Referenced by COneSeqRange::Add(), CSeqsRange::Add(), SSeqTableContent::Add(), CSeqFetchQueue::Add(), CRangeUnion< CBGZFPos >::add_range(), CAlignmentSmear::AddAlignment(), CDensityMap< CntType >::AddAlignments(), AddDomain(), SWGSFeatChunkInfo::SFeatureSet::AddFeatRange(), SWGSFeatChunkInfo::AddFeature(), SWGSFeatChunkInfo::SFeatureSet::AddFeature(), SLengthRange::AddLength(), CSelectionEvent::AddObjectSelection(), CHandleRangeMap::AddRange(), SLengthRange::AddRange(), CSubjectRanges::AddRange(), CHandleRange::AddRange(), CDensityMap< CntType >::AddRange(), CSegmentSmearGlyph::CSegMap::AddRange(), CSeqGraphicPane::AddRangeMarker(), CBamRefSeqChunkInfo::AddRefSeqRange(), SSeqTableConverter::AddToTable(), CFeatureGenerator::SImplementation::AdjustAlignment(), CFeatureGenerator::AdjustAlignment(), CFeatTrim::Apply(), CRecomputeIntervals::apply(), CBlobSplitterImpl::AttachToSkeleton(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::begin(), Blast_GetSeqLocInfoVector(), Blast_ScoreFreqNew(), BlastKarlinLHtoK(), BlastKmerBreakUpSequence(), BlastKmerGetKmerSet(), BlastKmerGetKmerSet2(), BOOST_AUTO_TEST_CASE(), CAlignCompare::SAlignment::BreakOnBoundaries(), CBlastKmerBuildIndex::Build(), BuildAlignDataSource(), CColumnLayout::BuildLayout(), CCompactLayout::BuildLayout(), CSGAlignmentDS::CalcAlnStat(), CSGFeatureDS::CalcFeatHistogram(), CScoreCache::CalculateScores(), CTestSeqBasedMethod::CalculateScores(), CColorTableMethod::CalculateScores(), BLASTer::CalculateSelfHitScores(), CAnnotTypes_CI::CAnnotTypes_CI(), CSeqGraphicPane::CanSetSwitchPoint(), CSGAlignmentDS::CanShowRange(), CCSraDb_Impl::CCSraDb_Impl(), CDenseSegHit::CDenseSegHit(), CGapCache::CGapCache(), CheckAdjustStartAndStop(), BlockMultipleAlignment::CheckAlignedBlock(), CheckCountRange(), CSnpTrack::CheckRange(), CVcfTrack::CheckRange(), CAlnMapPrinter::Chunks(), CkLabelType(), CGraphStatCollector_Graph::ClearRange(), UngappedAlignedBlock::Clone(), UnalignedBlock::Clone(), CMatePairGlyph::CMatePairGlyph(), CReadBlastApp::CollectRNAFeatures(), CReadBlastApp::CollectSimpleSeqs(), CScoreBuilder::ComputeScore(), CScoreBuilderBase::ComputeScore(), CAddFluComments::ConcatIds(), SSeqIdRange::const_iterator::const_iterator(), CRanges::Contain(), CSeq_loc_Conversion::Convert(), CConvertCDSToMiscFeat::Convert(), Convert_Seq_annot_Seq_loc_TotalRange(), CBadResiduesException::SBadResiduePositions::ConvertBadIndexesToString(), CBlobSplitterImpl::CopySequence(), CVCFVariantsBase::Count(), bm::rsc_sparse_vector< Val, SV >::count_range_notnull(), CreateAlignRow(), Threader::CreateCorDef(), CMacroBioData::CreateIterator(), CFeatureGenerator::CreateMicroIntrons(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), CreateObjectLocation(), CreatePairwiseSeqAlignFromMultipleRow(), CTrackConfigUtils::CreateRangeControl(), CSpliced_exon::CreateRowSeq_interval(), CSparseRowHandle::CreateSegmentIterator(), CAlnVecRowHandle::CreateSegmentIterator(), CSparseMultiDataSource::CreateSegmentIterator(), CSparseAlignment::CreateSegmentIterator(), CAlnVecMultiDataSource::CreateSegmentIterator(), CDensegGraphicDataSource::CreateSegmentIterator(), CSparseAlnGraphicDataSource::CreateSegmentIterator(), CAlnVecGraphicDataSource::CreateSegmentIterator(), CSparseAln::CreateSegmentIterator(), CPluginValueConstraint::CreateSeqLenRange(), CDeltaHelper::CreateSSR(), CComponentTrackFactory::CreateTracks(), CVarTrackFactory::CreateTracks(), CFeatureTrackFactory::CreateTracks(), CScaffoldTrackFactory::CreateTracks(), CSegmentMapTrackFactory::CreateTracks(), CSequenceTrackFactory::CreateTracks(), CGeneModelFactory::CreateTracks(), CVcfTrackFactory::CreateTracks(), CSegmentGlyph::CSegmentGlyph(), CSeqMap_CI::CSeqMap_CI(), CSNPDbPageIterator::CSNPDbPageIterator(), CSourceFeatureItem::CSourceFeatureItem(), CSparseIterator::CSparseIterator(), CVCFSlicedVariants::CVCFSlicedVariants(), CVCFVariant_CI::CVCFVariant_CI(), CVDBGraphDb_Impl::CVDBGraphDb_Impl(), BlockMultipleAlignment::DeleteBlock(), CommandProcessor::DoCommand_Highlight(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), CSFTransDS::DoTranslation(), CAlignMap::EditedSequence(), NSnpAnnot::EstimateSNPCount(), SAnnotSelector::ExcludeAnnotType(), SAnnotSelector::ExcludeFeatType(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractMaskingData(), BlockMultipleAlignment::ExtractRows(), SeqTreeAsnizer::fillAsnSeqTreeNode(), CFeatTableDS::SFeatureRow::FillIn(), FillInAlignmentData(), FillSetsRandomOne(), CVCFVariantsBase::Filter(), CAlignCollapser::FilterAlignments(), CCgiCookies::Find(), CVDBTableIndex::Find(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_insertion_point(), CFast5colReader::FindAnnots(), CLatLonMap_Base::FindClosestToLatLon(), CCompactSAMApplication::FindCompactAligns(), RowSourceTable::findEntries(), CSNPDb_Impl::FindSeq(), SequenceTable::findSequencesInTheGroup(), CSeqGraphicWidget::FindText(), CSeqGraphicPane::FindText(), CSeq_annot_SNP_Info::FirstIn(), CReadBlastApp::FixStrands(), SAnnotSelector::ForceAnnotType(), CGBSeqFormatter::FormatFeature(), CGBSeqFormatter::FormatReference(), fta_ranges_to_hist(), CCassandraFilteredPlan::Generate(), CFlatFileGenerator::Generate(), CSnpTrack::GenerateAsn1(), CFeatureTrack::GenerateAsn1(), CGeneModelTrack::GenerateAsn1(), CBinsGlyph::GenerateBinSignature(), CGeneMarkerGlyph::GenerateGeneMarkerSignature(), GenerateSignature(), CBinaryRangeCacheWithLock< Position, Value >::get_lock(), GetAlignedResidueIndexes(), CScoreBuilderBase::GetAlignLength(), CSeq_align::GetAlignLengthWithinRange(), CSGAlignmentDS::GetAlignmentCost(), BlockMultipleAlignment::GetAlignmentIndex(), CAlnVecRow::GetAlignmentTooltip(), CObjFingerprint::GetAlignSignature(), CBamRefSeqChunkInfo::GetAlignStartRange(), CSNPDbFeatIterator::GetAllele(), CAlnMap::GetAlnChunks(), CCSraRefSeqIterator::GetAlnOverToOpen(), CFast5colReader::GetAndUseAnnot(), CVDBGraphSeqIterator::GetAnnot(), CSGFeatureJob::GetAnnotNames(), CSGAlignmentJob::GetAnnotNames(), CSGSeqGraphJob::GetAnnotNames(), CEpigenomicsDS::GetAnnotNames(), CSGFeatureDS::GetAnnotNames(), CSGSegmentMapDS::GetAnnotNames(), CSGAlignmentDS::GetAnnotNames(), CSGGraphDS::GetAnnotNames(), CSGSnpDS::GetAnnotNames(), CSGFeatureJob::GetAnnotNames_var(), CSGFeatureDS::GetAnnotNames_var(), NSnpBins::GetBin(), BlockMultipleAlignment::GetBlock(), CFeatTrim::GetCdsFrame(), CInternalStopFinder::GetCDSNucleotideSequence(), BlockMultipleAlignment::GetCharacterTraitsAt(), CSNPDbSeqIterator::GetChunkForVersion(), CBamRefSeqInfo::GetChunkGraphRange(), SHitColoringParams::GetColorNorm(), CAddSecondary::GetCommand(), CObjFingerprint::GetComponentSignature(), CWGSDb_Impl::GetContigNameRowId(), CSNPDbSeqIterator::GetCoverageAnnot(), CSNPDbSeqIterator::GetCoverageGraph(), CVcfHeatmap::GetData(), CWigGraph::GetDataCoverage(), CDensityMap< CntType >::GetDensityMap(), GetDNAConv(), CSNPDbSeqIterator::GetEntry(), CBedCoverageGraph::GetEstimatedFeatureCount(), NSnpAnnot::GetFeat_CI(), CStdPrefetch::GetFeat_CI(), CSNPDbSeqIterator::GetFeatAnnot(), CObjFingerprint::GetFeatSignature(), CSeqTextDataSource::GetFeaturesAtPosition(), CVcfFeatureDS::GetFeaturesCountInRange(), SBamIndexRefIndex::GetFileRange(), CBamFileRangeSet::GetFileSize(), CGeneModelFeatJob::GetFilters(), CSGFeatureDS::GetFilters(), CSeq_align::GetFrameshiftsWithinRange(), CMultiAligner::SSegmentLoc::GetFrom(), CScoreBuilderBase::GetGapBaseCount(), CScoreBuilderBase::GetGapCount(), CSegmentSmearGlyph::CSegMap::GetGaps(), NSnpAnnot::GetGraph_CI(), CSGAlignmentDS::GetGraphCost(), CObjFingerprint::GetGraphSignature(), CVcfHistogram::GetHistogram(), CObjFingerprint::GetHistogramSignature(), CBinsGlyph::GetHTMLActiveAreas(), CGeneMarkerGlyph::GetHTMLActiveAreas(), CScoreBuilderBase::GetIdentityCount(), CSeq_align::GetIndelsWithinRange(), UnalignedBlock::GetIndexAt(), CAnnotType_Index::GetIndexRange(), CTableDataFTable::GetIntValue(), CVCFVariantsBase::GetLeftShiftedStartPos(), CGuiObjectInfoSeq_align::GetLinks(), CFeatureGenePanel::GetLocationForGene(), CSeqUtils::GetLocPlacements(), CWGSFeatureIterator::GetLocRange(), BlockMultipleAlignment::GetLoopLength(), CAnnotMapping_Info::GetMappedSeq_align(), CAutoDef::GetMasterLocation(), CVDBCursor::GetMaxRowId(), CScoreBuilderBase::GetMismatchCount(), CSparseGraph::GetMissingRegions(), CRawSeqDBSource::GetNext(), CClusterDBSource::GetNext(), CSeq_align::GetNonFrameshiftsWithinRange(), CPileUpGraph::GetNumberOfReads(), CSeq_align::GetNumFrameshiftsWithinRange(), CSeq_align::GetNumGapOpeningsWithinRange(), GetOverlappingFeatures(), CHandleRange::GetOverlappingRange(), CSNPDbSeqIterator::GetOverviewAnnot(), CSNPDbSeqIterator::GetOverviewGraph(), GetPackedFeatAnnot(), CScoreBuilderBase::GetPercentCoverage(), CScoreBuilderBase::GetPercentIdentity(), CWGSDb_Impl::GetProtAccRanges(), CWGSDb_Impl::GetProtAccRowId(), GetProteinConv(), GetProteinName(), CCrossAlnWidget::GetQueryVisibleRange(), CSeqTableReader::GetRange(), CClonePlacementGlyph::GetRange(), CLinkedFeatsGroup::GetRange(), CHistogramGlyph::GetRange(), CRsitesGlyph::GetRange(), SBamIndexParams::GetRangeIndexLevel(), CSeqGraphicWidget::GetRangeOrObjectSelection(), CCSraRefSeqIterator::GetRefLiterals(), CCgiContext::GetRequestValue(), CSGSegmentMapJob::GetSegmentMapLevels(), CSGSegmentMapDS::GetSegmentMapLevels(), CAlignSpanView::GetSelection(), CSNPDbFeatIterator::GetSeq_feat(), CAlnMap::GetSeqChunks(), CVDBGraphDb_Impl::GetSeqInfo(), CVDBGraphDb_Impl::GetSeqInfoAtRow(), CObjFingerprint::GetSeqLocSignature(), CAlnWriter::GetSeqString(), CSGSeqGraphJob::GetSeqtableAnnots(), CSGGraphDS::GetSeqtableAnnots(), CSeqDB::GetSequenceAsString(), CCSraShortReadIterator::GetShortBioseq(), CHitMatrixDataSource::GetStdSegRange(), SPsgCgiEntries::GetStringList(), CCrossAlnWidget::GetSubjectVisibleRange(), CSNPDbSeqIterator::GetTableFeatAnnots(), CMultiAligner::SSegmentLoc::GetTo(), CGeneMarkerGlyph::GetTooltip(), CGuiObjectInfoSeq_align::GetToolTip(), CGuiObjectInfoClone::GetToolTip(), CGuiObjectInfoPrimer::GetToolTip(), CSeq_align::GetTotalGapCountWithinRange(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), CLDBlockDS::GetTrackNames(), GetTrnaAnticodon(), CAlnSpanVertModel::GetValueAt(), CMultAlign::GetVariationAlignList(), CObjFingerprint::GetVcfVariantSignature(), CViewGraphic::GetVisibleRanges(), CSeqGraphicPane::GoBack(), CSeqGraphicPane::GoForward(), CGene::HarborsRange(), CSGSegmentMapDS::HasComponent(), CSGSegmentMapDS::HasScaffold(), CSGSegmentMapJob::HasSegmentMap(), CSGSegmentMapDS::HasSegmentMap(), SAnnotSelector::IncludeAnnotType(), SAnnotSelector::IncludedAnnotType(), SAnnotSelector::IncludedFeatType(), SAnnotSelector::IncludeFeatType(), CVcfHistogram::InitHistogramGlyph(), CViewGraphic::InitView(), CVcfTableView::InitView(), CSeq_loc_I::InsertInterval(), CAlignRangeCollection< CAlignRange< TSeqPos > >::IntersectFirst(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectFirst(), CHandleRange::IntersectingWith(), CAlignRangeCollection< CAlignRange< TSeqPos > >::IntersectSecond(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectSecond(), CRenderingContext::IntersectVisible(), CSeqDB_BitSet::IntersectWith(), ColumnResidueProfile::isAligned(), CLatLonMap_Base::IsClosestToLatLon(), CSGAlignmentDS::IsGraphCached(), CStringConstraint::IsInRange(), CLatLonMap_Base::IsNearLatLon(), CSGAlignmentDS::IsRangeCached(), CBlobSplitterImpl::IsWhole(), CSGAlignmentDS::LoadAlignFeats(), CSGAlignmentDS::LoadAlignments(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CSGAlignmentDS::LoadCoverageGraph(), CSGSnpDS::LoadData(), CEpigenomicsDS::LoadData(), CBinsDS::LoadData(), CSGHapmapDS::LoadData(), CSGFeatureDS::LoadFeatures(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CSGFeatureDS::LoadGeneModelFeatures(), CCSRARefSeqInfo::LoadRanges(), CCSRARefSeqInfo::LoadRefSeqChunk(), CSGSegmentMapDS::LoadSegmentMap(), CSGSegmentMapDS::LoadSegmentSmear(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CWGSDb_Impl::Lookup(), CAlnVecRow::LTH_OnLayoutChanged(), CSeqGraphicPane::LTH_ZoomOnRange(), CSeq_loc_CI_Impl::MakeBondA(), CSeq_loc_CI_Impl::MakeBondAB(), CSeq_loc_CI_Impl::MakeBondB(), CBlobSplitterImpl::MakeID2Chunk(), CBlobSplitterImpl::MakeLoc(), CSeq_loc_CI_Impl::MakeLoc(), CScoreSeqCoverage::MakeScore(), Map(), MapBlockFromConsensusToMaster(), MapSeq_feat(), CCpGIslands::MergeIslesWithin(), CHandleRange::MergeRange(), UnalignedBlock::MinResidues(), CSeqUtils::MixLocToLoc(), CSeqGraphicPane::ModifyMarker(), BlockMultipleAlignment::MoveBlockBoundary(), NcbiDumpIPRange(), NcbiIsInIPRange(), NcbiParseIPRange(), NcbiTrueIPRange(), SH2S_IoCoordinator::NewSession(), CSeqGraphicPane::NextPrevSplice(), SSNP_Info::NoMore(), SSNP_Info::NotThis(), StructureWindow::OnAlignStructures(), CHitMatrixWidget::OnColorByScore(), SequenceViewerWindow::OnHighlight(), CLDBlockGlyph::OnLeftDblClick(), CSeqGraphicPane::OnLeftDblClick(), CSeqGraphicPane::OnLeftUp(), CSeqGraphicWidget::OnModifyMarkerDlg(), CCrossAlignView::OnVisibleRangeChanged(), CDotMatrixView::OnVisibleRangeChanged(), CSeqGraphicWidget::OnZoomSelection(), CRangeUnion< CBGZFPos >::operator+=(), operator<<(), BlockMultipleAlignment::OptimizeBlock(), rapidjson::internal::GenericRegex< Encoding, Allocator >::Parse(), rapidjson::internal::GenericRegex< Encoding, Allocator >::ParseRange(), CGnomonAnnotator::Predict(), CWigGraph::Prefetch(), CSeqsRange::Print(), PrintFastaUnaligned(), PrintSAM(), PrintSAMUnaligned(), PrintTabular(), SBamIndexRefIndex::ProcessBin(), ProcessSAM(), CAlnWriter::ProcessSeqId(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), SBamIndexParams::RangeIsOnMinBinIndexLevel(), CGFFReader::Read(), ReadSequencesToBlast(), StructureObject::RealignStructure(), CCgiCookies::Remove(), CSeq_loc_CI_Impl::RemoveBond(), RowSourceTable::removeEntriesForCD(), CRichTextCtrl::RemoveFormatting(), CHistogramGraph::Render(), CRuler::Render(), CSeqGraphicPane::RenderVectorGraphics(), CExtendCDSToStop::ResetGenes(), CGnomonEngine::ResetRange(), TMaskedQueryRegions::RestrictToSeqInt(), ColumnResidueProfile::reweightColumnByRowWeights(), CAlignTabExportJob::Run(), CWiggleExportJob::Run(), CFeatureRetrievalJob::Run(), CDemoApp::Run(), CSampleAlnmgrApplication::Run(), s_AddCoalescedLocations(), s_AlignToSeqRanges(), s_ApplyPubMods(), s_ConvertBlastnMasks(), s_DetermineScanningOffsets(), s_EstimatedSize(), s_ExtractSeqidsAndRanges(), s_GetAlignmentTooltip(), s_GetAlnMapplingLocs(), s_GetCdsSequence(), s_GetComposition(), s_GetConcatenatedExon(), s_GetFeatureKey(), s_GetMatrixScoreProbs(), s_GetPssmScoreProbs(), s_GetQuerySequence(), s_GetRetainedRange(), s_GetRnaMappingLocs(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetSplicedSegIdentityMismatch(), s_GetTrimmedMappedFeat(), s_IntersectionLength(), s_MaskQuerySeq(), CBinaryRangeCacheWithLock< Position, Value >::s_Overlaps(), s_PassesFilter(), s_RangeContains(), s_Render_SeqFeat(), s_SeqDBMapNA2ToNA8(), s_SeqDBMapNcbiNA8ToBlastNA8(), s_SeqDBMaskSequence(), s_SeqLoc2MaskedSubjRanges(), s_SequenceGetProteinRange(), s_SequenceGetTranslatedRange(), s_SimpleRand(), s_SplitRange(), s_WindowSwapRange(), AlignmentUtility::ScoreRowByPSSM(), CSeqTextWidget::ScrollToText(), CSRSearch_Impl< index_t >::searchOneMismatch(), CSeqGraphicPane::SelectOnlyThisObject(), CWGSFeatureIterator::SelectRowRange(), SeqDB_UnpackAmbiguities(), SeqLocToBioseq(), CVDBGraphSeqIterator::SeqTableIsSmaller(), compile_time_bits::bitset_traits< _Ty, _Size, u_type >::set_range(), CAnnotMapping_Info::SetAnnotObjectRange(), CRangeMapIterator< Traits >::SetBegin(), CSegmentGlyph::SetComponentRanges(), CAlnMultiModel::SetCurrentMethod(), CCassandraFilteredPlan::SetFilterRanges(), CChainer::CChainerImpl::SetGenomicRange(), CBlobSplitterImpl::SetLoc(), CSegmentGlyph::SetMappedRanges(), CwxSeqMarkerSetDlg::SetMarkerRange(), CSeqGraphicPane::SetMarkers(), CCrossAlnWidget::SetQueryVisibleRange(), CHitMatrixPane::SetQueryVisibleRange(), CHitMatrixWidget::SetQueryVisibleRange(), CSeq_loc_I::SetRange(), SSeqMapSelector::SetRange(), CQueryOptionsArgs::SetRange(), CMappedFeatOrObject::SetRange(), CSegmentSmearGlyph::CSegMap::SetRange(), CDummyLayoutObject::SetRange(), CDummyGlyph::SetRange(), CRuler::SetRange(), CDataMiningPanel::SetRange(), CSeqMarkHandler::SetRange(), CMarker::SetRange(), CSeq_data_SplitInfo::SetSeq_data(), CMacroRep::SetSeqRange(), CCrossAlnWidget::SetSubjectVisibleRange(), CHitMatrixPane::SetSubjectVisibleRange(), CHitMatrixWidget::SetSubjectVisibleRange(), COligoSpecificityTemplate::SetTemplateRange(), CAnnotMapping_Info::SetTotalRange(), CCdsForMrnaPlugin::setUpFeatureIterator(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), LinkHspTestFixture::setupLinkHspInputBlastn(), SetupSubjects_OMF(), CTempTrackProxy::SetVisitedRange(), CDataTrack::SetVisRange(), sGenerateFields(), BlockMultipleAlignment::ShiftRow(), CReadBlastApp::short_proteins(), CStatusBarService::ShowStatusProgress(), CMessageSlot::ShowStatusProgress(), sParseRange(), BlockMultipleAlignment::SplitBlock(), CBlobSplitterImpl::SplitPieces(), CCassandraFullscanPlan::SplitTokenRangesForLimits(), SGraphMaker::Start(), CSeq_annot_Info::StartSortedIterator(), sx_HasMoreProducts(), TotalFrameShift(), transform_range(), CAlignmentAssistant::TranslateLocations(), TSeqLocVector2Packed_seqint(), CSparseGraph::Update(), CPileUpGraph::UpdateAlignStats(), CAlnMultiModel::UpdateOnScoringChanged(), CValidError_bioseq::ValidateSeqFeatContext(), CSpliceProblems::ValidateSpliceCdregion(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CBlastDB_FastaFormatter::Write(), CAlnWriter::WriteAlignDenseSeg(), CWriteDB_GiMaskData::WriteMask(), CAlnWriter::WriteSparseAlign(), CVecscreen::AlnInfo::x_add_aligns(), SWGSCreateInfo::x_AddFeatures(), SWGSCreateInfo::x_AddFeaturesDirect(), SWGSCreateInfo::x_AddFeaturesSplit(), CFeat_CI::x_AddFeaturesWithId(), CSGAnnotJob::x_AddGraphToMap(), CLinearSelHandler::x_AddToSelection(), CTextSelHandler::x_AddToSelection(), CEditObjectSeq_feat::x_AdjustCircularGene(), x_AdjustGraphRange(), x_AdjustRange(), CSourceModParser::x_ApplyMods(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CSGCalcFeatHistJob::x_CalcFeatHistRecursive(), CLayoutPWAlign::x_CalcIntervals(), CRuler::x_CalcStartStopOffsets(), CScoringJob::x_CalculateAlignmentScores(), CSeqGraphicPane::x_ChangeSwitchPoint(), CCDSTranslationProblems::x_CheckForRaggedEnd(), CDebugDumpViewer::x_CheckLocation(), CTotalRangeThread::x_CheckPoint(), CVisibleRange::x_Clamp(), CSGAlignStatJob::x_CollectAlignStats(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), x_CollectCoverageGraph(), CAnnot_Collector::x_CollectMapped(), x_CollectOverviewGraph(), CAnnot_Collector::x_CollectSegments(), CFlatGatherer::x_CollectSourceFeatures(), CSeqDBOIDList::x_ComputeFilters(), CSGFeatureJob::x_CreateAndFilterCrossOriginGlyphs(), CWGSSeqIterator::x_CreateDataChunk(), CMacroBioData::x_CreateFeatIterator(), CWGSSeqIterator::x_CreateFeaturesChunk(), CGFFReader::x_CreateGeneFeatures(), x_CreateLocalCDDEntryChunk(), CFeatureGraph::x_CreateMapRanges(), CSGAlignStatJob::x_CreatePileUpGraphs(), SWGSCreateInfo::x_CreateProtSet(), CGeneModelFactory::x_CreateTracksWithFilters(), CWigGraph::x_DecodeDelta(), CVCFVariantsBase::x_DeserializeDescr_Range(), CNCMessageHandler::x_DoCmd_Get(), CComponentSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CGeneMarkerGlyph::x_Draw(), CLDBlockGlyph::x_Draw(), CHistogramGlyph::x_Draw(), CMatePairGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CLinkedFeatsGroup::x_DrawFeatureBar(), CAlignGlyph::x_DrawUnalignedBar(), CAlignGlyph::x_DrawUnalignedRowSequence(), CSGAlignStatJob::x_Execute(), CVcfFeatureJob::x_Execute(), x_ExpandRange(), CAdjustForConsensusSpliceSite::x_ExtendStartOfExon(), CAdjustForConsensusSpliceSite::x_ExtendStopOfExon(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), x_FillResidueFrequencies(), CSeq_annot_Finder::x_Find(), CFast5colReader::x_FindAnnots(), CTSE_Info::x_FindSeq_feat(), CAlnVecRow::x_ForEachAlnSeg(), CDisplaySeqalign::x_FormatAlnBlastInfo(), CDisplaySeqalign::x_FormatAlnHSPLinks(), CFtableFormatter::x_FormatLocation(), CFlatItemFormatter::x_FormatRefLocation(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CRuler::x_GenerateLabelPositions(), CWGSResolver_VDB::x_GetAccPrefixes(), CSGAlignmentJob::x_GetAlignments(), CAlnVecRow::x_GetAlignmentTooltip(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CSeqDBVol::x_GetAmbigSeq(), CWigGraph::x_GetBigWigData(), CBinsGlyph::x_GetBinRange(), x_GetClusterGapLocations(), CCreateGeneModelTask::x_GetCommand(), CSixFramesTransTrack::x_GetCurrentTransRange(), CAlnGraphic::x_GetEffectiveRange(), CSnpTrack::x_GetFeat_CI(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CAutoDef::x_GetFeatureClauses(), CTSE_Info::x_GetFeaturesById(), CSnpTrack::x_GetGraph_CI(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CRuler::x_GetPositionLabel(), CCSraShortReadIterator::x_GetQualityGraph(), CCSraShortReadIterator::x_GetQualityGraphAnnot(), CCSraShortReadIterator::x_GetReadData(), CVectorTrimPanel::x_GetRetainedRange(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps(), CDistances::x_GetSelfScores(), CSequenceSearchJob::x_GetSequence(), CAlnTableDS::x_GetStartStop(), CCreateGeneModelTask::x_Group_By_GeneID(), x_HasFeatIds(), x_HasFeatType(), CAlnVecRow::x_HitTest(), CLinearSelHandler::x_HitTest(), CTextSelHandler::x_HitTest(), CCSraShortReadIterator::x_Init(), CWGSScaffoldIterator::x_Init(), CWGSProteinIterator::x_Init(), CWGSFeatureIterator::x_Init(), CWGSGiIterator::x_Init(), CWGSSeqIterator::x_Init(), CAnnotTypes_CI::x_Init(), CAnnot_Collector::x_Initialize(), CAnnot_Collector::x_Initialize0(), SAnnotSelector::x_InitializeAnnotTypesSet(), CAnnotType_Index::x_InitIndexTables(), CDisplaySeqalign::x_InitSeqUrl(), CAlignRangeCollection< CAlignRange< TSeqPos > >::x_IntersectFirst(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_IntersectFirst(), CAlignRangeCollection< CAlignRange< TSeqPos > >::x_IntersectSecond(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_IntersectSecond(), CSegmentMapTrackFactory::x_IsChromosome(), x_IsOverlappingRange(), CLayeredLayout::x_LayerByPos(), CAlignmentTrack::x_LoadAlignedSeqFeats(), CID2SNPProcessor_Impl::x_LoadChunk(), CBatchFeatJob::x_LoadFeatProducts(), CFeatureTrack::x_LoadFeatures(), CIntronTrack::x_LoadFeatures(), CSGSegmentSmearJob::x_LoadFromDeltaSeqs(), CSGSegmentSmearJob::x_LoadFromNA(), CSGSeqGraphJob::x_LoadSeqTable(), CColumnarVCFReaderApp::x_LoadSerializedData(), CVDBGraphSeqIterator::x_MakeGraph(), CVDBGraphSeqIterator::x_MakeTable(), CTSE_Info::x_MapChunkByFeatId(), CTSE_Info::x_MapChunkByFeatType(), CFeaturePropagator::x_MapLocation(), CAnnot_Collector::x_MatchRange(), CSeqTextView::x_MergeObjects(), CFeatTableView::x_MergeObjects(), CViewGraphic::x_MergeObjects(), CSGSegmentMapJob::x_MergeSeqSegments(), CWGSSeqIterator::x_NormalizeSeqRange(), CGlWidgetBase::x_OnScrollX(), CGlWidgetBase::x_OnScrollY(), CColumnarVCFReaderApp::x_ParseRange(), x_ParseSNP_Info(), CRegEx::x_ParseSquare(), CBinsJob::x_PreFetchFtable(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CWig2tableApplication::x_PreprocessValues(), CGenBankLoadOptionPanel::x_ProccessText(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CFilterColumnsDlg::x_ProcessSelectionPattern(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CLinearSelHandler::x_RemoveFromSelection(), CTextSelHandler::x_RemoveFromSelection(), CAlnVecRow::x_RenderAlign(), CRuler::x_RenderAllPosLabels(), CFeaturePanel::x_RenderFeatureGrid(), CAlnVecRow::x_RenderGraph(), CAlnVecRow::x_RenderInserts(), CRuler::x_RenderOriginAndMetric(), CRuler::x_RenderRange(), CRuler::x_RenderScale(), CAlnVecRow::x_RenderTracks(), CAlnVecRow::x_RenderUnaligned(), CGFFReader::x_ResolveLoc(), CSGAlnQualityScore::x_RetrieveQualityMap(), x_RoundRange(), CFastaRetrieveLocJob::x_Run(), CWigGraph::x_RunBigWigScript(), CSeqGraphicWidget::x_SaveVectorImage(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchObjects(), CAnnot_Collector::x_SearchRange(), CAnnot_Collector::x_SearchSegments(), CSequenceSearchJob::x_SearchSequence(), CVDBGraphSeqIterator::x_SeqTableIsSmaller(), CBioseqContext::x_SetLocation(), CAdjustForConsensusSpliceSite::x_ShiftExonPairBackward(), CAdjustForConsensusSpliceSite::x_ShiftExonPairForward(), CMacroBioData_FeatIntervalIter::x_StepToNextFeat(), CRuler::x_ToDisplay(), CRuler::x_ToModel(), CAdjustForConsensusSpliceSite::x_TrimStartOfExon(), CAdjustForConsensusSpliceSite::x_TrimStopOfExon(), CBinsGlyph::x_UpdateBoundingBox(), CGeneMarkerGlyph::x_UpdateBoundingBox(), CScatterPlotGlyph::x_UpdateBoundingBox(), CLDBlockGlyph::x_UpdateBoundingBox(), CAlignGlyph::x_UpdateBoundingBox(), CAlignSmearGlyph::x_UpdateBoundingBox(), CCommentGlyph::x_UpdateBoundingBox(), CLinkedFeatsGroup::x_UpdateBoundingBox(), CHistogramGlyph::x_UpdateBoundingBox(), CMatePairGlyph::x_UpdateBoundingBox(), CRsitesGlyph::x_UpdateBoundingBox(), CSegmentGlyph::x_UpdateBoundingBox(), CScoringJob::x_UpdateBuffer(), CSnpTrack::x_UpdateData(), CEpigenomicsTrack::x_UpdateData(), CFeatureTrack::x_UpdateData(), CSequenceTrack::x_UpdateData(), CVarTrack::x_UpdateData(), CSixFramesTransTrack::x_UpdateData(), CVcfTrack::x_UpdateData(), CRuler::x_UpdateMappingByPane(), CHitMatrixDataSource::x_UpdateScoreMap(), CGlWidgetBase::x_UpdateScrollbars(), CSeq_loc::x_UpdateTotalRange(), CSingleFeatValidator::x_ValidateRptUnitRangeVal(), CPolyASiteValidator::x_ValidateSeqFeatLoc(), CPolyASignalValidator::x_ValidateSeqFeatLoc(), CVcfWriter::x_WriteData(), XGapToSeqLocEx(), CWiggleReader::xPreprocessValues(), CSeqGraphicRenderer::ZoomOnRange(), and CSeqGraphicWidget::ZoomOnRange().
