetchApp::LookUpGI(), CFeatCompareJob_Align::Run(), CDemoApp::Run(), CFeatTreeSampleApp::Run(), s_GetRnaMappingLocs(), s_SetSelection(), CBioseqIndex::x_DefaultSelector(), x_GetAnnotSelector(), and CFeatureGraph::x_StartJob().

Extract optional zoom level suffix from named annotation string.

returns true if zoom level explicitly defined in the full_name argument. The accession string without zoom level will be written by acc_ptr pointer if it's not null. Zoom level will be written by zoom_level_ptr pointer if it's not null. Absent zoom level will be represented by value 0. Wildcard zoom level will be represented by value -1.

Definition at line 965 of file annot_selector.cpp.

References CSeq_annot::ExtractZoomLevel().

Referenced by CGraphUtils::CalcGraphLevels(), NSnpAnnot::GetGraph_CI(), CGBDataLoader_Native::GetNamedAnnotAccessions(), SAnnotSelector::HasIncludedOnlyNamedAnnotAccessions(), SAnnotSelector::IncludedAnnotName(), SAnnotSelector::IncludeNamedAnnotAccession(), CProcessor_AnnotInfo::LoadBlob(), s_CreateNAChunk(), CHistogramGlyph::SetAnnotName(), CSnpJob::x_FetchGraphs(), CAnnot_Collector::x_FoundAllNamedAnnotAccessions(), and CId2ReaderBase::x_UpdateLoadedSet().

Set annot type, include all subtypes.

Definition at line 840 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, CAnnotType_Index::GetAnnotTypeRange(), i, SAnnotSelector::m_AnnotTypesBitset, and SAnnotSelector::SetAnnotType().

Referenced by CAnnotTypes_CI::CAnnotTypes_CI(), SAnnotSelector::ExcludeFeatSubtype(), SAnnotSelector::ExcludeFeatType(), SAnnotSelector::IncludeFeatSubtype(), and SAnnotSelector::IncludeFeatType().

Returns the current depth, which may vary depending on flags.

If fIncludeGivenEntry is set, it returns the current depth relative to the initially given seq-entry (or initially given bioseq-set), where the given has depth "0", its direct children have depth "1", and so on. If fIncludeGivenEntry is NOT set, then the returned values are 1 less. That is, "0" for direct descendents of the given, "1" for the direct descendents of those, etc.

See also

fIncludeGivenEntry

Definition at line 205 of file seq_entry_ci.cpp.

References _ASSERT, CSeq_entry_CI::fIncludeGivenEntry, CSeq_entry_CI::m_Flags, CSeq_entry_CI::m_Parent, and CSeq_entry_CI::m_SubIt.

return end position of current segment in sequence (exclusive)

Definition at line 679 of file seq_map_ci.hpp.

References SSeqMapSelector::m_Length, SSeqMapSelector::m_Position, and CSeqMap_CI::m_Selector.

Referenced by CGapAnalysis::AddBioseqGaps(), CValidError_bioseq::GapByGapInst(), CSeqVector_CI::GetGapSizeForward(), CAdvancedAlignCleanup::GetProsplignCompartments(), CResolveRequest::Process(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_NewGapItem(), UpdateSeqLength(), CAnnot_Collector::x_CollectMapped(), CFlatGatherer::x_CollectSourceDescriptors(), CComponentSearchJob::x_DoSearch(), CSeqVector_CI::x_FillCache(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSeqVector_CI::x_IncSeg(), CSeqVector_CI::x_InitSeg(), CSeqMap_CI::x_Prev(), CSequenceTrack::x_RenderGaps(), CSplign::x_RunOnCompartment(), CAnnot_Collector::x_SearchMapped(), CSequenceAmbigTrimmer::x_SegmentGetEndInclusive(), CSeqVector_CI::x_SetPos(), CVectorTrimPanel::x_SetSeqData(), CSequenceAmbigTrimmer::x_SliceBioseq(), CSeqVector_CI::x_UpdateCacheDown(), CSeqVector_CI::x_UpdateCacheUp(), and CSeqVector_CI::x_UpdateSeg().

Definition at line 192 of file graph_ci.cpp.

References CSeq_graph_Base::GetGraph(), CAnnotObject_Ref::GetMappingInfo(), CMappedGraph::GetOriginalGraph(), CAnnotMapping_Info::IsPartial(), CMappedGraph::m_GraphRef, CMappedGraph::m_MappedGraph, and CMappedGraph::MakeMappedGraph().

Referenced by NSnpAnnot::EstimateSNPCount(), CSGAnnotJob::x_AddGraphObject(), CSnpJob::x_FetchGraphs(), CVectorTrimPanel::x_TrimSeqGraphData(), and CReportTrim::x_TrimSeqGraphData().

return length of current segment

Definition at line 672 of file seq_map_ci.hpp.

References SSeqMapSelector::m_Length, and CSeqMap_CI::m_Selector.

Referenced by CGapAnalysis::AddBioseqGaps(), CAlignmentAssistant::AdjustBioseq(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CSeqMap::CanResolveRange(), CGapCache::CGapCache(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CFeatGapInfo::CollectGaps(), CEditSequence::CreateControls(), CSeqMap_CI::GetRefEndPosition(), CDemoApp::Run(), s_NewGapItem(), CSeq_loc_Conversion::SetConversion(), CEditSeqEndsWithAlign::TrimBeforeAfter(), UpdateSeqLength(), CGapAnalysis::x_AddGapsFromBases(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CSeqMap_CI::x_Push(), CVectorTrimPanel::x_SetSeqData(), CSequenceAmbigTrimmer::x_SliceBioseq(), and CSeqVector_CI::x_UpdateSeg().

Reimplemented from CSeq_feat_Handle.

Definition at line 183 of file mapped_feat.cpp.

References CSeq_feat_Base::GetLocation(), CMappedFeat::GetMappedLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), CAnnotMapping_Info::IsMappedLocation(), and CMappedFeat::m_MappingInfoPtr.

Referenced by CFeatTree::AddFeaturesFor(), CReportTrim::AdjustAndTranslate(), CEditSequence::AdjustFeatureLocations(), AdjustSingleFeature(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), BOOST_AUTO_TEST_CASE(), BuildFeatureSeqTableFromSeqEntry(), CheckAdjustStart(), CheckAdjustStartAndStop(), CheckAdjustStop(), variation::CVariationUtil::CheckExonBoundary(), CLDBlockGlyph::CLDBlockGlyph(), CAnnotCompare::CompareFeats(), CWriteUtil::CompareFeatures(), CFeatureGenerator::CreateMicroIntrons(), CSourceFeatureItem::CSourceFeatureItem(), CAnnotationASN1::ExtractModels(), variation::CVariationUtil::FindLocationProperties(), CValidError_bioseq::GapByGapInst(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), GetAlignmentForRna(), CGeneFinder::GetAssociatedGeneInfo(), GetBestOverlappingFeat(), CFeatureGenerator::SImplementation::GetCds(), CInternalStopFinder::GetCDSNucleotideSequence(), GetCdsOnMrna(), variation::CVariationUtil::GetEffectiveTranscriptLength(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), GetFeatureProtein(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CSeqUtils::GetMappingInfo(), GetMrnasForGene(), GetOverlappingFeatures(), GetParentFeature(), CSeqTextDataSourceInterval::GetSeqData(), CFlatFileGenerator::GetSeqFeatText(), CValidError_imp::GetTSACDSOnMinusStrandErrors(), CValidError_bioseqset::IsCDSProductInGPS(), NSnp::IsSnpKnown(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), MakemRNAforCDS(), SFeatLengthPredicate::operator()(), SFeatSortPredicate::operator()(), SChildLess::operator()(), operator<<(), CGeneFinder::CGeneSearchPlugin::processMainLoop(), variation::CVariationUtil::RemapToAnnotatedTarget(), CNewCleanup_imp::ResynchPeptidePartials(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CFeatureRetrievalJob::Run(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_CdsCountAmbiguities(), s_CdsLength(), s_CdsStopCodon(), s_CheckQuals_cdregion(), s_CodingPropensity(), s_CoincidingGapFeatures(), s_CollectBestOverlaps(), s_GetCdregionPlusUpstream(), s_GetFeatureKey(), s_GetFeatureKeyLinkLocation(), s_GetLinkFeatureKey(), s_GetOverlap(), s_PrematureStopCodon(), s_TitleFromSegment(), s_Utrs(), CCleanup::SetGenePartialByLongestContainedFeature(), SetTranslExcept(), CValidError_bioseq::ValidateFeatPartialInContext(), CVcfWriter::WriteAnnot(), CGuiObjectInfoSeq_feat::x_AddExtraInfo(), CFeatureItem::x_AddQualCodedBy(), CFeatureItem::x_AddQualOperon(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CGvfWriteRecord::x_AssignAttributeEndRange(), CGvfWriteRecord::x_AssignAttributeStartRange(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_CopyCDSFromCDNA(), CSGFeatureJob::x_CreateAndFilterCrossOriginGlyphs(), CSGFeatureJob::x_CreateCloneFeature(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeatSmear(), CSGFeatureJob::x_CreateFeature1(), CSGFeatureJob::x_CreateFeatures(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), COrfSearchJob::x_DoSearch(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), variation_ref::CHgvsParser::x_general_pos(), variation::CHgvsParser::x_general_pos(), CCdregionValidator::x_HasGoodParent(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CBioseqIndex::x_InitFeats(), CValidError_bioseq::x_IsSameAsCDS(), CBatchFeatJob::x_LoadFeatProducts(), CMacroFunction_FeatStrandednessConstraint::x_Match(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CNewCleanup_imp::x_MoveCDSFromNucAnnotToSetAnnot(), CValidError_bioseq::x_PartialAdjacentToIntron(), variation::CHgvsParser::x_PlacementCoordsToStr(), CReportTrim::x_RetranslateCDS(), CFlatFeatureRetrieveJob::x_Run(), variation_ref::CHgvsParser::x_SeqLocToStr(), CBioseqContext::x_SetHasMultiIntervalGenes(), x_ToBlastVec(), CValidError_bioseq::x_ValidateAbuttingRNA(), CSingleFeatValidator::x_ValidateGeneXRef(), CVcfWriter::x_WriteFeature(), CGff3Writer::xAssignFeature(), CGff2Writer::xAssignFeatureAttributeIsOrdered(), CGff2Writer::xAssignFeatureAttributePartial(), CGff2Writer::xAssignFeatureEndpoints(), CGtfWriter::xAssignFeatureMethod(), CGtfWriter::xAssignFeaturesCds(), CGtfWriter::xAssignFeaturesGene(), CGff2Writer::xAssignFeatureStrand(), CGff3Writer::xAssignFeatureStrand(), CGtfWriter::xAssignFeaturesTranscript(), CFeatTableEdit::xConvertToGeneralIds(), CGffIdGenerator::xExtractFeatureLocation(), CGff2Writer::xGenerateMissingTranscript(), CExonNumberAssigner::xInitialize(), CFeatTableEdit::xPutErrorMissingLocustag(), CFeatTableEdit::xPutErrorMissingProteinId(), CFeatTableEdit::xPutErrorMissingTranscriptId(), CGtfWriter::xWriteFeatureExons(), CGff3Writer::xWriteFeatureGeneric(), CGff3Writer::xWriteFeatureProtein(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteFeatureTrna(), CGff3Writer::xWriteNucleotideFeature(), CGff3Writer::xWriteNucleotideFeatureTransSpliced(), and CGff3Writer::xWriteProteinFeature().

Feature mapped to the master sequence.

WARNING! The function is rather slow and should be used with care.

Definition at line 152 of file mapped_feat.cpp.

References CMappedFeat::GetSeq_feat().

Referenced by CLinkUtils::AddDbxrefLinksForSNP(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CReportEntry::CReportEntry(), CExploreProcess::DoOneBioseq(), CSnpTrack::GenerateAsn1(), CFeatureTrack::GenerateAsn1(), CGeneModelTrack::GenerateAsn1(), CSeqUtils::GetCdsMappingInfoFromRna(), CGeneXrefsFromFeats::GetCommand(), CGuiObjectInfoVariation::GetLinks(), CSeqUtils::GetMappingInfo(), GetOverlappingFeatures(), GetProtAndRnaForCDS(), CLinkedFeatsGroup::GetTooltip(), CAsn2FastaApp::HandleSeqEntry(), CWriteUtil::IsTransspliced(), CSelectFeatureDlg::OnFeatureEdit(), SChildLess::operator()(), CFeatIdRemapper::RemapIds(), variation::CVariationUtil::RemapToAnnotatedTarget(), CFeatureLoadingJob::Run(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_AdjustToAnnotatedCDS(), s_GetFeatureKey(), s_GetRnaMappingLocs(), variation::CHgvsParser::CContext::SetId(), variation_ref::CHgvsParser::CContext::SetId(), ProjectCDS::transform_align(), CFeatureItem::x_AddQualsIdx(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGAlignmentJob::x_CreateGeneModels(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CAnnotGetter::x_GetCompleteSeqAnnot(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CAutoDef::x_GetFeatureClauses(), CSelectFeatureDlg::x_LoadFeatures(), CFeatureSearchJob::x_SearchFeatures(), CReportEntry::x_SetFeature(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CGtfWriter::xAssignFeaturesCds(), and CGff3Writer::xWriteFeatureCds().

Definition at line 684 of file annot_selector.hpp.

References SAnnotSelector::m_NamedAnnotAccessions.

Referenced by CPSGDataLoader_Impl::GetAnnotRecordsNAOnce(), SCacheInfo::GetBlob_idsSubkey(), CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce(), CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce(), CId1Reader::LoadSeq_idBlob_ids(), CId2ReaderBase::LoadSeq_idBlob_ids(), s_FormatCall(), CReaderRequestResult::s_KeyBlobIds(), CAnnot_Collector::x_FoundAllNamedAnnotAccessions(), CScope_Impl::x_GetAnnotRef_Info(), and CSGAnnotJob::x_LoadCoverageGraph().

Get original feature with unmapped location/product.

Definition at line 146 of file mapped_feat.cpp.

References CSeq_feat_Handle::GetOriginalSeq_feat().

Referenced by CReportTrim::AdjustAndTranslate(), CEditSequence::AdjustFeatureLocations(), AdjustSingleFeature(), CModifyStructuredComment::apply_to_seq_and_feat(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), BOOST_AUTO_TEST_CASE(), CFeatureItemBase::CFeatureItemBase(), CLDBlockGlyph::CLDBlockGlyph(), CAnnotCompare::CompareFeats(), CConvertCDSToProt::Convert(), Convert_Seq_loc_Seq_feat(), CCdsToMatPeptide::ConvertInner(), CSourceFeatureItem::CSourceFeatureItem(), CExploreProcess::DoOneBioseq(), CAnnotationASN1::ExtractModels(), CmRNAAndCDSIndex::FindMatchmRNA(), CFeatTableEdit::GenerateLocusTags(), NSnp::GetAlleles(), CPubField::GetApplyObjects(), CSrcTableColumnBase::GetApplyObjects(), GetBestMrnaForCds(), GetBioSourceForBioseq(), NSnp::GetBitfield(), CValidError_imp::GetCDSGivenProduct(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), GetFeatureProtein(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CGeneModelFeatJob::GetFilters(), NSnp::GetLength(), CSeqUtils::GetMappingInfo(), GetmRNAForProduct(), CValidError_imp::GetmRNAGivenProduct(), GetMrnasForGene(), CCleanup::GetNormalizableGeneQualPairs(), CPubField::GetObjects(), CSrcTableColumnBase::GetObjects(), GetOverlappingFeatures(), GetProductName(), GetPROTForProduct(), NSnp::GetRsid(), NSnp::GetTag(), CBulkCDS::GetValuesTableFromSeqEntry(), CFeatTableEdit::InferPartials(), NSnp::IsSnp(), NSnp::IsSnpKnown(), SFeatSortPredicate::operator()(), operator<<(), CFeatTableEdit::ProcessCodonRecognized(), CCdsForMrnaPlugin::processMainLoop(), CGeneFinder::CGeneSearchPlugin::processMainLoop(), CGeneFinder::ResolveGeneObjectId(), RestoreModelFromPublicMrnaFeature(), RetranslateCdregion(), CExtendCDSToStop::RetranslateCDSCommand(), CRevCompSequencesDlg::RevCompBioSeq(), CGffExportJob::Run(), CGtfExportJob::Run(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CDemoApp::Run(), CTestBMApp::Run(), CSampleLds2Application::Run(), s_Code_break(), s_CompareProtProdToTrans(), s_GetCdsByProduct(), s_GetMappedFeat(), s_GetProductName(), s_IsSelenocysteine(), s_PassesFilter(), s_RemoveTaxnameFromProtRef(), s_Render_SeqFeat(), s_SubsequentIntron(), CFixFeatureId::s_UpdateFeatureIds(), s_VerifyTree(), CGeneOverlapProcess::SeqEntryProcess(), CCleanup::SetGeneticCodes(), CCleanup::SetProteinName(), SetTranslExcept(), sGetCdsProductName(), CFeatTableEdit::SubmitFixProducts(), TrimSequenceAndAnnotation(), TrimStopsFromCompleteCDS(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddQualsCdregionIdx(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualTranslation(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeatSmear(), CGeneModelFeatJob::x_CreateFeaturesWithFilter(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CSourceItem::x_GatherInfo(), CFlatGatherer::x_GatherReferences(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CAutoDef::x_GetFeatureClauses(), CDeflineGenerator::x_GetGeneRefViaCDS(), CLDBlockJob::x_LoadFtable(), CSnpJob::x_PreFetchFtable(), CVectorTrimPanel::x_RetranslateCDS(), CReportTrim::x_RetranslateCDS(), CFeatureSearchJob::x_SearchFeatures(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CVectorTrimPanel::x_TrimSelected(), CValidError_bioseq::x_ValidateAbuttingRNA(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CMRNAValidator::x_ValidateMrnaGene(), CFeatTableEdit::xAdjustExistingParentGene(), CGtfWriter::xAssignFeatureAttributeTranscriptBiotype(), CGff3Writer::xAssignFeatureType(), CFeatTableEdit::xCreateMissingParentGene(), CFeatTableEdit::xFeatureAddQualifier(), CFeatTableEdit::xFeatureRemoveQualifier(), CFeatTableEdit::xFeatureSetProduct(), CFeatTableEdit::xGenerateMissingMrnaForCds(), CFeatTableEdit::xGetLinkedFeature(), CGff3Writer::xWriteFeatureProtein(), CBedWriter::xWriteFeaturesThreeFeatData(), and CGff3Writer::xWriteProteinFeature().

Get original graph with unmapped location/product.

Definition at line 70 of file graph_ci.hpp.

References CAnnotObject_Ref::GetGraph(), and CMappedGraph::m_GraphRef.

Referenced by BOOST_AUTO_TEST_CASE(), Convert_Seq_loc_Seq_graph(), CMappedGraph::GetA(), CMappedGraph::GetB(), CMappedGraph::GetComment(), CMappedGraph::GetComp(), CMappedGraph::GetGraph(), CMappedGraph::GetNumval(), CMappedGraph::GetTitle(), CMappedGraph::GetTitle_x(), CMappedGraph::GetTitle_y(), CMappedGraph::IsSetA(), CMappedGraph::IsSetB(), CMappedGraph::IsSetComment(), CMappedGraph::IsSetComp(), CMappedGraph::IsSetTitle(), CMappedGraph::IsSetTitle_x(), CMappedGraph::IsSetTitle_y(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CMappedGraph::MakeMappedGraph(), CMappedGraph::MakeMappedGraphData(), CMappedGraph::MakeMappedLoc(), CRevCompSequencesDlg::RevCompBioSeq(), CDemoApp::Run(), CEditSeqEndsWithAlign::TrimQualityScores(), CAlignmentAssistant::TrimQualityScores(), CReportTrim::TrimSeqGraphs(), TrimSequenceAndAnnotation(), CVectorTrimPanel::x_TrimSeqGraphs(), and CValidError_graph::x_ValidateGraphOnDeltaBioseq().

Get original alignment.

Definition at line 225 of file align_ci.cpp.

References _ASSERT, CAnnotTypes_CI::Get(), CAnnotObject_Ref::GetAlign(), and CAnnotObject_Ref::IsAlign().

Referenced by BOOST_AUTO_TEST_CASE(), Convert_Seq_loc_Seq_align(), CwxDemoAlignTableFrame::InitData(), CSequenceEditingEventHandler::RemoveSegGaps(), CDemoApp::Run(), CSampleLds2Application::Run(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CApplyRNAITSDlg::x_GetAlignments(), CApplyRNAITSDlg::x_IsThereAlignment(), CApplyRNAITSDlg::x_SetupAlnMgr(), and CVectorTrimPanel::x_TrimAlignments().

Reimplemented from CSeq_feat_Handle.

Definition at line 167 of file mapped_feat.cpp.

References CSeq_feat_Handle::GetPartial(), CAnnotMapping_Info::IsMapped(), CAnnotMapping_Info::IsPartial(), and CMappedFeat::m_MappingInfoPtr.

Referenced by CFeatTableEdit::InferPartials(), CNewCleanup_imp::ResynchPeptidePartials(), CDemoApp::Run(), s_CdsFlags(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddQualPartial(), CFeatureItem::x_AddQualsProt(), CFeatTableEdit::xAdjustExistingParentGene(), and CGff2Writer::xAssignFeatureAttributePartial().

Definition at line 373 of file seq_vector_ci.hpp.

References CSeqVector_CI::x_CacheOffset(), and CSeqVector_CI::x_CachePos().

Referenced by CProtProp::AACount(), CSeqVector::CanGetRange(), CSeqVector_CI::GetGapSizeBackward(), CSeqVector_CI::GetGapSizeForward(), GetMRNATranslationProblems(), CSeqVector::GetSeqData(), CSeqVector_CI::GetSeqData(), CSeqVector_CI::HasZeroGapBefore(), CSeqVector_CI::operator!=(), operator+(), CSeqVector_CI::operator+=(), operator-(), CSeqVector_CI::operator-=(), CSeqVector_CI::operator<(), CSeqVector_CI::operator<=(), CSeqVector_CI::operator==(), CSeqVector_CI::operator>(), CSeqVector_CI::operator>=(), s_CalcDistanceUntilNextSignificantGapOrEnd(), CSeqVector_CI::SetCoding(), CSeqVector_CI::SetRandomizeAmbiguities(), CSeqVector_CI::SetStrand(), CSeqVector_CI::SkipGap(), CSeqVector_CI::SkipGapBackward(), CGapAnalysis::x_AddGapsFromBases(), CFeaturePropagator::x_CdsStopAtStopCodon(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeqVector_CI::x_NextCacheSeg(), CSeqVector_CI::x_PrevCacheSeg(), CSeqVector_CI::x_SetPos(), CSeqVector_CI::x_ThrowOutOfRange(), CSeqVector_CI::x_UpdateCacheDown(), CSeqVector_CI::x_UpdateCacheUp(), CValidError_graph::x_ValidateGraphValues(), and CFastaOstream::x_WriteSequence().

return position of current segment in sequence

Definition at line 665 of file seq_map_ci.hpp.

References SSeqMapSelector::m_Position, and CSeqMap_CI::m_Selector.

Referenced by CGapAnalysis::AddBioseqGaps(), CSeqMap::CanResolveRange(), CGapCache::CGapCache(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CFeatGapInfo::CollectGaps(), CValidError_bioseq::GapByGapInst(), CSeqVector_CI::GetGapSizeBackward(), CAdvancedAlignCleanup::GetProsplignCompartments(), CSeqMap_CI::IsValid(), CSeqMap_CI::operator<(), CSeqMap_CI::operator==(), CSeqMap_CI::operator>(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_NewGapItem(), CSeq_loc_Conversion::SetConversion(), UpdateSeqLength(), CGapAnalysis::x_AddGapsFromBases(), CAnnot_Collector::x_CollectMapped(), CAnnot_Collector::x_CollectSegments(), CFlatGatherer::x_CollectSourceDescriptors(), CSeqVector_CI::x_DecSeg(), CComponentSearchJob::x_DoSearch(), CSGSegmentMapJob::x_Execute(), CSeqVector_CI::x_FillCache(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CSeqVector_CI::x_InitSeg(), CSGSegmentSmearJob::x_LoadFromDeltaSeqs(), CSGSegmentSmearJob::x_LoadGaps(), CSeqMap_CI::x_Next(), CSeqVector_CI::x_PrevCacheSeg(), CSequenceTrack::x_RenderGaps(), CSplign::x_RunOnCompartment(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchSegments(), CSequenceAmbigTrimmer::x_SegmentGetEndInclusive(), CSeqMap_CI::x_Select(), CSeqVector_CI::x_SetPos(), CVectorTrimPanel::x_SetSeqData(), CSeqMap_CI::x_SettleNext(), CSequenceAmbigTrimmer::x_SliceBioseq(), CSeqVector_CI::x_UpdateCacheDown(), CSeqVector_CI::x_UpdateCacheUp(), and CSeqVector_CI::x_UpdateSeg().

Reimplemented from CSeq_feat_Handle.

Definition at line 176 of file mapped_feat.cpp.

References CMappedFeat::GetMappedLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeq_feat_Base::GetProduct(), CAnnotMapping_Info::IsMappedProduct(), and CMappedFeat::m_MappingInfoPtr.

Referenced by BOOST_AUTO_TEST_CASE(), DeleteProteinAndRenormalizeNucProtSet(), GetBestCdsForMrna(), CSeqUtils::GetCdsMappingInfoFromRna(), CEditSequence::GetFeatures(), variation::GetFocusLocusIDs(), GetProteinString(), variation::GetUniquePrimaryTranscriptId(), SChildLess::operator()(), operator<<(), CTabularFormatter_SeqId::Print(), CResolveRequest::Process(), variation::CVariationUtil::RemapToAnnotatedTarget(), CDemoApp::Run(), s_CheckQuals_cdregion(), s_CollectBestOverlaps(), s_GetCdsSequence(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_GetProductFlagFromCDSProductNames(), s_GetRnaMappingLocs(), s_TitleFromSegment(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_bioseqset::ValidateGenProdSet(), CFeatureItem::x_AddQualProteinConflict(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CSeq_id_Resolver__LRG::x_Create(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGFeatureJob::x_CreateFeature1(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFeatureItem::x_GetAssociatedProtInfo(), CFeatureItem::x_GetAssociatedProtInfoIdx(), variation::CHgvsParser::x_header(), variation::CVariationUtil::CCdregionIndex::x_Index(), CReportEntry::x_SetFeature(), CVectorTrimPanel::x_TrimSelected(), CCdregionValidator::x_ValidateFarProducts(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xWriteFeatureCds(), and CGff3Writer::xWriteFeatureProtein().

Reimplemented from CSeq_feat_Handle.

Definition at line 208 of file mapped_feat.cpp.

References CSeq_id_Handle::GetHandle(), CAnnotMapping_Info::GetProductId(), CSeq_feat_Handle::GetProductId(), CAnnotMapping_Info::IsMappedProduct(), and CMappedFeat::m_MappingInfoPtr.

Referenced by GetAlignmentForRna(), s_GetDbxrefFromProduct(), CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualsCdregion(), CFeatureItem::x_AddQualsCdregionIdx(), CFeatureItem::x_AddQualsProt(), CBioseqIndex::x_InitFeats(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xAssignFeatureAttributeTranscriptId(), CGffIdGenerator::xExtractFarAccession(), and CGffIdGenerator::xGetIdForCds().

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

Definition at line 292 of file seq_map_ci.cpp.

References NCBI_THROW, CSeqMap_CI::x_GetSegment(), CSeqMap::x_GetSeq_literal(), and CSeqMap_CI::x_GetSeqMap().

Referenced by CSeqVector_CI::GetGapSeq_literal(), CAdvancedAlignCleanup::GetProsplignCompartments(), CGapInfo< CBlastTabular >::IntersectsNonBridgeableGap(), CDemoApp::Run(), s_NewGapItem(), UpdateSeqLength(), CSequenceTrack::x_RenderGaps(), CSplign::x_RunOnCompartment(), CVectorTrimPanel::x_SetSeqData(), CSequenceAmbigTrimmer::x_SliceBioseq(), and CFastaOstream::x_WriteSequence().

Definition at line 700 of file seq_map_ci.hpp.

References CSeqMap_CI_SegmentInfo::GetRefMinusStrand(), and CSeqMap_CI::x_GetSegmentInfo().

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), CTextItemSeq_loc::CreateObject(), CSeqMap_CI::GetData(), CDemoApp::Run(), CSeq_loc_Conversion::SetConversion(), CAnnot_Collector::x_CollectMapped(), CSeqVector_CI::x_FillCache(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CSeqMap_CI::x_Push(), and CAnnot_Collector::x_SearchMapped().

Definition at line 693 of file seq_map_ci.hpp.

References CSeqMap_CI_SegmentInfo::GetRefPosition(), and CSeqMap_CI::x_GetSegmentInfo().

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), CTextItemSeq_loc::CreateObject(), CSeqMap_CI::GetData(), CSeqMap_CI::GetRefEndPosition(), CDemoApp::Run(), CSeq_loc_Conversion::SetConversion(), CAnnot_Collector::x_CollectMapped(), CSeqVector_CI::x_FillCache(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CSeqMap_CI::x_Push(), and CAnnot_Collector::x_SearchMapped().

The following function makes sense only when the segment is a reference to another seq.

Definition at line 312 of file seq_map_ci.cpp.

References CSeq_id_Handle::GetHandle(), NCBI_THROW, CSeqMap_CI::x_GetSegment(), and CSeqMap_CI::x_GetSeqMap().

Referenced by CSeqMap::CanResolveRange(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CBioseq_Handle::ContainsSegment(), CTextItemSeq_loc::CreateObject(), GetSwitchPoint(), CResolveRequest::Process(), CDemoApp::Run(), CAnnot_Collector::x_CollectMapped(), CFlatGatherer::x_CollectSourceDescriptors(), CFlatGatherer::x_DoMultipleSections(), CComponentSearchJob::x_DoSearch(), CIdMapperScope::x_Init(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CAnnot_Collector::x_SearchMapped(), and CMasterContext::x_SetBaseName().

Get original alignment handle.

Definition at line 233 of file align_ci.cpp.

References CAnnotTypes_CI::GetAnnot(), and CAnnotTypes_CI::GetIterator().

Referenced by BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), CSequenceEditingEventHandler::RemoveSegGaps(), s_DivvyUpAlignments_ProcessAnnot(), CReportTrim::TrimAlignments(), TrimSequenceAndAnnotation(), CSGAlignmentJob::x_GetAlignments(), CSGAlignmentJob::x_GetAlignSmear(), CwxAnnotConfigDlg::x_InitAnnotList(), and CVectorTrimPanel::x_TrimAlignments().

Definition at line 326 of file seqdesc_ci.cpp.

References CSeq_descr_CI::GetSeq_entry_Handle(), and CSeqdesc_CI::m_Entry.

Referenced by AddModToDefline(), AddModVectorToDefline(), AddOrgToDefline(), CLoadSecondaryAccessions::apply(), COrgGeneralPanel::ApplyCommand(), ApplySrcTableToSeqEntry(), AutodefSeqEntryNoTitle(), CSequenceEditingEventHandler::ChangeToGenomicDna(), CreateMolInfoDesc(), CAddSecondary::GetCommand(), CEditHistory::GetCommand(), CEditObjectSeq_desc::GetEditCommand(), GetSynchronizeProductMolInfoCommand(), InstantiateProteinTitles(), CBarcodeTool::OnAddKeyword(), CCompareWithBiosample::OnClickOk(), CBarcodeTool::OnRemoveKeyword(), CMacroFunction_Autodef::s_AutodefBioseqsNoTitle(), CMacroFunction_Autodef::s_AutodefSequenceNoTitle(), CMacroFunction_Autodef::s_AutodefSetsNoTitle(), CMacroFunction_ParseToStructComm::TheFunction(), CMacroFunction_MakeBoldXrefs::TheFunction(), CMacroFunction_AutodefComplete::TheFunction(), UpdateOneDefLine(), CSubmissionWizard::x_ApplyOrReplaceDescriptorToRecord(), and CSubmissionWizard::x_ApplySourceDescriptorToRecord().

Get current seq-feat.

Reimplemented from CSeq_feat_Handle.

Definition at line 135 of file mapped_feat.cpp.

References CCreatedFeat_Ref::GetMappedFeature(), CSeq_feat_Handle::GetOriginalSeq_feat(), CAnnotMapping_Info::IsMapped(), CMappedFeat::m_MappedFeat, and CMappedFeat::m_MappingInfoPtr.

Referenced by AdjustSingleFeature(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCdsMatchInfo::AssignMatch(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CFixForTransSplicing::CollectProteinNames(), CCleanup::FixGeneXrefSkew(), GetChangeStrainForwardingCommand(), CFixForTransSplicing::GetCommand(), CGeneCache::GetGeneFromCache(), CMappedFeat::GetMappedFeature(), GetReverseComplimentSequenceCommand(), GetRmCultureNotesCommand(), CValidError_imp::GetTSACDSOnMinusStrandErrors(), CNewCleanup_imp::ProtSeqBC(), CCleanup::RepairXrefs(), CFeatTreeSampleApp::Run(), s_HasPromoter(), CCleanup::SetGenePartialByLongestContainedFeature(), CSeqTextPane::STG_RenderFeatureExtras(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_bioseqset::ValidateGenProdSet(), CAnnot_Collector::x_GetMappedObject(), CAutoDefFeatureClause::x_GetProductName(), variation::CVariationUtil::CCdregionIndex::x_Index(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CCorrectRNAStrandDlg::x_ReverseFeatures(), CBioseqContext::x_SetTaxname(), CCdregionValidator::x_ValidateFarProducts(), CSingleFeatValidator::x_ValidateGeneXRef(), CGff2Writer::xAssignFeatureAttributePartial(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), and CFastaOstreamEx::xWriteFeature().

Get original feature handle.

Definition at line 71 of file mapped_feat.hpp.

Referenced by CExportTableDlg::AddCdsGeneMrnaTable(), CFeatTree::AddFeature(), CEditSequence::AdjustFeatureLocations(), CSplitCDSwithTooManyXs::AdjustSingleCDS(), AdjustSingleFeature(), CConvertBadCdsAndRnaToMiscFeat::apply(), CRemoveGenomeProjectsDB::apply_to_seq_and_feat(), CRemoveStructuredComment::apply_to_seq_and_feat(), CModifyStructuredComment::apply_to_seq_and_feat(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), BuildFeatureSeqTableFromSeqEntry(), CBulkCDS::CBulkCDS(), CBulkGene::CBulkGene(), CBulkRna::CBulkRna(), CFeatureItemBase::CFeatureItemBase(), ChangeFeat(), CRemoveFeaturesDlg::CountProteinsBeforeRemoval(), CExtendCDSToStop::ExtendmRNA(), CAnnotationASN1::ExtractModels(), IEditingActionFeat::FindOrCreateProtFeat(), IEditingActionFeat::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CValidError_bioseq::GapByGapInst(), NSearchFeatPanel::GatherFeatures(), CFixForTransSplicing::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), IEditingActionFeat::GoToProtFeature(), CRestoreRNAediting::OnApply(), CBioseqEditor::OnDeleteBiosourceFeat(), CSubPrep_panel::RemoveAllFeatures(), CSeq_annot_EditHandle::ReorderFtable(), CExtendCDSToStop::ResetGenes(), CFeatCompareJob_Location::Run(), CDemoApp::Run(), CFixFeatureId::s_UpdateFeatureIds(), CCleanup::SetProteinName(), CMacroFunction_RemoveAllFeatures::TheFunction(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CFeatTree::x_GetInfo(), CBioseqIndex::x_InitFeats(), CNewCleanup_imp::x_MoveCDSFromNucAnnotToSetAnnot(), CReportTrim::x_RetranslateCDS(), and CVcfWriter::x_WriteData().

Fill the buffer string with the count bytes of sequence data starting with current iterator position.

Definition at line 720 of file seq_vector_ci.cpp.

References _ASSERT, buffer, CSeqVector_CI::CanGetRange(), count, CSeqVector_CI::GetPos(), CSeqVector_CI::m_Cache, CSeqVector_CI::m_CacheEnd, CSeqVector_CI::m_TSE, min(), NCBI_THROW_FMT, CSeqVector_CI::x_GetSize(), and CSeqVector_CI::x_NextCacheSeg().

Definition at line 651 of file seq_map_ci.hpp.

References CSeqMap_CI_SegmentInfo::GetType(), and CSeqMap_CI::x_GetSegmentInfo().

Referenced by CGapAnalysis::AddBioseqGaps(), CSeqMap::CanResolveRange(), CGapCache::CGapCache(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CFeatGapInfo::CollectGaps(), CEditSequence::CreateControls(), CTextItemSeq_loc::CreateObject(), GetAllSwitchPoints(), CAdvancedAlignCleanup::GetProsplignCompartments(), CSGSegmentMapJob::GetSegmentMapLevels(), GetSwitchPoint(), CSGSegmentMapJob::HasSegmentMap(), CSeqVector_CI::IsInGap(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), CSeqTranslator::TranslateToProtein(), TrimSeqData(), UpdateSeqLength(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CComponentSearchJob::x_DoSearch(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), CSeqVector_CI::x_FillCache(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CIdMapperScope::x_Init(), CSingleFeatValidator::x_IsMostlyNs(), CSGSegmentSmearJob::x_LoadGaps(), CSequenceTrack::x_RenderGaps(), CSplign::x_RunOnCompartment(), CVectorTrimPanel::x_SetSeqData(), CSequenceAmbigTrimmer::x_SliceBioseq(), and CFastaOstream::x_WriteSequence().

Definition at line 903 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, CSeqFeatData_Base::e_not_set, CSeqFeatData::eSubtype_any, SAnnotTypeSelector::GetAnnotType(), SAnnotTypeSelector::GetFeatSubtype(), SAnnotTypeSelector::GetFeatType(), CAnnotType_Index::GetSubtypeIndex(), CSeqFeatData::GetTypeFromSubtype(), and SAnnotSelector::m_AnnotTypesBitset.

Referenced by SAnnotSelector::ExcludeFeatSubtype(), SAnnotSelector::IncludeFeatSubtype(), and SAnnotSelector::MatchType().

Definition at line 883 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, CSeqFeatData_Base::e_not_set, SAnnotTypeSelector::GetAnnotType(), SAnnotTypeSelector::GetFeatType(), CAnnotType_Index::GetFeatTypeRange(), i, SAnnotSelector::m_AnnotTypesBitset, and type.

Referenced by SAnnotSelector::ExcludeFeatType(), SAnnotSelector::IncludeFeatType(), and SAnnotSelector::MatchType().

Include feature subtype in the search.

Definition at line 814 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetSubtypeIndex(), SAnnotSelector::IncludedFeatSubtype(), SAnnotSelector::m_AnnotTypesBitset, SAnnotTypeSelector::SetFeatSubtype(), and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by CLinkUtils::AddDbxrefLinksForSNP(), CFeatTree::AddFeaturesFor(), CFeatTableEdit::AnnotHasAllLocusTags(), variation::CVariationUtil::CheckExonBoundary(), CmRNACDSLinker::CompleteHalfFormedXrefPairs(), NSearchFeatPanel::GatherFeatures(), CFeatTableEdit::GenerateLocusTags(), CFeatTableEdit::GenerateMissingMrnaForCds(), CFeatTableEdit::GenerateMissingParentFeaturesForEukaryote(), CFeatTableEdit::GenerateProteinAndTranscriptIds(), CDataLoader::GetCDDAnnots(), CSeqUtils::GetCdsMappingInfoFromRna(), variation::CVariationUtil::GetEffectiveTranscriptLength(), CGuiObjectInfoVariation::GetLinks(), CSeqUtils::GetMrnaForCds(), GetMrnasForGene(), GetProteinWeights(), CFeatTableEdit::InferPartials(), CFeatTableEdit::InstantiateProducts(), IsInScope(), CmRNACDSLinker::LinkByLabelAndLocation(), CSGAlignmentDS::LoadAlignFeats(), CResolveRequest::Process(), CFeatTableEdit::ProcessCodonRecognized(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), s_GetCdsProductSel(), s_GetMappedFeat(), s_Render_SeqFeat(), CReportEntry::SetAlignment(), CFeatTableEdit::SubmitFixProducts(), CValidError_bioseq::ValidateBioseqContext(), CLinkUtils::x_AddDbxrefFeatureLinks(), variation_ref::CHgvsParser::x_general_pos(), variation::CHgvsParser::x_general_pos(), CFeatureSearchJob::x_SearchFeatures(), CReportEntry::x_SetFeature(), CFeatureGraph::x_StartJob(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), and CFeatTableEdit::xGenerateMissingGeneForSubtype().

Include feature type in the search.

Definition at line 780 of file annot_selector.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_not_set, SAnnotSelector::ForceAnnotType(), SAnnotTypeSelector::GetAnnotType(), CAnnotType_Index::GetFeatTypeRange(), i, SAnnotSelector::IncludedFeatType(), SAnnotSelector::m_AnnotTypesBitset, SAnnotTypeSelector::SetFeatType(), and SAnnotSelector::x_InitializeAnnotTypesSet().

Referenced by CFeatureGenerator::CreateMicroIntrons(), CFeatTableEdit::GenerateMissingParentFeaturesForEukaryote(), CGeneModelFeatJob::GetFilters(), variation::GetFocusLocusIDs(), GetProteinWeights(), variation::GetUniquePrimaryTranscriptId(), IsInScope(), CCleanup::MoveProteinSpecificFeats(), CInfluenzaSet::OkToMakeSet(), CTabularFormatter_ProtRef::Print(), variation::CVariationUtil::RemapToAnnotatedTarget(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), s_GetFeaturesForRange(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_MoveProteinSpecificFeats(), variation::CHgvsParser::CContext::SetId(), variation_ref::CVariationUtil::SetVariantProperties(), CFeatTableEdit::SubmitFixProducts(), CSeq_id_Resolver__LRG::x_Create(), CGeneModelFeatJob::x_Execute(), CNaSeqlocHelper::x_GetCDS(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), variation::CHgvsParser::x_header(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CFlatFeatureRetrieveJob::x_Run(), CFeatureSearchJob::x_SearchFeatures(), CDeflineGenerator::x_SetTitleFromNM(), CIdResolver::x_TryProcessLRG(), CFeatTableEdit::xGenerateMissingGeneForChoice(), and CGff3Writer::xWriteProteinSequence().

Definition at line 548 of file annot_selector.cpp.

References ExtractZoomLevel(), SAnnotSelector::m_NamedAnnotAccessions, and NCBI_THROW_FMT.

Referenced by CGraphUtils::CalcGraphLevels(), CGBObjectLoader::Execute(), NSearchFeatPanel::GatherFeatures(), CSGSnpDS::GetAnnotNames(), CSeqUtils::GetAnnotSelector(), NSnpBins::GetBinSelector(), NSnpAnnot::GetFeat_CI(), NSnpAnnot::GetGraph_CI(), CSeqUtils::GetMrnaForCds(), CGBDataLoader_Native::GetNamedAnnotAccessions(), CNAUtils::GetNATrackInfo(), CPubseqReader::LoadSeq_idBlob_ids(), CDemoApp::Run(), s_GetAnnotSelector(), s_GetRnaMappingLocs(), CAsn2FlatApp::x_AddSNPAnnots(), CBioseqIndex::x_DefaultSelector(), CSnpJob::x_FetchFtable(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CMacroBioData::x_GetAnnotSelector(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CSGAnnotJob::x_LoadCoverageGraph(), and CFeatureGenerator::x_SetAnnotName().

check if any named annot accession is included in the search

Definition at line 689 of file annot_selector.hpp.

References SAnnotSelector::m_NamedAnnotAccessions.

Referenced by CPSGDataLoader_Impl::GetAnnotRecordsNAOnce(), CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce(), SAnnotSelector::HasIncludedOnlyNamedAnnotAccessions(), SAnnotSelector::IncludedAnnotName(), SAnnotSelector::IsIncludedNamedAnnotAccession(), CDataLoader::IsRequestedAnyNA(), CId1Reader::LoadSeq_idBlob_ids(), CId2ReaderBase::LoadSeq_idBlob_ids(), CReader::LoadSeq_idBlob_ids(), CPubseqReader::LoadSeq_idBlob_ids(), CBlob_Annot_Info::Matches(), CDemoApp::Run(), s_FormatCall(), CReaderRequestResult::s_KeyBlobIds(), CAnnot_Collector::x_FoundAllNamedAnnotAccessions(), CScope_Impl::x_GetAnnotRef_Info(), CSGAnnotJob::x_LoadCoverageGraph(), CAnnot_Collector::x_SearchLoc(), and CAnnot_Collector::x_SearchMaster().

true if current position of CSeqVector_CI is inside of sequence gap

Definition at line 486 of file seq_vector_ci.hpp.

References CSeqMap::eSeqGap, CSeqMap_CI::GetType(), and CSeqVector_CI::m_Seg.

Referenced by CGenbankFormatter::FormatSequence(), CSeqVector_CI::GetGapSeq_literal(), CSeqVector_CI::GetGapSizeBackward(), CSeqVector_CI::GetGapSizeForward(), CSequenceTrack::GetTooltip(), CSeqVector::IsInGap(), s_CalcDistanceUntilNextSignificantGapOrEnd(), CSeqVector_CI::SkipGap(), and CSeqVector_CI::SkipGapBackward().

Reimplemented from CSeq_feat_Handle.

Definition at line 158 of file mapped_feat.cpp.

References CAnnotMapping_Info::IsMapped(), CAnnotMapping_Info::IsPartial(), CSeq_feat_Handle::IsSetPartial(), and CMappedFeat::m_MappingInfoPtr.

Referenced by BOOST_AUTO_TEST_CASE(), CFeatTableEdit::InferPartials(), CNewCleanup_imp::ResynchPeptidePartials(), CDemoApp::Run(), s_CdsFlags(), s_TitleFromSegment(), ProjectCDS::transform_align(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddQualPartial(), CFeatureItem::x_AddQualsProt(), CFeatTableEdit::xAdjustExistingParentGene(), and CGff2Writer::xAssignFeatureAttributePartial().

Definition at line 105 of file graph_ci.cpp.

References CMappedGraph::GetLoc(), CAnnotObject_Ref::GetMappingInfo(), CMappedGraph::GetOriginalGraph(), CAnnotMapping_Info::IsMapped(), CMappedGraph::m_GraphRef, CMappedGraph::m_MappedGraph, CMappedGraph::MakeMappedGraphData(), CConstRef< C, Locker >::Reset(), and tmp.

Referenced by CMappedGraph::GetGraph(), and CMappedGraph::GetMappedGraph().

Definition at line 131 of file graph_ci.cpp.

References CopyGraphData(), CSeq_graph_Base::C_Graph::e_Byte, CSeq_graph_Base::C_Graph::e_Int, CSeq_graph_Base::C_Graph::e_Real, CByte_graph_Base::GetAxis(), CInt_graph_Base::GetAxis(), CReal_graph_Base::GetAxis(), CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetComp(), CSeq_graph_Base::GetGraph(), CSeq_graph_Base::C_Graph::GetInt(), CMappedGraph::GetMappedGraphRanges(), CByte_graph_Base::GetMax(), CInt_graph_Base::GetMax(), CReal_graph_Base::GetMax(), CByte_graph_Base::GetMin(), CInt_graph_Base::GetMin(), CReal_graph_Base::GetMin(), CMappedGraph::GetOriginalGraph(), CSeq_graph_Base::C_Graph::GetReal(), CByte_graph_Base::GetValues(), CInt_graph_Base::GetValues(), CReal_graph_Base::GetValues(), CSeq_graph_Base::IsSetComp(), ITERATE, CSeq_graph_Base::C_Graph::Reset(), CByte_graph_Base::SetAxis(), CInt_graph_Base::SetAxis(), CReal_graph_Base::SetAxis(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::C_Graph::SetInt(), CByte_graph_Base::SetMax(), CInt_graph_Base::SetMax(), CReal_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CInt_graph_Base::SetMin(), CReal_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::C_Graph::SetReal(), CByte_graph_Base::SetValues(), CInt_graph_Base::SetValues(), CReal_graph_Base::SetValues(), and CSeq_graph_Base::C_Graph::Which().

Referenced by CMappedGraph::MakeMappedGraph().

Definition at line 65 of file graph_ci.cpp.

References CMappedGraph::GetLoc(), CAnnotMapping_Info::GetMappedSeq_loc(), CAnnotObject_Ref::GetMappingInfo(), CMappedGraph::GetOriginalGraph(), CAnnotMapping_Info::IsMapped(), CMappedGraph::m_Collector, CAnnot_Collector::m_CreatedMapped, CMappedGraph::m_GraphRef, CMappedGraph::m_MappedGraph, CMappedGraph::m_MappedLoc, CAnnotMapping_Info::MappedSeq_locNeedsUpdate(), CCreatedFeat_Ref::ReleaseRefsTo(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), CCreatedFeat_Ref::ResetRefsFrom(), and CAnnotMapping_Info::UpdateMappedSeq_loc().

Referenced by CMappedGraph::GetLoc().

Mapped alignment, not the original one.

Definition at line 202 of file align_ci.cpp.

References _ASSERT, CAnnotTypes_CI::Get(), CAnnotObject_Ref::GetAlign(), CAnnotMapping_Info::GetMappedSeq_align(), CAnnotObject_Ref::GetMappingInfo(), CAnnotObject_Ref::IsAlign(), CAnnotMapping_Info::IsMapped(), CAlign_CI::m_MappedAlign, CObject::ReferencedOnlyOnce(), and CConstRef< C, Locker >::Reset().

Move to the next object in iterated sequence.

Restricted postfix operators.

They allow only get value from old position by operator*, like in commonly used copying cycle: CSeqVector_CI src; for ( ... ) { *dst++ = *src++; }

Definition at line 169 of file seq_vector_ci.hpp.

References rapidjson::value.

Mapped alignment, not the original one.

Definition at line 219 of file align_ci.cpp.

Definition at line 414 of file seq_vector_ci.cpp.

References AutoArray< X, Del >::get(), CSeqVector_CI::GetCoding(), CSeqVector_CI::m_BackupData, CSeqVector_CI::m_BackupEnd, CSeqVector_CI::m_BackupPos, CSeqVector_CI::m_Cache, CSeqVector_CI::m_CacheData, CSeqVector_CI::m_CacheEnd, CSeqVector_CI::m_CachePos, CSeqVector_CI::m_CaseConversion, CSeqVector_CI::m_Coding, CSeqVector_CI::m_Randomizer, CSeqVector_CI::m_ScannedEnd, CSeqVector_CI::m_ScannedStart, CSeqVector_CI::m_Scope, CSeqVector_CI::m_Seg, CSeqVector_CI::m_SeqMap, CSeqVector_CI::m_Strand, CSeqVector_CI::m_TSE, CSeqVector_CI::x_BackupPos(), CSeqVector_CI::x_BackupSize(), CSeqVector_CI::x_CacheOffset(), CSeqVector_CI::x_CachePos(), CSeqVector_CI::x_CacheSize(), CSeqVector_CI::x_InitializeCache(), CSeqVector_CI::x_ResetBackup(), and CSeqVector_CI::x_ResetCache().

Definition at line 163 of file annot_selector.cpp.

References SAnnotSelector::m_AdaptiveDepthFlags, SAnnotSelector::m_AdaptiveTriggers, SAnnotSelector::m_AnnotTypesBitset, SAnnotSelector::m_CollectCostOfLoading, SAnnotSelector::m_CollectNames, SAnnotSelector::m_CollectSeq_annots, SAnnotSelector::m_CollectTypes, SAnnotSelector::m_ExactDepth, SAnnotSelector::m_ExcludeAnnotsNames, SAnnotSelector::m_ExcludedTSE, SAnnotSelector::m_ExcludeExternal, SAnnotSelector::m_ExcludeIfGeneIsSuppressed, SAnnotSelector::m_FeatComparator, SAnnotSelector::m_FeatProduct, SAnnotSelector::m_FilterBits, SAnnotSelector::m_FilterMask, SAnnotSelector::m_HasWildcardInAnnotsNames, SAnnotSelector::m_IgnoreFarLocationsForSorting, SAnnotSelector::m_IgnoreStrand, SAnnotSelector::m_IncludeAnnotsNames, SAnnotSelector::m_LimitObject, SAnnotSelector::m_LimitObjectType, SAnnotSelector::m_LimitTSE, SAnnotSelector::m_MaxSearchSegments, SAnnotSelector::m_MaxSearchSegmentsAction, SAnnotSelector::m_MaxSearchTime, SAnnotSelector::m_MaxSize, SAnnotSelector::m_NamedAnnotAccessions, SAnnotSelector::m_NoMapping, SAnnotSelector::m_OverlapType, SAnnotSelector::m_ResolveDepth, SAnnotSelector::m_ResolveMethod, SAnnotSelector::m_SNPScaleLimit, SAnnotSelector::m_SortOrder, SAnnotSelector::m_SourceLoc, SAnnotSelector::m_UnresolvedFlag, and AutoPtr< X, Del >::reset().

Check if iterator points to an object.

Definition at line 239 of file feat_ci.hpp.

References CAnnotTypes_CI::Rewind(), and CFeat_CI::Update().

Referenced by CCleanup::FixGeneXrefSkew(), GetMrnasForGene(), GetRmCultureNotesCommand(), CSeq_annot_EditHandle::ReorderFtable(), CCompareSeqRegions::Rewind(), CFeatTreeSampleApp::Run(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), CFixFeatureId::s_UpdateFeatureIds(), CFeat_CI::x_AddFeaturesWithId(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CAutoDef::x_Is5SList(), and CAutoDef::x_IsSingleMiscFeat().

Definition at line 45 of file graph_ci.cpp.

References _ASSERT, CAnnotObject_Ref::IsGraph(), CMappedGraph::m_Collector, CMappedGraph::m_GraphRef, CMappedGraph::m_MappedGraph, CMappedGraph::m_MappedLoc, CRef< C, Locker >::Reset(), and CConstRef< C, Locker >::Reset().

Referenced by CAnnot_Collector::x_GetMappedObject(), and CGraph_CI::x_Update().

Definition at line 86 of file mapped_feat.cpp.

References _ASSERT, CAnnotObject_Ref::GetAnnotIndex(), CAnnotObject_Ref::GetAnnotObject_Info(), CAnnotObject_Ref::GetMappingInfo(), CAnnotObject_Ref::GetSeq_annot_Handle(), CAnnotObject_Ref::IsFeat(), CSeq_feat_Handle::IsPlainFeat(), CAnnotObject_Info::IsRegular(), CAnnotObject_Ref::IsSNPTableFeat(), CAnnotObject_Ref::IsSortedSeqTableFeat(), CSeq_feat_Handle::IsSortedTableFeat(), CSeq_feat_Handle::IsTableFeat(), CSeq_feat_Handle::IsTableSNP(), CSeq_feat_Handle::kNoAnnotObjectInfo, CSeq_feat_Handle::m_CreatedFeat, CAnnot_Collector::m_CreatedOriginal, CSeq_feat_Handle::m_CreatedOriginalFeat, CSeq_feat_Handle::m_FeatIndex, CMappedFeat::m_MappedFeat, CMappedFeat::m_MappingInfoPtr, CSeq_feat_Handle::m_Seq_annot, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), and CCreatedFeat_Ref::ResetRefs().

Referenced by CFeat_CI::Update(), and CAnnot_Collector::x_GetMappedObject().

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower level of segments.

It's meaningful in cases when features on segments are also annotated on master sequence. Setting this flag will avoid duplicates, and speed up loading. Annotation iterator will look for annotations of special types, by default it's gene, mrna, and cds. If any annotation from those types is found the iterator will treat this as annotated sequence, and not look for more annotations on subsegments. This option works in addition to SetResolveDepth(), so subsegment resolution stops when either specified depth is reached, or if any adaptive trigger annotation is found. Adaptive depth flag has no effect if 'exact depth' is set.

Note, that trigger annotations on one segment has no effect on adaptive resolution of another segment. So, for example, if Master sequence A has segments B1 and B2, while B1 has segments C11 and C12, and B2 has segments C21 and C22:
|————— A —————-|
|—— B1 ——||—— B2 ——|
|- C11 -||- C12 -||- C21 -||- C22 -|
Also, there are genes only on sequences B1, C11, C12, C21, and C22. For simplicity, there are no other adaptive trigger annotations. In this case annotation iterator in 'adaptive' mode will return genes and other annotations from sequences A, B1, B2, C21, and C22. It will skip searching on C11, and C12 because trigger feature will be found on B1.

See also

SetResolveDepth(), SetExactDepth(), SetAdaptiveTrigger(), GetAdaptiveDepth()

Definition at line 624 of file annot_selector.cpp.

References SAnnotSelector::GetDefaultAdaptiveDepthFlags(), SAnnotSelector::kAdaptive_None, SAnnotSelector::m_AdaptiveDepthFlags, and rapidjson::value.

Referenced by CFeatTree::AddFeaturesFor(), CGraphUtils::CalcGraphLevels(), CFeatureGenerator::CreateMicroIntrons(), ExtractExtraIds(), CSeqUtils::GetAnnotSelector(), NSnpBins::GetBinSelector(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeqUtils::GetMrnaForCds(), GetMrnasForGene(), GetOverlappingFeatures(), CAsn2FastaApp::HandleSeqEntry(), CResolveRequest::Process(), variation::CVariationUtil::RemapToAnnotatedTarget(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), CFeatTreeSampleApp::Run(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_GetRnaMappingLocs(), s_SetSelection(), CFeatureGenerator::SImplementation::x_CopyAdditionalFeatures(), CBioseqIndex::x_DefaultSelector(), CFlatGatherer::x_GatherFeaturesOnRange(), x_GetAnnotSelector(), CMacroBioData::x_GetAnnotSelector(), CDisplaySeqalign::x_GetFeatureInfo(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), and CAnnotWriterApp::xTweakAnnotSelector().

Set annotation type (feat, align, graph)

Definition at line 127 of file annot_selector.hpp.

References SAnnotTypeSelector::GetAnnotType(), SAnnotTypeSelector::SetAnnotType(), and SAnnotSelector::x_ClearAnnotTypesSet().

Referenced by CFeatTree::AddFeaturesFor(), CSequenceTrackFactory::CreateTracks(), SAnnotSelector::ForceAnnotType(), CEpigenomicsDS::GetAnnotNames(), NSnpBins::GetBinSelector(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), NSnp::IsSnpKnown(), CDemoApp::Run(), CBioseqContext::x_CheckForShowComments(), CDensityMapDS::x_GetAnnotSelector(), and CSGAnnotJob::x_LoadCoverageGraph().

Collect available annot names rather than annots.

See also

CAnnotTypes_CI::GetAnnotNames()

Definition at line 734 of file annot_selector.hpp.

References SAnnotSelector::m_CollectNames, and rapidjson::value.

Referenced by CGraphUtils::CalcGraphLevels(), CAlignmentTrackFactory::CreateTracks(), CSGAlignmentJob::GetAlignType(), CSGFeatureJob::GetAnnotNames(), CEpigenomicsDS::GetAnnotNames(), CSGSnpDS::GetAnnotNames(), CSGFeatureJob::GetAnnotNames_var(), CSeqUtils::GetAnnotSelector(), CSGAlignmentDS::GetDataLoader(), NSnpAnnot::GetGraph_CI(), CNAUtils::GetNATrackInfo(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), CLDBlockDS::GetTrackNames(), CDemoApp::Run(), CSnpJob::x_FetchGraphs(), CAlignTabExportPage2::x_StartAlignNamesJob(), and CAlignTabExportPage2::x_StartNAAlignNamesJob().

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetResolveDepth() only.

By default this flag is not set, and annotations iterators will also return annotations from above levels. This flag, when set, overrides 'adaptive depth' flag.

Examples: SetResolveDepth(0)

• only direct annotations on the sequence will be found. SetResolveDepth(1), SetExactDepth(false) (default)
• find annotations on the sequence, and its direct segments. SetResolveDepth(1), SetExactDepth(true)
• find annotations on the direct segments.

See also

SetResolveDepth(), SetAdaptiveDepth(), SetAdaptiveTrigger()

Definition at line 434 of file annot_selector.hpp.

References SAnnotSelector::m_ExactDepth, and rapidjson::value.

Referenced by ExtractExtraIds(), NSnpBins::GetBinSelector(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeqUtils::GetMrnaForCds(), MapSeq_feat(), C5ColExportJob::Run(), CGffExportJob::Run(), CGtfExportJob::Run(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), s_GetRnaMappingLocs(), and CAnnotWriterApp::xTweakAnnotSelector().

External annotations for the Object Manger are annotations located in top level Seq-entry different from TSE with the sequence they annotate.

They can be excluded from search by SetExcludeExternal() option.

Exclude all external annotations from the search. Effective only when no Seq-entry/Bioseq/Seq-annot limit is set.

Definition at line 568 of file annot_selector.hpp.

References SAnnotSelector::m_ExcludeExternal.

Referenced by CSeqUtils::GetAnnotSelector(), NSnpAnnot::GetGraph_CI(), CAsn2FastaApp::HandleSeqEntry(), NSnp::IsSnpKnown(), CResolveRequest::Process(), CDemoApp::Run(), CTestBMApp::Run(), CFastaOstreamEx::x_AddProteinNameAttribute(), CBioseqIndex::x_DefaultSelector(), CSnpJob::x_FetchGraphs(), and x_GetAnnotSelector().

Set feature subtype (also set annotation and feat type)

Definition at line 145 of file annot_selector.hpp.

References SAnnotTypeSelector::SetFeatSubtype(), and SAnnotSelector::x_ClearAnnotTypesSet().

Referenced by CFeatTree::AddFeaturesFor(), CVarTrackFactory::CreateTracks(), CFeatureTrackFactory::CreateTracks(), CGeneModelFactory::CreateTracks(), NSearchFeatPanel::GatherFeatures(), CSGSnpDS::GetAnnotNames(), GetBestCdsForMrna(), GetBestMrnaForCds(), GetOverlappingFeatures(), NSnp::IsSnpKnown(), CSelectFeatureDlg::OnFeatureEdit(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CTestTranscript_CountCdregions::RunTest(), s_GetCdsProductSel(), ProjectCDS::transform_align(), CDensityMapDS::x_GetAnnotSelector(), CMacroBioData::x_GetAnnotSelector(), CValidError_bioseq::x_IsMicroRNA(), CSelectFeatureDlg::x_LoadFeatures(), and x_ToBlastVec().

Set feature type (also set annotation type to feat)

Definition at line 137 of file annot_selector.hpp.

References SAnnotTypeSelector::SetFeatType(), and SAnnotSelector::x_ClearAnnotTypesSet().

Referenced by AddDefaultSentinelFeats(), CGeneModelFactory::CreateTracks(), CAnnotationASN1::ExtractModels(), CGeneModelFeatJob::GetFilters(), GetOverlappingFeatures(), CSelectFeatureDlg::OnFeatureEdit(), CNewCleanup_imp::ProtSeqBC(), CDemoApp::Run(), CSampleObjmgrApplication::Run(), s_RemoveTaxnameFromProtRef(), CFeatureItem::x_AddQualsProt(), CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CDensityMapDS::x_GetAnnotSelector(), CMacroBioData::x_GetAnnotSelector(), CSelectFeatureDlg::x_LoadFeatures(), CFlatFeatureRetrieveJob::x_Run(), CBioseqContext::x_SetTaxname(), and CDeflineGenerator::x_SetTitleFromNM().

Select segment type(s)

Definition at line 179 of file seq_map_ci.hpp.

References flags, and SSeqMapSelector::m_Flags.

Referenced by CGapAnalysis::AddBioseqGaps(), CAlignmentAssistant::AdjustBioseq(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CDiscrepancyContext::BuildSeqSummary(), CSeqMap::CanResolveRange(), CBioseq_Handle::ContainsSegment(), CEditSequence::CreateControls(), CValidError_bioseq::GapByGapInst(), CAdvancedAlignCleanup::GetProsplignCompartments(), CEditSequence::OnAccept(), CValidError_bioseq::PctNs(), CResolveRequest::Process(), CSeqMap::ResolvedRangeIterator(), CDemoApp::Run(), s_CreateGapMapIter(), CSeqMap_CI::SetFlags(), CEditSeqEndsWithAlign::TrimBeforeAfter(), CFlatGatherer::x_GatherReferences(), CBioseqIndex::x_InitGaps(), and CSeq_loc_Mapper::x_InitializeSeqMap().

Remove restrictions on the parent object of annotations.

Definition at line 221 of file annot_selector.cpp.

References SAnnotSelector::eLimit_None, SAnnotSelector::m_LimitObject, SAnnotSelector::m_LimitObjectType, SAnnotSelector::m_LimitTSE, CConstRef< C, Locker >::Reset(), and CTSE_Handle::Reset().

Referenced by SAnnotSelector::SetLimitSeqAnnot(), SAnnotSelector::SetLimitSeqEntry(), SAnnotSelector::SetLimitTSE(), CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

Limit annotations to those from the seq-annot only.

Definition at line 264 of file annot_selector.cpp.

References SAnnotSelector::eLimit_Seq_annot_Info, CSeq_annot_Handle::GetTSE_Handle(), SAnnotSelector::m_LimitObject, SAnnotSelector::m_LimitObjectType, SAnnotSelector::m_LimitTSE, CConstRef< C, Locker >::Reset(), SAnnotSelector::SetLimitNone(), and CSeq_annot_Handle::x_GetInfo().

Referenced by CAnnotTypes_CI::CAnnotTypes_CI(), MapSeq_feat(), CDemoApp::Run(), and CGff3Writer::x_WriteSeqAnnotHandle().

Limit annotations to those from the TSE only.

Definition at line 231 of file annot_selector.cpp.

References SAnnotSelector::eLimit_TSE_Info, SAnnotSelector::m_LimitObject, SAnnotSelector::m_LimitObjectType, SAnnotSelector::m_LimitTSE, CConstRef< C, Locker >::Reset(), SAnnotSelector::SetLimitNone(), and CTSE_Handle::x_GetTSE_Info().

Referenced by CSequenceUpdater::ExtendOneEndOfSequence(), CValidError_imp::GetCDSGivenProduct(), CValidError_imp::GetmRNAGivenProduct(), CSequenceUpdater::NoChange(), CSequenceUpdater::Replace(), CGeneFinder::ResolveGeneObjectId(), CDemoApp::Run(), CSampleObjmgrApplication::Run(), s_GetBestProtFeature(), s_HasAlignment(), s_SetSelection(), CGeneOverlapProcess::SeqEntryProcess(), CGeneFeatTreeProcess::SeqEntryProcess(), SAnnotSelector::SetLimitTSE(), SAnnotSelector::SetSearchExternal(), CFlatGatherer::x_CollectSourceFeatures(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CSequenceUpdater::x_MapOldAndImportedFeatsThroughNewAlign(), and CSequenceUpdater::x_ReplaceIdInOldFeatures().

Definition at line 157 of file seq_map_ci.hpp.

References SSeqMapSelector::m_LinkUsedTSE.

Referenced by CSeqVector_CI::CanGetRange(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeqMap_CI::CSeqMap_CI(), CAsn2FastaApp::HandleSeqEntry(), LoadSequencesToScope(), CNewCleanup_imp::ProtSeqBC(), CFastaOstream::WriteSequence(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CSeq_loc_Mapper::x_InitializeSeqMap(), and CSeqVector_CI::x_InitSeg().

Definition at line 404 of file seq_vector_ci.hpp.

References AutoArray< X, Del >::get(), CSeqVector_CI::m_Cache, CSeqVector_CI::m_CacheData, CSeqVector_CI::m_CacheEnd, CSeqVector_CI::m_CachePos, offset, ncbi::grid::netcache::search::fields::size, and CSeqVector_CI::x_SetPos().

Referenced by CSeqVector_CI::GetSeqData(), operator+(), CSeqVector_CI::operator+=(), operator-(), CSeqVector_CI::operator-=(), CSeqVector_CI::SkipGap(), CSeqVector_CI::SkipGapBackward(), CSeqVector::x_GetIterator(), and CFastaOstream::x_WriteSequence().

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

See also

SetResolveMethod()

Definition at line 304 of file annot_selector.hpp.

References SAnnotSelector::eResolve_All, and SAnnotSelector::SetResolveMethod().

Referenced by AddDefaultSentinelFeats(), CFeatTree::AddFeaturesFor(), CGraphUtils::CalcGraphLevels(), CFeatureGenerator::CreateMicroIntrons(), CRemoveFeatChecker::Do(), ExtractExtraIds(), CSeqUtils::GetAnnotSelector(), NSnpBins::GetBinSelector(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeqUtils::GetMrnaForCds(), GetOverlappingFeatures(), CAsn2FastaApp::HandleSeqEntry(), IsInScope(), NSnp::IsSnpKnown(), MapSeq_feat(), CResolveRequest::Process(), variation::CVariationUtil::RemapToAnnotatedTarget(), CXcompareAnnotsApplication::Run(), CSampleLds2Application::Run(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), CTestSingleAln_All::RunTest(), s_ExtendEntriesFromAlignments(), s_GetRnaMappingLocs(), s_SetSelection(), CLinkUtils::x_AddDbxrefFeatureLinks(), CFeatureGenerator::SImplementation::x_CopyAdditionalFeatures(), CBioseqIndex::x_DefaultSelector(), CFlatGatherer::x_GatherFeaturesOnRange(), x_GetAnnotSelector(), CMacroBioData::x_GetAnnotSelector(), CDisplaySeqalign::x_GetFeatureInfo(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CBioseqContext::x_Init(), and CAnnotWriterApp::xTweakAnnotSelector().

Set max depth of resolving seq-map.

Definition at line 151 of file seq_map_ci.hpp.

References SSeqMapSelector::m_MaxResolveCount.

Referenced by CGapAnalysis::AddBioseqGaps(), CSeqMap::BeginResolved(), CSeqMap::CanResolveRange(), CBioseq_Handle::ContainsSegment(), CSeqMap::EndResolved(), CValidError_bioseq::GapByGapInst(), CAdvancedAlignCleanup::GetProsplignCompartments(), CSGSegmentMapJob::GetSegmentMapLevels(), CSGSegmentMapJob::HasSegmentMap(), CResolveRequest::Process(), CNewCleanup_imp::ProtSeqBC(), CSeqMap::ResolvedRangeIterator(), CDemoApp::Run(), s_CreateGapMapIter(), CSeqMap_I::sx_AdjustSelector(), CFlatGatherer::x_GatherReferences(), CGencollIdMapper::x_Init_SeqLocMappers(), and CBioseqIndex::x_InitGaps().

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

Zero means look for annotations directly pointing to the sequence. One means to look on direct segments of the sequence too. By default the limit is set to kIntMax, meaning no restriction.

See also

SetExactDepth(), SetAdaptiveDepth(), GetResolveDepth()

Definition at line 327 of file annot_selector.hpp.

References depth, and SAnnotSelector::m_ResolveDepth.

Referenced by AddDefaultSentinelFeats(), CSequenceTrackFactory::CreateTracks(), ExtractExtraIds(), NSnpBins::GetBinSelector(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeqUtils::GetMrnaForCds(), MapSeq_feat(), C5ColExportJob::Run(), CGffExportJob::Run(), CGtfExportJob::Run(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_CountCdregions::RunTest(), s_GetRnaMappingLocs(), CGeneOverlapProcess::SeqEntryProcess(), CGeneFeatTreeProcess::SeqEntryProcess(), CFlatGatherer::x_CollectSourceFeatures(), CBioseqIndex::x_DefaultSelector(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnRange(), CSeqTest::x_TestAllCdregions(), and CAnnotWriterApp::xTweakAnnotSelector().

SetResolveMethod() controls visibility of subsegments depending on whether it's packaged together with master sequence.

eResolve_None means to skip all subsegments completely. It has the same effect as calling SetResolveDepth(0). eResolve_TSE means to look on 'near' segments, packaged in the Same TSE (top level Seq-entry). eResolve_All lifts any restriction of segments by packaging. This option works in addition to 'resolve depth', 'adaptive depth', and 'exact depth'.

See also

SetResolveNone(), SetResolveTSE(), SetResolveAll(), SetResolveDepth(), SetExactDepth(), SetAdaptiveDepth(), SetUnresolvedFlag().

Definition at line 282 of file annot_selector.hpp.

References SAnnotSelector::m_ResolveMethod.

Referenced by CDemoApp::Run(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveNone(), SAnnotSelector::SetResolveTSE(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), and CDensityMapDS::x_GetAnnotSelector().

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

See also

SetResolveMethod()

Definition at line 297 of file annot_selector.hpp.

References SAnnotSelector::eResolve_TSE, and SAnnotSelector::SetResolveMethod().

Referenced by GetBestCdsForMrna(), GetBestMrnaForCds(), GetMrnasForGene(), GetOverlappingFeatures(), GetProteinWeights(), variation::GetUniquePrimaryTranscriptId(), CTabularFormatter_ProtRef::Print(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_SetSelection(), variation::CHgvsParser::CContext::SetId(), SAnnotSelector::SetSearchExternal(), CSeq_id_Resolver__LRG::x_Create(), CNaSeqlocHelper::x_GetCDS(), variation::CHgvsParser::x_header(), CDeflineGenerator::x_SetTitleFromNM(), and CIdResolver::x_TryProcessLRG().

Set sequence data.

The buffer is converted from buffer_coding to seq_data_coding and put into the new seq-data. NOTE: Some seq-data types (Gap) and encodings (Ncbipna, Ncbipaa) are not supported.

Definition at line 937 of file seq_map_ci.cpp.

References buffer, CODING_PACK_CASE, NCBI_THROW, CSeq_data_Base::SelectionName(), CSeqMap_I::SetSeq_data(), and CSeqMap_CI::x_UpdateLength().

Referenced by CAlignmentAssistant::AdjustBioseq(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CSeqMap_I::InsertData(), CEditSequence::OnAccept(), and CEditSeqEndsWithAlign::TrimBeforeAfter().

Set sort order of annotations.

eSortOrder_None - do not sort annotations for faster retrieval. eSortOrder_Normal - default. Sort by start (increasing), then by length (decreasing). eSortOrder_Reverse - sort by end (decresing), then length (decreasing).

Definition at line 234 of file annot_selector.hpp.

References SAnnotSelector::m_SortOrder.

Referenced by CAnnotTypes_CI::CAnnotTypes_CI(), CFeatTableEdit::GenerateLocusTags(), CAsn2FastaApp::HandleSeqEntry(), IsInScope(), CDemoApp::Run(), s_SetSelection(), CVcfWriter::SetAnnotSelector(), CFastaOstreamEx::x_AddProteinNameAttribute(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CVcfWriter::x_WriteData(), CGff2Writer::xAssignFeatureAttributeProduct(), and CFeatTableEdit::xGenerateLocusIdsRegenerate().

Set method of handling unresolved seq-ids.

A seq-id may be unresolvable due to EResolveMethod restrictions. E.g. a seq-id may be a far reference, while the annotations for this seq-id are stored in the master sequence TSE. eIgnoreUnresolved - default, do not search for annotations on unresolved seq-ids. eSearchUnresolved - search for annotations on unresolved seq-ids. eFailUnresolved - throw CAnnotException exception if a seq-id can not be resolved.

See also

SetSearchExternal()

Definition at line 541 of file annot_selector.hpp.

References SAnnotSelector::m_UnresolvedFlag.

Referenced by CDemoApp::Run().

Definition at line 68 of file seq_map_ci.cpp.

Definition at line 56 of file seq_map_ci.cpp.

Definition at line 1113 of file seq_vector.cpp.

References CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbieaa, CSeqVectorTypes::eCaseConversion_lower, CSeqVectorTypes::eCaseConversion_none, CSeqVectorTypes::eCaseConversion_upper, CSeqportUtil::GetCodeIndexFromTo(), CSeqportUtil::GetIndexComplement(), CSeqportUtil::GetMapToIndex(), i, CSeqportUtil::IsCodeAvailable(), ncbi::grid::netcache::search::fields::key, kMax_UChar, min(), CSeqVectorTypes::sm_TrivialTable, table, tolower(), and toupper().

Referenced by CSeqVector_CI::x_FillCache(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), and CSeqVector::x_GetPacked8SeqData().

Definition at line 1074 of file seq_vector.cpp.

References CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbipaa, CSeq_data_Base::e_Ncbipna, CSeq_data_Base::e_Ncbistdaa, CSeq_data_Base::e_not_set, CSeqVectorTypes::eCaseConversion_lower, and NCBI_THROW_FMT.

Referenced by CSeqVector::GetGapChar(), CSeqVector_CI::GetGapChar(), CSeqVector_CI::x_FillCache(), and CSeqVector::x_GetPacked2naSeqData().

Definition at line 256 of file feat_ci.cpp.

References CSeqFeatData::eSubtype_any, SAnnotSelector::GetFeatProduct(), SAnnotTypeSelector::GetFeatSubtype(), CTSE_Handle::GetFeaturesWithId(), CTSE_Handle::GetFeaturesWithXref(), CAnnotType_Index::GetIndexRange(), CAnnotType_Index::GetSubtypeForIndex(), i, CFeat_CI::Rewind(), CFeat_CI::x_AddFeatures(), CTSE_Handle::x_GetTSE_Info(), and CTSE_Info::x_HasFeaturesWithId().

Referenced by CFeat_CI::CFeat_CI().

Definition at line 331 of file seq_vector_ci.hpp.

References AutoArray< X, Del >::get(), CSeqVector_CI::m_CacheData, and CSeqVector_CI::m_CacheEnd.

Referenced by CSeqVector_CI::operator=(), CSeqVector_CI::SetCoding(), CSeqVector_CI::SetRandomizeAmbiguities(), CSeqVector_CI::SetStrand(), CSeqVector_CI::x_CacheEndPos(), CSeqVector_CI::x_NextCacheSeg(), CSeqVector_CI::x_PrevCacheSeg(), and CSeqVector_CI::x_SetPos().

Definition at line 85 of file seqdesc_ci.cpp.

References CSeq_inst_Base::eRepr_ref, CScope::GetBioseqHandle(), CSeq_loc::GetId(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Repr(), CSeq_ext_Base::GetRef(), CBioseq_Handle::GetScope(), CSeq_ext_Base::IsRef(), CBioseq_Handle::IsSetInst_Ext(), CBioseq_Handle::IsSetInst_Repr(), CSeqdesc_CI::m_Ref, and CBioseq_Handle::Reset().