template<typename Mapped , typename Position = int>
Definition at line 553 of file rangemap.hpp.
◆ const_iterator [3/3]template<typename Mapped , typename Position = int>
Definition at line 615 of file rangemap.hpp.
◆ iterator [1/5] ◆ iterator [2/5] ◆ iterator [3/5] ◆ iterator [4/5]template<typename Mapped , typename Position = int>
Definition at line 552 of file rangemap.hpp.
◆ iterator [5/5]template<typename Mapped , typename Position = int>
Definition at line 614 of file rangemap.hpp.
◆ key_type [1/3] ◆ key_type [2/3]template<typename Mapped , typename Position = int>
Definition at line 550 of file rangemap.hpp.
◆ key_type [3/3]template<typename Mapped , typename Position = int>
Definition at line 612 of file rangemap.hpp.
◆ mapped_type [1/5]template<typename Position , typename Mapped >
Definition at line 65 of file rangemap.hpp.
◆ mapped_type [2/5] ◆ mapped_type [3/5] ◆ mapped_type [4/5]template<typename Mapped , typename Position = int>
Definition at line 548 of file rangemap.hpp.
◆ mapped_type [5/5]template<typename Mapped , typename Position = int>
Definition at line 610 of file rangemap.hpp.
◆ non_const_iterator [1/2] ◆ non_const_iterator [2/2] ◆ pointer [1/3] ◆ pointer [2/3] ◆ pointer [3/3] ◆ position_type [1/10] ◆ position_type [2/10] ◆ position_type [3/10] ◆ position_type [4/10]template<class Position >
Definition at line 120 of file range.hpp.
◆ position_type [5/10]template<class Position >
Definition at line 391 of file range.hpp.
◆ position_type [6/10]template<typename Position , typename Mapped >
Definition at line 63 of file rangemap.hpp.
◆ position_type [7/10] ◆ position_type [8/10] ◆ position_type [9/10]template<typename Mapped , typename Position = int>
Definition at line 546 of file rangemap.hpp.
◆ position_type [10/10]template<typename Mapped , typename Position = int>
Definition at line 608 of file rangemap.hpp.
◆ range_type [1/5]template<typename Position , typename Mapped >
Definition at line 64 of file rangemap.hpp.
◆ range_type [2/5] ◆ range_type [3/5] ◆ range_type [4/5]template<typename Mapped , typename Position = int>
Definition at line 547 of file rangemap.hpp.
◆ range_type [5/5]template<typename Mapped , typename Position = int>
Definition at line 609 of file rangemap.hpp.
◆ reference [1/3] ◆ reference [2/3] ◆ reference [3/3] ◆ select_value [1/3] ◆ select_value [2/3]template<typename Mapped , typename Position = int>
Definition at line 557 of file rangemap.hpp.
◆ select_value [3/3]template<typename Mapped , typename Position = int>
Definition at line 619 of file rangemap.hpp.
◆ size_type [1/3] ◆ size_type [2/3]template<typename Mapped , typename Position = int>
Definition at line 545 of file rangemap.hpp.
◆ size_type [3/3]template<typename Mapped , typename Position = int>
Definition at line 607 of file rangemap.hpp.
◆ TConstIteratorTraits ◆ TIteratorTraits [1/3] ◆ TIteratorTraits [2/3] ◆ TIteratorTraits [3/3] ◆ TLevelIter [1/3] ◆ TLevelIter [2/3] ◆ TLevelIter [3/3] ◆ TLevelMap [1/5]template<typename Position , typename Mapped >
Definition at line 113 of file rangemap.hpp.
◆ TLevelMap [2/5]template<typename Position , typename Mapped >
Definition at line 123 of file rangemap.hpp.
◆ TLevelMap [3/5] ◆ TLevelMap [4/5]template<typename Mapped , typename Position = int>
Definition at line 559 of file rangemap.hpp.
◆ TLevelMap [5/5]template<typename Mapped , typename Position = int>
Definition at line 621 of file rangemap.hpp.
◆ TLevelMapI [1/3] ◆ TLevelMapI [2/3]template<typename Mapped , typename Position = int>
Definition at line 560 of file rangemap.hpp.
◆ TLevelMapI [3/3]template<typename Mapped , typename Position = int>
Definition at line 622 of file rangemap.hpp.
◆ TLevelMapRef [1/2] ◆ TLevelMapRef [2/2] ◆ TMapTraits [1/2] ◆ TMapTraits [2/2] ◆ TNCIteratorTraits [1/2] ◆ TNCIteratorTraits [2/2] ◆ TParent [1/5]template<class Position >
Definition at line 390 of file range.hpp.
◆ TParent [2/5]template<typename Position , typename Mapped >
Definition at line 110 of file rangemap.hpp.
◆ TParent [3/5]template<typename Position , typename Mapped >
Definition at line 120 of file rangemap.hpp.
◆ TParent [4/5]template<typename Mapped , typename Position = int>
Definition at line 542 of file rangemap.hpp.
◆ TParent [5/5]template<typename Mapped , typename Position = int>
Definition at line 604 of file rangemap.hpp.
◆ TRange ◆ TRangeMap [1/3]template<typename Position , typename Mapped >
Definition at line 112 of file rangemap.hpp.
◆ TRangeMap [2/3]template<typename Position , typename Mapped >
Definition at line 122 of file rangemap.hpp.
◆ TRangeMap [3/3] ◆ TRangeMapRef [1/2] ◆ TRangeMapRef [2/2] ◆ TRangeMapTraits [1/3] ◆ TRangeMapTraits [2/3]template<typename Mapped , typename Position = int>
Definition at line 555 of file rangemap.hpp.
◆ TRangeMapTraits [3/3]template<typename Mapped , typename Position = int>
Definition at line 617 of file rangemap.hpp.
◆ TSelectIter [1/3] ◆ TSelectIter [2/3] ◆ TSelectIter [3/3] ◆ TSelectMap [1/5]template<typename Position , typename Mapped >
Definition at line 114 of file rangemap.hpp.
◆ TSelectMap [2/5]template<typename Position , typename Mapped >
Definition at line 124 of file rangemap.hpp.
◆ TSelectMap [3/5] ◆ TSelectMap [4/5]template<typename Mapped , typename Position = int>
Definition at line 556 of file rangemap.hpp.
◆ TSelectMap [5/5]template<typename Mapped , typename Position = int>
Definition at line 618 of file rangemap.hpp.
◆ TSelectMapI [1/3] ◆ TSelectMapI [2/3]template<typename Mapped , typename Position = int>
Definition at line 558 of file rangemap.hpp.
◆ TSelectMapI [3/3]template<typename Mapped , typename Position = int>
Definition at line 620 of file rangemap.hpp.
◆ TSelectMapRef [1/3] ◆ TSelectMapRef [2/3] ◆ TSelectMapRef [3/3] ◆ TSeqRangetypedefs for sequence ranges
Definition at line 419 of file range.hpp.
◆ TSignedSeqRange ◆ TThisType [1/5] ◆ TThisType [2/5]template<class Position >
Definition at line 121 of file range.hpp.
◆ TThisType [3/5]template<class Position >
Definition at line 392 of file range.hpp.
◆ TThisType [4/5] ◆ TThisType [5/5] ◆ TTraits ◆ value_type [1/5]template<typename Position , typename Mapped >
Definition at line 66 of file rangemap.hpp.
◆ value_type [2/5] ◆ value_type [3/5] ◆ value_type [4/5]template<typename Mapped , typename Position = int>
Definition at line 549 of file rangemap.hpp.
◆ value_type [5/5]template<typename Mapped , typename Position = int>
Definition at line 611 of file rangemap.hpp.
◆ EFlagstemplate<class Position >
◆ AbuttingWith()template<class Position >
◆ begin() [1/4] ◆ begin() [2/4] ◆ begin() [3/4] ◆ begin() [4/4] ◆ CAlignRange() [1/2]template<class Position >
◆ CAlignRange() [2/2] ◆ clear() ◆ CombinationWith()template<class Position >
◆ CombinationWithAbutting()template<class Position >
◆ CombineWith()template<class Position >
Definition at line 345 of file range.hpp.
Referenced by CGraphRanges::AddRange(), CHit::AddUpSubHits(), CFeatHistogramDS::CFeatHistogramDS(), CIdRangeMap::CIdRangeMap(), CModelExon::Extend(), CAnnotMapping_Info::GetMappedSeq_align(), CClonePlacementGlyph::GetRange(), CFeatGlyph::GetRange(), CLinkedFeatsGroup::GetRange(), CHistogramGlyph::GetRange(), CSeq_align::GetSeqRange(), CHitMatrixDataSource::GetStdSegRange(), CSparseAlignment::Init(), CModelCluster< Model >::Insert(), CGnomonAnnotator::Predict(), readGFF3(), s_SeqLocToTotalRangesInfoMapByStrand(), CModelCluster< Model >::Splice(), CSparseAln::x_Build(), CFeatGlyph::x_DrawFeatureBar(), CAllOtherFeaturesTrack::x_OnAllJobsFinished(), CTrackContainer::x_OnJobCompleted(), CAlignedFeatureGraph::x_PlaceCluster(), CUnorderedSplitter::x_SplitDeltaExt(), and CMatePairGlyph::x_UpdateBoundingBox().
◆ CombineWithAbutting()template<class Position >
Definition at line 302 of file align_range.hpp.
References _ASSERT, CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstToOpen(), CAlignRange< Position >::IsAbutting(), CAlignRange< Position >::IsDirect(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::m_Length, r(), CAlignRange< Position >::SetFirstFrom(), and CAlignRange< Position >::SetSecondFrom().
Referenced by CAlignRange< Position >::CombinationWithAbutting(), and CAlignRangeCollection< CAlignRange< TSeqPos > >::insert().
◆ COpenRange() [1/2]template<class Position >
Definition at line 128 of file range.hpp.
◆ COpenRange() [2/2]template<class Position >
Definition at line 124 of file range.hpp.
◆ CRange() [1/3]template<class Position >
Definition at line 402 of file range.hpp.
◆ CRange() [2/3]template<class Position >
Definition at line 398 of file range.hpp.
◆ CRange() [3/3]template<class Position >
Definition at line 395 of file range.hpp.
◆ CRangeMap()template<typename Mapped , typename Position = int>
Definition at line 563 of file rangemap.hpp.
◆ CRangeMapBase() ◆ CRangeMapIterator() [1/2] ◆ CRangeMapIterator() [2/2] ◆ CRangeMultimap()template<typename Mapped , typename Position = int>
Definition at line 625 of file rangemap.hpp.
◆ DECLARE_OPERATOR_BOOL() ◆ Empty() [1/2]template<class Position >
◆ Empty() [2/2]template<class Position >
Definition at line 148 of file range.hpp.
Referenced by CAlignCollapser::AddAlignment(), CGeneModel::AddExon(), CGraphRanges::AddRange(), CHandleRange::AddRange(), CDepthCollection::AddRange(), CDensityMap< CntType >::AddRange(), CBamFileRangeSet::AddRanges(), AddSupport(), CChain::CalculateDropLimits(), CFeatHistogramDS::CFeatHistogramDS(), CChainer::CChainerImpl::CheckCompatibility(), CheckSparseAln(), CCDSInfo::Clip(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), CModelExon::CModelExon(), IAlnMultiDataSource::CollectAlignStats(), CGeneModel::CombineCdsInfo(), CCDSInfo::CombineWith(), CSeq_loc_Conversion::CombineWith(), SPhyloCSFSlice::CompactRange(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CComponentTrackFactory::CreateTracks(), CVarTrackFactory::CreateTracks(), CFeatureTrackFactory::CreateTracks(), CScaffoldTrackFactory::CreateTracks(), CSegmentMapTrackFactory::CreateTracks(), CGeneModelFactory::CreateTracks(), CVcfTrackFactory::CreateTracks(), CGeneModel::CutExons(), CDataLoader::DetailsToChoice(), CEquivRange::Distance(), CAlignGlyph::DrawPWAlignElem(), DumpSparseAln(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CEquivRange::Empty(), CAlignCollapser::FilterAlignments(), CGeneSelector::FilterGenes(), CChainer::CChainerImpl::FilterOutTandemOverlap(), CChainer::CChainerImpl::FindAltsForGeneSeeds(), FindPolyA(), FindStartsStops(), CGeneModel::FShiftedLen(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CGnomonEngine::GetAnnot(), CVDBGraphSeqIterator::GetAnnot(), CParse::GetGenes(), CGuiObjectInfoSeq_align::GetInsertionRanges(), SBamIndexRefIndex::GetLimitRange(), CHandleRange::GetOverlappingRange(), CHandleRange::GetRight(), CGnomonEngine::GetScore(), CEditScript::GetScore(), CSeq_align::GetSeqRange(), CHitMatrixDataSource::GetStdSegRange(), CHandleRange::GetStrandsFlag(), CChain::HarborsNested(), CGene::HarborsNested(), CSeqScores::Init(), CSeq_loc_I::InsertInterval(), CHandleRange::IntersectingWith(), CCddInputData::CHit::IntersectWith(), CSeq_loc_CI::IsEmpty(), IAlnSegment::IsGap(), CChain::MainPeaks(), CChainer::CChainerImpl::MakeChains(), CEditScript::MakeEditScript(), Map(), CGnomonAnnotator_Base::MapModelsToOrigContig(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CAlignMap::MapRangeEditedToOrig(), CAlignMap::MapRangeOrigToEdited(), CSeqUtils::MixLocToLoc(), CTestNameToInfoMapLoader::operator()(), SOutsideRange::operator()(), ParseAttributes(), CGnomonAnnotator::Predict(), readGFF3(), CAlignModel::RecalculateAlignMap(), CAlignCollapser::RemoveNotSupportedIntronsFromProt(), CAlignMarkHandler::Render(), CRuler::Render(), CChainer::CChainerImpl::ReplicatePStops(), CChain::RestoreReasonableConfirmedStart(), s_AlignDist(), s_MapSlaveFeatureToMaster(), s_SeqLocToTotalRangesInfoMapByStrand(), CClippedScorer::ScoreAlignments(), CSNPDbGraphIterator::Select(), CSNPDbPageIterator::Select(), CFeatureSearchJob::SeqLocToString(), CVDBGraphSeqIterator::SeqTableIsSmaller(), CChain::SetConfirmedEnds(), CChain::SetConsistentCoverage(), CChainer::CChainerImpl::SetFlagsForChains(), CCDSInfo::SetReadingFrame(), CAlignCompare::SAlignment::Slice(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), SModelData::SModelData(), CEquivRangeBuilder::SplitIntersections(), CSeq_align::SplitOnLongDiscontinuity(), CBlobSplitterImpl::SplitPieces(), SGraphMaker::Start(), ProjectCDS::transform_align(), DoNotBelieveFrameShiftsWithoutCdsEvidence::transform_align(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), TrimAlignment::TrimTranscript(), CMultAlign::Variations(), CHit::VerifyHit(), CAnnot_Collector::x_AddPostMappings(), CAnnot_Collector::x_AddPostMappingsCvt(), CPhrap_Read::x_AddQualityFeat(), CMultiAligner::x_AlignProfileProfileUsingHit(), CAlignMarkHandler::x_AlnRangeFromSeqRange(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), CAlignGlyph::x_CalcIntervals(), CScoringJob::x_CalculateAlignmentScores(), CHitMatrixDataSource::x_CalculateHitsRange(), CDenseg_CI::x_CheckSegment(), CSparse_CI::x_CheckSegment(), CAnnot_Collector::x_CollectMapped(), CSGAlignStatJob::x_CreatePileUpGraphs(), CGeneModelFactory::x_CreateTracksWithFilters(), CVCFVariantsBase::x_DeserializeDescr_Range(), CMatePairGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CAlignGlyph::x_DrawGaps(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CAlignGlyph::x_DrawMultiAlign(), CCdsGlyph::x_DrawProjectedProtSeq(), CFeatGlyph::x_DrawProjectedRuler(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawUnalignedBar(), CAlignGlyph::x_DrawUnalignedRowSequence(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CDisplaySeqalign::x_GetFeatureInfo(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CDistances::x_GetSelfScores(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CSeqGlyph::x_IntersectVisible(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CColumnarVCFReaderApp::x_LoadSerializedData(), CMappingRange::x_Map_Fuzz(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSparse_CI::x_NextSegment(), CTextSelHandler::x_OnChangeSelRange(), CLinearSelHandler::x_OnEndSelRange(), CTextSelHandler::x_OnEndSelRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CMultiAligner::x_RealignBlocks(), CAlnVecRow::x_RenderAlignSegments(), CAlignGlyph::x_RenderAveragableScores(), CGraphOverlay::x_RenderContent(), CGraphTrack::x_RenderContent(), CTraceGraphTrack::x_RenderContent(), CRuler::x_RenderRange(), CRuler::x_RenderScale(), CSeqGraphicPane::x_RenderTooltipConnector(), CAnnot_Collector::x_SearchMapped(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CGraphOverlay::x_UpdateBoundingBox(), CGraphTrack::x_UpdateBoundingBox(), CFeatureTrack::x_UpdateData(), CGeneModelTrack::x_UpdateData(), CSeqGlyph::x_Visible_V(), and CHitMatrixWidget::x_ZoomToHits().
◆ empty() ◆ end() [1/2] ◆ end() [2/2] ◆ erase() [1/2] ◆ erase() [2/2] ◆ find() [1/2] ◆ find() [2/2] ◆ Find() ◆ FirstContains()template<class Position >
◆ FirstLevelIter() ◆ get_max_length()template<typename Position , typename Mapped >
◆ GetEmpty() [1/2] ◆ GetEmpty() [2/2]template<class Position >
◆ GetEmptyFrom() [1/2]template<class Position >
◆ GetEmptyFrom() [2/2]template<class Position >
◆ GetEmptyLength() [1/2] ◆ GetEmptyLength() [2/2]template<class Position >
Definition at line 302 of file range.hpp.
◆ GetEmptyTo() [1/2]template<class Position >
◆ GetEmptyTo() [2/2]template<class Position >
◆ GetEmptyToOpen() [1/2]template<class Position >
◆ GetEmptyToOpen() [2/2]template<class Position >
◆ GetFirstFrom()template<class Position >
Definition at line 109 of file align_range.hpp.
References CAlignRange< Position >::m_FirstFrom.
Referenced by CDenseSegHit::CDenseSegHit(), CheckPairwiseAln(), CAlignRange< Position >::CombineWithAbutting(), DumpPairwiseAln(), CAlignRange< Position >::GetFirstRange(), CDiagHitElement::GetQueryStart(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IntersectingWith(), CAlignRange< Position >::IntersectWith(), CAlignRange< Position >::IsAbutting(), operator<<(), CAlignRange< Position >::operator==(), s_GetSplicedSegIdentityMismatch(), s_TranslatePairwise(), s_TranslatePairwiseToAlnCoords(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimSecondFrom(), CDiagRangeCollection::TrimSecondTo(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), CSparseAln::x_Build(), CRuler::x_CalcStartStopOffsets(), CDiagRangeCollection::x_Diff(), CAlnMixMerger::x_Merge(), CRuler::x_RenderAllPosLabels(), CRuler::x_RenderOriginAndMetric(), CRuler::x_RenderScale(), CRuler::x_UpdateMappingByPane(), and CMergedPairwiseAln::x_ValidNeighboursOnFirstDim().
◆ GetFirstPosBySecondPos()template<class Position >
◆ GetFirstRange()template<class Position >
◆ GetFirstTo()template<class Position >
Definition at line 117 of file align_range.hpp.
References CAlignRange< Position >::GetFirstToOpen().
Referenced by CDenseSegHit::CDenseSegHit(), CAlignRange< Position >::GetFirstRange(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IntersectingWith(), CAlignRange< Position >::IntersectWith(), s_GetSplicedSegIdentityMismatch(), s_TranslatePairwiseToAlnCoords(), CRuler::x_CalcStartStopOffsets(), CRuler::x_RenderAllPosLabels(), CRuler::x_RenderScale(), and CRuler::x_UpdateMappingByPane().
◆ GetFirstToOpen()template<class Position >
Definition at line 113 of file align_range.hpp.
References CAlignRange< Position >::m_FirstFrom, and CAlignRange< Position >::m_Length.
Referenced by CAlignRange< Position >::CombineWithAbutting(), ConvertStdsegToPairwiseAln(), CAlignRange< Position >::FirstContains(), CAlignRange< Position >::GetFirstTo(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IsAbutting(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), CSparseAln::x_Build(), CDiagRangeCollection::x_Diff(), and CMergedPairwiseAln::x_ValidNeighboursOnFirstDim().
◆ GetFrom()template<class Position >
Definition at line 134 of file range.hpp.
Referenced by CSeq_loc_Conversion_Set::Convert(), DumpPairwiseAln(), SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), SBamIndexRefIndex::GetAlnOverStarts(), CVDBGraphSeqIterator::GetAnnot(), SBamIndexParams::GetBinRange(), CBamRawAlignIterator::GetCIGARPos(), SBamIndexRefIndex::GetLimitRange(), CPagedFile::GetPage(), CBamRawAlignIterator::GetRefSeqPos(), CSNPDbFeatIterator::GetSNPPosition(), CSeq_loc::GetStart(), SBamIndexRefIndex::ProcessBin(), s_CompareRanges(), CBinaryRangeCacheWithLock< Position, Value >::s_Overlaps(), s_SetSplitQuerySeqInterval(), CSNPDbGraphIterator::Select(), CSNPDbPageIterator::Select(), CSplitQueryBlk::SetChunkBounds(), CAnnot_Collector::x_CollectMapped(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CCSraShortReadIterator::x_GetQualityGraph(), CCSraShortReadIterator::x_GetReadData(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps(), CVDBGraphSeqIterator::x_MakeGraph(), CVDBGraphSeqIterator::x_MakeTable(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CBamRawAlignIterator::x_NeedToSkip(), CAnnot_Collector::x_SearchMapped(), CVDBGraphSeqIterator::x_SeqTableIsSmaller(), and CSplitQueryTestFixture::x_ValidateChunkBounds().
◆ GetInterval() ◆ GetLength() [1/2]template<class Position >
Definition at line 150 of file align_range.hpp.
References CAlignRange< Position >::m_Length.
Referenced by CDiagHitElement::GetQueryLength(), CDiagHitElement::GetSubjectLength(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IsAbutting(), operator<<(), CAlignRange< Position >::operator==(), CRuler::Render(), s_TranslateAnchorToAlnCoords(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimFirstTo(), CDiagRangeCollection::TrimSecondFrom(), CDiagRangeCollection::TrimSecondTo(), CSparseAln::x_Build(), CAlnMixMerger::x_Merge(), and CRuler::x_RenderAllPosLabels().
◆ GetLength() [2/2]template<class Position >
Definition at line 158 of file range.hpp.
Referenced by CMultAlign::AddAlignment(), CSAM_CIGAR_Formatter::AddRow(), AlignModelToSeqalign(), CAlnGraphic::AlnGraphicDisplay(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CBlobSplitterImpl::AttachToSkeleton(), BlastKmerGetKmerSet(), BlastKmerGetKmerSet2(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CColumnLayout::BuildLayout(), CEquivRangeBuilder::CalcMatches(), CTestSeqBasedMethod::CalculateScores(), CChain::CalculateSupportAndWeightFromMembers(), CAlignModel::CAlignModel(), CAnnotObject_Ref::CAnnotObject_Ref(), CChainer::CChainerImpl::CDNACounts(), CGeneModel::CdsInvariant(), CLocMapper_Default::CGappedRange::CGappedRange(), check_no_overlaps(), CChainer::CChainerImpl::CheckCompatibility(), CAlignCollapser::CleanSelfTranscript(), CGraphStatCollector_Graph::ClearRange(), CChain::ClipChain(), CChain::ClipLowCoverageUTR(), IAlnMultiDataSource::CollectAlignStats(), CChain::CollectTrustedmRNAsProts(), CombineCorrectionsAndIndels(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertSeqLocsToPairwiseAln(), ConvertStdsegToPairwiseAln(), CSeq_loc_Conversion::CSeq_loc_Conversion(), EffectiveExonLength(), NSnpAnnot::EstimateSNPCount(), CMacroEngineParallel::Exec(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CFeatTableDS::SFeatureRow::FillIn(), CAlignCollapser::FilterAlignments(), FindPolyTail(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CSeqGraphicWidget::FindText(), CSeqGraphicPane::FindText(), CGBSeqFormatter::FormatFeature(), CAlignMap::FShiftedLen(), CSparseAlignment::GetAlnSeqString(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CGeneModel::GetCdsDnaSequence(), CBamRawAlignIterator::GetCIGARRefSize(), CBamRawAlignIterator::GetCIGARShortSize(), CSeq_loc::GetCircularLength(), CAlignCollapser::GetCollapsedAlgnments(), CVcfHeatmap::GetData(), CWigGraph::GetDataCoverage(), CSeq_loc_Conversion::GetDstPoint(), CBedCoverageGraph::GetEstimatedFeatureCount(), CShowBlastDefline::GetFormattingInfo(), NSnpAnnot::GetGraph_CI(), CSGAlignmentDS::GetGraphCost(), CAlnStatGlyph::GetHTMLActiveAreas(), CHistogramGlyph::GetHTMLActiveAreas(), CLocMapper_Default::CGappedRange::GetIdentity(), CGuiObjectInfoSeq_align::GetInsertionRanges(), CTableDataFTable::GetIntValue(), CSeq_featHandler::GetLabel(), NSnp::GetLength(), CCddInputData::CHitSegment::GetLength(), CSparseGraph::GetMissingRegions(), CPileUpGraph::GetNumberOfReads(), CPagedFile::GetPage(), GetProteinName(), GetProteinWeight(), CDenseSegHitElement::GetQueryLength(), CStdSegHitElement::GetQueryLength(), CCSraShortReadIterator::GetShortLen(), CSNPDbFeatIterator::GetSNPLength(), CDenseSegHitElement::GetSubjectLength(), CStdSegHitElement::GetSubjectLength(), GetUnalignedRegionLength(), CMultAlign::GetVariationAlignList(), CGeneModel::HasCompatibleOverlap(), CCrossPanelIR::HitTest(), CSparseAlignment::Init(), SChunkTranslator::Init(), CAlnGraphic::Init(), CBlastFormatUtil::InsertSubjectScores(), CSeq_align::IntronLengthRange(), CGeneModel::isCompatible(), CSGAlignmentDS::IsGraphCached(), CSeq_loc_CI::IsPoint(), CSeqGlyph::LessBySeqSize(), CmRNACDSLinker::LinkByLabelAndLocation(), CChainer::CChainerImpl::LRCanChainItoJ(), CChain::MainPeaks(), CBlobSplitterImpl::MakeID2Chunk(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CEquivRangeBuilder::Merge(), ProteinWithBigHole::model_predicate(), CGeneModel::MutualExtension(), CSeqGraphicWidget::OnGoToMarker(), CwxExportVectorImageDlg::OnSaveClick(), CAlignSort::SAlignExtractor::operator()(), operator<<(), PatchTargetSequence(), CChain::PeaksAndLimits(), CGnomonAnnotator::Predict(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_AlignLengthRatio::Print(), CGFFReader::Read(), readGFF3(), CDense_seg::RemapToLoc(), CLinearSelHandler::Render(), RestoreModelReadingFrame(), CChain::RestoreReasonableConfirmedStart(), RetrievePartsOfLargeChromosome(), CChainer::CChainerImpl::RightLeft(), s_CreateObjList(), s_FindGaps(), s_GetQuerySequence(), NSearchFeatPanel::s_GetSeq_TotalRangeLabel(), s_GetSeq_TotalRangeLabel(), s_GetUncoveredLength(), s_PassesFilter(), s_Render_SeqFeat(), variation::CVariationUtil::s_ResolveIntronicOffsets(), CExpansionScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CGnomonEngine::SelectBestReadingFrame(), SeqLocAllowed(), CReportEntry::SetCds(), CBlastTabularInfo::SetFields(), SSeqMapSelector::SetRange(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CBlobSplitterImpl::SplitPieces(), sx_CalcFeatChunkPages(), CLocMapper_Default::CGappedRange::ToString(), CutShortPartialExons::transform_align(), CGeneModel::TrimEdgesToFrameInOtherAlignGaps(), CSparseGraph::Update(), CPileUpGraph::UpdateAlignStats(), CEditScript::VerifyScript(), CGuiObjectInfoSeq_feat::x_AddGroupLocationRows(), CGuiObjectInfoSeq_feat::x_AddLocationRows(), CMultiAligner::x_AlignProfileProfileUsingHit(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), CMultiAligner::x_BuildAlignmentIterative(), CPhyTreeCalc::x_CalcAlnSegInfo(), CScoringJob::x_CalculateAlignmentScores(), CCDSTranslationProblems::x_CheckForRaggedEnd(), CVisibleRange::x_Clamp(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CAlnSpanVertModel::x_ConvertRowsToSpans(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CInversionMergeAligner::x_CreateDiscAlignment(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGAlignStatJob::x_CreatePileUpGraphs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CWigGraph::x_DecodeDelta(), CDisplaySeqalign::x_DoFills(), CComponentSearchJob::x_DoSearch(), CCpgSearchJob::x_DoSearch(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CHistogramGlyph::x_Draw(), CMatePairGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CLinkedFeatsGroup::x_DrawChildrenOnParent(), CCrossPanelIR::x_DrawCrossAlignment(), CFeatGlyph::x_DrawFeatureBar(), CLinkedFeatsGroup::x_DrawFeatureBar(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeqGlyph::x_DrawInnerLabelColumns(), CSeqGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithXPinned(), CVcfGlyph::x_DrawLabelWithXPinned(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CAlignGlyph::x_DrawPWAlign(), CCrossPanelIR::x_DrawSequence(), CVcfGlyph::x_DrawVariationBar(), CSGAlignStatJob::x_Execute(), CSGFeatureJob::x_Execute(), CSGSegmentMapJob::x_Execute(), CSFTranslationJob::x_Execute(), CVcfFeatureJob::x_Execute(), CSnpJob::x_FetchGraphs(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CDisplaySeqalign::x_FillInserts(), CMultiAligner::x_FindConservedColumns(), CMultiAligner::x_FindConstraints(), COligoSpecificityCheck::x_FindOverlappingHSP(), CCIGAR_Formatter::x_FormatLine(), CSGAlignmentJob::x_GetAlignments(), CAlnVecRow::x_GetAlignmentTooltip_Gap(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CWigGraph::x_GetBigWigData(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CCSraShortReadIterator::x_GetQualityGraph(), CSeq_loc_Mapper_Base::x_GetRangeLength(), CCSraShortReadIterator::x_GetReadData(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps(), CDistances::x_GetSelfScores(), CSequenceSearchJob::x_GetSequence(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CAlignedFeatureGraph::x_GetTooltip(), CAlnVecRow::x_GetTooltipSequence(), CGuiObjectInfoSeq_align::x_GetTooltipSequence(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CShowBlastDefline::x_InitDeflineTable(), CSeq_loc_Mapper::x_InitGCSequence(), CSparse_CI::x_InitSegment(), COligoSpecificityCheck::x_IsPcrLengthInRange(), CAlignmentTrack::x_LoadAlignedSeqFeats(), CBatchFeatJob::x_LoadFeatProducts(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), CVDBGraphSeqIterator::x_MakeTable(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), x_MatchSubHits(), variation_ref::CHgvsParser::x_nuc_inv(), CAlignedFeatureGraph::x_PlaceCluster(), CAlnSpanVertModel::x_PopulateRows(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CMultiAligner::x_RealignBlocks(), CSeqGraphicPane::x_RenderTooltipConnector(), CFastaRetrieveLocJob::x_Run(), CInversionMergeAligner::x_RunMerger(), CMagicBlastResults::x_SetInfo(), CUnorderedSplitter::x_SplitDeltaExt(), CBinsGlyph::x_UpdateBoundingBox(), CGeneMarkerGlyph::x_UpdateBoundingBox(), CScatterPlotGlyph::x_UpdateBoundingBox(), CLDBlockGlyph::x_UpdateBoundingBox(), CAlnStatGlyph::x_UpdateBoundingBox(), CAlignGlyph::x_UpdateBoundingBox(), CAlignSmearGlyph::x_UpdateBoundingBox(), CClonePlacementGlyph::x_UpdateBoundingBox(), CFeatGlyph::x_UpdateBoundingBox(), CHistogramGlyph::x_UpdateBoundingBox(), CLayoutTrack::x_UpdateBoundingBox(), CMatePairGlyph::x_UpdateBoundingBox(), CNamedGroup::x_UpdateBoundingBox(), CRsitesGlyph::x_UpdateBoundingBox(), CSegmentGlyph::x_UpdateBoundingBox(), CTraceGlyph::x_UpdateBoundingBox(), CVcfGlyph::x_UpdateBoundingBox(), CAlignmentTrack::x_UpdateData(), CSixFramesTransTrack::x_UpdateData(), CGraphOverlay::x_UpdateLegend(), CHistogramGlyph::x_UpdateLegend(), CValidError_align::x_ValidateAlignPercentIdentity(), CSplitQueryTestFixture::x_ValidateChunkBounds(), CGff3Writer::xAssignAlignmentDensegGap(), and CSeqGraphicWidget::ZoomOnRange().
◆ GetLevelIter() ◆ GetLevelIterEnd() ◆ GetPositionMax() [1/2]template<class Position >
◆ GetPositionMax() [2/2]template<class Position >
◆ GetPositionMin() [1/2]template<class Position >
◆ GetPositionMin() [2/2]template<class Position >
Definition at line 246 of file range.hpp.
◆ GetRange() ◆ GetSecondFrom()template<class Position >
Definition at line 121 of file align_range.hpp.
References CAlignRange< Position >::m_SecondFrom.
Referenced by CDenseSegHit::CDenseSegHit(), CAlignRange< Position >::GetSecondRange(), CDiagHitElement::GetSubjectStart(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IntersectSecondWith(), CAlignRange< Position >::IsAbutting(), operator<<(), CAlignRange< Position >::operator==(), CRuler::Render(), s_GetSplicedSegIdentityMismatch(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimFirstTo(), CDiagRangeCollection::TrimSecondFrom(), CSparseAln::x_Build(), CDiagRangeCollection::x_DiffSecond(), CAlnMixMerger::x_Merge(), CRuler::x_RenderOriginAndMetric(), CRuler::x_UpdateMappingByPane(), and CMergedPairwiseAln::x_ValidNeighboursOnSecondDim().
◆ GetSecondPosByFirstPos()template<class Position >
◆ GetSecondRange()template<class Position >
◆ GetSecondTo()template<class Position >
◆ GetSecondToOpen()template<class Position >
◆ GetSelectIter() ◆ GetSelectIterEnd() ◆ GetTo()template<class Position >
◆ GetToOpen()template<class Position >
Definition at line 138 of file range.hpp.
Referenced by CDensityMap< CntType >::AddRange(), CSAM_CIGAR_Formatter::AddRow(), BOOST_AUTO_TEST_CASE(), CAlignCompare::SAlignment::BreakOnBoundaries(), CdsTrnaOverlapStr(), CFeatHistogramDS::CFeatHistogramDS(), CIdRangeMap::CIdRangeMap(), CreateAlignRow(), CSegmentGlyph::CSegmentGlyph(), CSparseIterator::CSparseIterator(), CAlignGlyph::DrawPWAlignElem(), DumpPairwiseAln(), SAnnotObject_Key::end(), CPrefetchSeqData::Execute(), SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), CCSraRefSeqIterator::GetAlnOverToOpen(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CVDBGraphSeqIterator::GetAnnot(), CSNPDbSeqIterator::GetEntry(), CFeatHistogramDS::GetLimit(), SBamIndexRefIndex::GetLimitRange(), CGuiObjectInfoSeq_align::GetLinks(), CSparseGraph::GetMissingRegions(), GetProteinName(), CMaskedRangeSet::GetRanges(), CCSraRefSeqIterator::GetRefLiterals(), CGuiObjectInfoSeq_align::GetSeqString(), CDensegGraphicDataSource::GetSeqString(), CSparseAln::GetSeqString(), CSeqDB::GetSequenceAsString(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CAnnotMapping_Info::GetToOpen(), CBlobSplitterImpl::IsWhole(), CBam2Seq_graph::MakeSeq_entry(), CHandleRange::MergeRange(), SSNP_Info::NoMore(), SSNP_Info::NotThis(), CLDBlockGlyph::OnLeftDblClick(), CPairwise_CI::operator bool(), SSortSourceByLoc::operator()(), operator<<(), PatchTargetSequence(), PrintSAM(), PrintTabular(), CAlignMarkHandler::Render(), CLinearSelHandler::Render(), TMaskedQueryRegions::RestrictToSeqInt(), s_CheckAbutting(), s_CompareRanges(), s_GetCigarString(), CBinaryRangeCacheWithLock< Position, Value >::s_Overlaps(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SetSplitQuerySeqInterval(), CVDBGraphSeqIterator::SeqTableIsSmaller(), CSplitQueryBlk::SetChunkBounds(), CBlobSplitterImpl::SetLoc(), CwxSeqMarkerSetDlg::SetMarkerRange(), SGraphMaker::Start(), CFeatHistogramDS::Update(), CPileUpGraph::UpdateAlignStats(), CSGAnnotJob::x_AddGraphToMap(), CInlineLayout::x_BuildLayout1Row(), CDensityMap< score_type >::x_CalcNbins(), CAdvancedAlignCleanup::x_CleanupProsplignAsGenomic(), CSGAlignStatJob::x_CollectAlignStats(), x_CollectCoverageGraph(), CAnnot_Collector::x_CollectMapped(), CAnnot_Collector::x_CollectSegments(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CAlignGlyph::x_ConvertAlnTaillRngToSeqRng(), CSGAlignStatJob::x_CreatePileUpGraphs(), CLDBlockGlyph::x_Draw(), CFeatGlyph::x_DrawAdditionalInfo(), CVcfGlyph::x_DrawAdditionalInfo(), CFeatGlyph::x_DrawFeatureBar(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithYPinned(), CVcfGlyph::x_DrawLabelWithYPinned(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawUnalignedBar(), CGuiObjectInfoSeq_align::x_GetAlignmentTooltip_Insert(), CDensegGraphicDataSource::x_GetAlnStringFromCigar(), CAnnotObject_Less::x_GetExtremes(), CAlignMarkHandler::x_HitTest(), CAlignMarkHandler::x_InitDeltaMap(), CBlastHitMatrix::x_InitPort(), CDenseg_CI::x_InitSegment(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CID2SNPProcessor_Impl::x_LoadBlob(), CVDBGraphSeqIterator::x_MakeGraph(), CVDBGraphSeqIterator::x_MakeTable(), CBamRawAlignIterator::x_NeedToSkip(), CSNPDbGraphIterator::x_Next(), CWGSSeqIterator::x_NormalizeSeqRange(), CLinearSelHandler::x_OnChangeSelRange(), CTextSelHandler::x_OnChangeSelRange(), CAlnSpanVertModel::x_PopulateRows(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CRuler::x_RenderAllPosLabels(), CAlignGlyph::x_RenderAveragableScores(), CRuler::x_RenderBackground(), CAlnVecRow::x_RenderInserts(), CAlignGlyph::x_RenderNonAveragableScores(), CRuler::x_RenderOriginAndMetric(), x_RoundRange(), CWigGraph::x_RunBigWigScript(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchSegments(), CVDBGraphSeqIterator::x_SeqTableIsSmaller(), CHitMatrixWidget::x_SetPortLimits(), CSeqGraphicRenderer::x_SetupModelLimits(), CAlignMarkHandler::x_UpdateMarks(), CSeq_loc::x_UpdateTotalRange(), CSeq_annot_SortedIter::x_Valid(), CSplitQueryTestFixture::x_ValidateChunkBounds(), CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk(), CHitMatrixWidget::x_ZoomToHits(), and CSeqGraphicWidget::ZoomOnRange().
◆ GetWhole()template<class Position >
◆ GetWholeFrom()template<class Position >
◆ GetWholeLength()template<class Position >
Definition at line 268 of file range.hpp.
◆ GetWholeTo()template<class Position >
◆ GetWholeToOpen()template<class Position >
Definition at line 260 of file range.hpp.
◆ insert() [1/2]template<typename Mapped , typename Position = int>
◆ insert() [2/2]template<typename Mapped , typename Position = int>
Definition at line 629 of file rangemap.hpp.
References map_checker< Container >::end(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::insertLevel(), CRangeMapIterator< Traits >::m_LevelIter, CRangeMapIterator< Traits >::m_Range, CRangeMapIterator< Traits >::m_SelectIter, CRangeMapIterator< Traits >::m_SelectIterEnd, CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::m_SelectMap, NCBI_THROW, and rapidjson::value.
Referenced by CSeq_loc_Conversion_Set::x_Add(), CPhrap_Contig::x_AddAlignRanges(), and CTSE_Info::x_MapAnnotObject().
◆ insertLevel() ◆ IntersectingWith() [1/2]template<class Position >
◆ IntersectingWith() [2/2]template<class Position >
Definition at line 331 of file range.hpp.
Referenced by CFeatureGenerator::SImplementation::AdjustAlignment(), BuildAlignDataSource(), CEquivRange::CalcRelativeDuo(), CChain::CalculateSupportAndWeightFromMembers(), CChain::CChain(), CChainer::CChainerImpl::CheckCompatibility(), CChainer::CChainerImpl::CombineCompatibleChains(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CCDSInfo::Cut(), NSnpAnnot::EstimateSNPCount(), CChainer::CChainerImpl::FilterOutChimeras(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CChainer::CChainerImpl::FindOverlappingWithTrusted(), CGetFeature::GetFeatInfo(), CChain::HarborsNested(), CGene::HarborsRange(), CSeqScores::Init(), CEquivRange::IntersectingWith(), CGeneModel::IntersectingWith(), CHandleRange::IntersectingWith(), CHandleRange::IntersectingWithTotalRange(), C2DLayoutEngine::Layout(), CChainer::CChainerImpl::MakeChains(), CAlignFilter::Match(), CDepthCollection::MinDepthForRange(), CSeqGraphicPane::OnSearchTip(), CGnomonAnnotator::Predict(), CTestSingleAln_All::RunTest(), s_Distance(), s_GetUncoveredLength(), s_IsOverlapping(), s_MergeRangeList(), s_SeqIntervalToSeqLocInfo(), s_SetSplitQuerySeqInterval(), CReportEntry::SetCds(), CChain::SetConfirmedStartStopForCompleteProteins(), CEquivRangeBuilder::SplitIntersections(), CBlobSplitterImpl::SplitPieces(), CMultiAligner::x_AssignRPSResFreqs(), CVecscreen::x_BuildNonOverlappingRange(), CSeqGraphicPane::x_ChangeSwitchPoint(), CFeatureGenerator::SImplementation::x_CheckMatch(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CQuerySet::x_ContainsAlignment(), CSGAlignmentJob::x_CreateCAlignGlyph(), CInversionMergeAligner::x_CreateDiscAlignment(), CDisplaySeqalign::x_DisplayRowDataSet(), CCrossPanelIR::x_DrawCrossAlignment(), CFeatGlyph::x_DrawFeatureBar(), CTranslationGlyph::x_Intersecting(), CLayeredLayout::x_LayerBySize(), CVecscreen::x_MergeInclusiveSeqalign(), CVecscreen::x_MergeLowerRankSeqalign(), CAllOtherFeaturesTrack::x_OnAllJobsFinished(), CTrackContainer::x_OnJobCompleted(), CDisplaySeqalign::x_PrintFeatures(), CDisplaySeqalign::x_ProcessRowDataSet(), CInversionMergeAligner::x_RunMerger(), and COligoSpecificityCheck::x_SavePrimerInfo().
◆ IntersectionWith() [1/2]template<class Position >
◆ IntersectionWith() [2/2]template<class Position >
Definition at line 312 of file range.hpp.
Referenced by CDepthCollection::AddRange(), CFeatTrim::Apply(), CEquivRange::Distance(), CHandleRange::GetOverlappingRange(), GetTrnaAnticodon(), CRenderingContext::IntersectVisible(), CRenderingContext::IntersectVisible_Y(), CCddInputData::CHit::IntersectWith(), CTrackContainer::NoSubtrackEver(), SOutsideRange::operator()(), CTrackContainer::RemoveEmptyTracks(), TMaskedQueryRegions::RestrictToSeqInt(), s_AlignDist(), CClippedScorer::ScoreAlignments(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), x_AdjustRange(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), CQuerySet::x_ContainsAlignment(), CSeqGlyph::x_DrawInnerLabelColumns(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawMultiAlign(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CRangeCollection< TSeqPos >::x_IntersectWith(), CRangeSet< CPairwiseAln::TPos >::x_IntersectWith(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_MatchSubHits(), CTrackContainer::x_ReinitTrack(), CSeqGraphicPane::x_RenderTooltipConnector(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CUnorderedSplitter::x_TrimRows(), CSixFramesTransTrack::x_UpdateData(), CVcfWriter::x_WriteData(), CGff2Writer::xAssignFeatureAttributePartial(), CGff3Writer::xWriteNucleotideFeature(), and CGff3Writer::xWriteProteinFeature().
◆ IntersectSecondWith()template<class Position >
◆ IntersectWith() [1/2]template<class Position >
◆ IntersectWith() [2/2]template<class Position >
◆ IsAbutting()template<class Position >
Definition at line 287 of file align_range.hpp.
References CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstToOpen(), CAlignRange< Position >::GetLength(), CAlignRange< Position >::GetSecondFrom(), CAlignRange< Position >::GetSecondToOpen(), CAlignRange< Position >::IsDirect(), r(), and swap().
Referenced by CAlignRange< Position >::CombineWithAbutting(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges().
◆ IsDirect()template<class Position >
Definition at line 96 of file align_range.hpp.
References CAlignRange< Position >::fReversed, and CAlignRange< Position >::m_Flags.
Referenced by CheckPairwiseAln(), CAlignRange< Position >::CombineWithAbutting(), DumpPairwiseAln(), CDiagHitElement::GetSubjectStrand(), CAlignRange< Position >::IsAbutting(), operator<<(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwiseToAlnCoords(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimSecondFrom(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), CSparseAln::x_Build(), and CRuler::x_RenderOriginAndMetric().
◆ IsFirstDirect()template<class Position >
◆ IsFirstReversed()template<class Position >
◆ IsNegative() [1/2]template<class Position >
Definition at line 67 of file range.hpp.
◆ IsNegative() [2/2]template<class Position >
Definition at line 78 of file range.hpp.
◆ IsReversed()template<class Position >
◆ IsWhole()template<class Position >
Definition at line 284 of file range.hpp.
Referenced by CGraphRanges::AddRange(), CVisibleRange::Clamp(), CComponentTrackFactory::CreateTracks(), CScaffoldTrackFactory::CreateTracks(), CSegmentMapTrackFactory::CreateTracks(), CSourceFeatureItem::CSourceFeatureItem(), CGBSeqFormatter::FormatFeature(), CGBSeqFormatter::FormatReference(), CFlatFileGenerator::Generate(), CSparseAln::GetAlnSeqString(), CAlnWriter::GetSeqString(), CSparseAln::GetSeqString(), CSeq_loc_I::InsertInterval(), CSeq_loc_CI::IsWhole(), CResolveRequest::Process(), s_GetQuerySequence(), s_GetUncoveredLength(), CValidError_bioseq::ValidateSeqFeatContext(), CVisibleRange::x_Clamp(), CFtableFormatter::x_FormatLocation(), CFlatItemFormatter::x_FormatRefLocation(), CPairwise_CI::x_Init(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CDenseg_CI::x_InitIterator(), CPairwise_CI::x_InitSegment(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSeq_loc_Mapper_Base::x_PushSourceRange(), CGff2Writer::xAssignFeatureAttributeCodeBreak(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff3Writer::xAssignSourceEndpoints(), CGff3Writer::xWriteFeatureCds(), and CGff3Writer::xWriteSequenceHeader().
◆ IsWholeFrom()template<class Position >
Definition at line 276 of file range.hpp.
◆ IsWholeTo()template<class Position >
Definition at line 280 of file range.hpp.
◆ NotEmpty() [1/2]template<class Position >
◆ NotEmpty() [2/2]template<class Position >
Definition at line 152 of file range.hpp.
Referenced by CChain::AddAllMembersAndCoverage(), CDepthCollection::AddRange(), AlignModelToSeqalign(), CFeatTrim::Apply(), Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), CChain::CalculateSupportAndWeightFromMembers(), CChain::CChain(), CAlignCollapser::CleanSelfTranscript(), CGeneModel::Clip(), CChain::ClipChain(), CChain::ClipToCap(), CChain::ClipToPolyA(), CollectAttributes(), CVCFVariantsBase::Count(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CVCFVariant_CI::CVCFVariant_CI(), CGeneModel::Extend(), CBlastDBExtractor::ExtractFasta(), CChainer::CChainerImpl::FilterOutChimeras(), CChainer::CChainerImpl::FindContainedAlignments(), CChainer::CChainerImpl::FindGeneSeeds(), CChainer::CChainerImpl::FindOverlappingWithTrusted(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), FindStartsStops(), CSeqGraphicWidget::FindText(), CSeqGraphicPane::FindText(), CDensegGraphicDataSource::GetAlnSeqString(), CParse::GetGenes(), CGeneModel::GetInDels(), CGnomonEngine::GetScore(), CSeqDB::GetSequenceAsString(), GetWallLimits(), CCDSInfo::HasStart(), CCDSInfo::HasStop(), CSeqScores::Init(), CAlignCollapser::InitContig(), CBlastFormatUtil::InsertSubjectScores(), CCDSInfo::MapFromEditedToOrig(), CCDSInfo::MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CEquivRange::NotEmpty(), CAlnMultiWidget::OnUpdateZoomSelection(), CGeneModel::OpenLeftEnd(), CGeneModel::OpenRightEnd(), ParseAttributes(), CChain::PeaksAndLimits(), CGnomonAnnotator::Predict(), printGFF3(), readGFF3(), CCDSInfo::Remap(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), RestoreModelAttributes(), CChain::RestoreReasonableConfirmedStart(), TMaskedQueryRegions::RestrictToSeqInt(), s_ConvertBlastnMasks(), s_GetQuerySequence(), CChain::SetBestPlacement(), CChain::SetConsistentCoverage(), CBlastTabularInfo::SetFields(), CChainer::CChainerImpl::SetFlagsForChains(), CCDSInfo::SetStop(), CAlignMap::ShrinkToRealPoints(), CAlignMap::ShrinkToRealPointsOnEdited(), spliced_exon(), CSeq_align::SplitOnLongDiscontinuity(), CutShortPartialExons::transform_align(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CGeneModel::TrimEdgesToFrameInOtherAlignGaps(), TrimAlignment::TrimProtein(), TrimAlignment::TrimTranscript(), CMultAlign::Variations(), CMultiAligner::x_AlignProfileProfileUsingHit(), CDenseg_CI::x_CheckSegment(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CLinkedFeatsGroup::x_DrawFeatureBar(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAlignMarkHandler::x_HitRangeBorder(), CAlignMarkHandler::x_InitDeltaMap(), CRangeCollection< TSeqPos >::x_IntersectWith(), CRangeSet< CPairwiseAln::TPos >::x_IntersectWith(), CGBDataLoader_Native::x_MakeContentMask(), CLinearSelHandler::x_OnSelectCursor(), CTextSelHandler::x_OnSelectCursor(), CLinearSelHandler::x_OnStartSel(), CTextSelHandler::x_OnStartSel(), CTraceGraph::x_RenderContour(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CUnorderedSplitter::x_TrimRows(), CVcfWriter::x_WriteData(), CGff2Writer::xAssignFeatureAttributePartial(), and CAlnMultiWidget::ZoomToSelection().
◆ operator!=() [1/3] ◆ operator!=() [2/3]template<class Position >
◆ operator!=() [3/3]template<class Position >
Definition at line 219 of file range.hpp.
◆ operator&()template<class Position >
Definition at line 323 of file range.hpp.
◆ operator&=()template<class Position >
Definition at line 327 of file range.hpp.
◆ operator()() [1/9]template<class TAlignRange >
◆ operator()() [2/9]template<class TAlignRange >
◆ operator()() [3/9]template<class TAlignRange >
◆ operator()() [4/9] ◆ operator()() [5/9]template<class TAlignRange >
◆ operator()() [6/9]template<class TAlignRange >
◆ operator()() [7/9]template<class TAlignRange >
◆ operator()() [8/9]template<class TAlignRange >
◆ operator()() [9/9]template<class TAlignRange >
◆ operator*() ◆ operator+()template<class Position >
Definition at line 375 of file range.hpp.
◆ operator++() ◆ operator+=()template<class Position >
Definition at line 371 of file range.hpp.
◆ operator->() ◆ operator<()template<class Position >
Definition at line 223 of file range.hpp.
◆ operator<<()template<class Position >
Definition at line 426 of file range.hpp.
◆ operator<=()template<class Position >
Definition at line 228 of file range.hpp.
◆ operator=()template<class Position >
Definition at line 408 of file range.hpp.
◆ operator==() [1/3] ◆ operator==() [2/3]template<class Position >
◆ operator==() [3/3]template<class Position >
Definition at line 215 of file range.hpp.
◆ operator>()template<class Position >
Definition at line 233 of file range.hpp.
◆ operator>=()template<class Position >
Definition at line 238 of file range.hpp.
◆ operator[]()template<typename Mapped , typename Position = int>
◆ SecondContains()template<class Position >
◆ Set() [1/2]template<class Position >
◆ Set() [2/2]template<class Position >
Definition at line 188 of file range.hpp.
Referenced by CAlnGraphic::AlnGraphicDisplay(), CSparseAlignment::Clear(), CAlnVecPrinter::ClustalStyle(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CComponentTrackFactory::CreateTracks(), CScaffoldTrackFactory::CreateTracks(), CSegmentMapTrackFactory::CreateTracks(), FindPolyTail(), CScore_EdgeExonInfo::Get(), CRsitesGlyph::GetHTMLActiveAreas(), CLegendItemGlyph::GetHTMLActiveAreas(), CAlignFormatUtil::GetMasterCoverage(), CSeqTableReader::GetRange(), CAlnVecRow::GetRowStatistics(), CAdvancedAlignCleanup::GetSplignCompartments(), CSparseSegment::Init(), CAlnGraphic::Init(), CSeqGraphicWidget::OnSetSeqMarkerForSelDlg(), CAlnVecPrinter::PopsetStyle(), CRenderingContext::PrepareContext(), CPhrap_Read::ReadQuality(), s_FixMinusStrandRange(), s_GetCountIdentityMismatch(), s_ProcessAlignSet(), CSeqTextWidget::ScrollToText(), CwxExportVectorImageDlg::SetSeqRange(), TSeqLocVector2Packed_seqint(), CSixFramesTransTrack::Update(), CAlnVwrApp::View8(), CVecscreen::x_BuildNonOverlappingRange(), CHitMatrixDataSource::x_CalculateHitsRange(), CSeq_loc::x_CalculateTotalRangeCheckId(), CAnnot_Collector::x_CollectMapped(), CSGAlignStatJob::x_CreatePileUpGraphs(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CAlignGlyph::x_DrawMultiAlign(), CVecscreen::x_GetAlnInfo(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CDistances::x_GetSelfScores(), CAlnVecRow::x_GetTooltipSequence(), CGuiObjectInfoSeq_align::x_GetTooltipSequence(), CGraphOverlay::x_LoadSettings(), CGraphTrack::x_LoadSettings(), CSeq_loc_Mapper_Base::x_MapNextRange(), CVecscreen::x_MergeLowerRankSeqalign(), CSixFramesTransTrack::x_OnContentIconClicked(), CSixFramesTransTrack::x_OnGeneticIconClicked(), CSixFramesTransTrack::x_OnSettingIconClicked(), CDisplaySeqalign::x_OutputSeq(), CColumnarVCFReaderApp::x_ParseRange(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CMultiAligner::x_RealignBlocks(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchRange(), CSixFramesTransTrack::x_UpdateData(), and x_UpdateRanges().
◆ SetBegin() [1/2] ◆ SetBegin() [2/2] ◆ SetDirect()template<class Position >
◆ SetEnd() ◆ SetFirstDirect()template<class Position >
◆ SetFirstFrom()template<class Position >
◆ SetFirstReversed()template<class Position >
◆ SetFrom()template<class Position >
Definition at line 170 of file range.hpp.
Referenced by SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), SBamAlignInfo::get_cigar_alignment(), SBamIndexRefIndex::GetAlnOverStarts(), CVDBGraphSeqIterator::GetAnnot(), CBamAlignIterator::GetCIGARAlignment(), CWGSSeqIterator::x_AddGap(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CWGSSeqIterator::x_CreateDataChunk(), CSNPDbFeatIterator::x_Excluded(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().
◆ SetLength() [1/2]template<class Position >
◆ SetLength() [2/2]template<class Position >
Definition at line 194 of file range.hpp.
Referenced by CSeq_loc_Conversion::ConvertInterval(), CreateAlignRow(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), SBamAlignInfo::get_cigar_alignment(), SBamIndexRefIndex::GetAlnOverStarts(), CWGSFeatureIterator::GetLocRange(), CCSRARefSeqInfo::LoadRefSeqChunk(), s_AlignToSeqRanges(), s_FindGaps(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CWGSSeqIterator::x_AddGap(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CQuerySet::x_ContainsAlignment(), CWGSSeqIterator::x_CreateDataChunk(), CInversionMergeAligner::x_CreateDiscAlignment(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps(), CLinearSelHandler::x_HitTest(), CAlignMarkHandler::x_HitTest(), CTextSelHandler::x_HitTest(), CAlignMarkHandler::x_InitDeltaMap(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSplign::x_MaskSequence(), CLinearSelHandler::x_OnEndSelRange(), CTextSelHandler::x_OnEndSelRange(), and CUnorderedSplitter::x_SplitDeltaExt().
◆ SetLengthDown()template<class Position >
◆ SetLevelIter() ◆ SetOpen()template<class Position >
Definition at line 184 of file range.hpp.
Referenced by CSparseAln::GetAlnSeqString(), CLDS2_Database::GetAnnots(), CSplitQueryBlk::GetChunkBounds(), s_SeqLocToTotalRangeInfoMap(), CAnnot_Collector::x_CollectMapped(), CDenseg_CI::x_InitSegment(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CAnnot_Collector::x_SearchMapped().
◆ SetReversed()template<class Position >
◆ SetSecondFrom()template<class Position >
◆ SetTo()template<class Position >
Definition at line 180 of file range.hpp.
◆ SetToOpen()template<class Position >
Definition at line 175 of file range.hpp.
Referenced by CBamRawAlignIterator::CBamRawAlignIterator(), CreateAlignRow(), DumpPairwiseAln(), SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), CVDBGraphSeqIterator::GetAnnot(), CSNPDbSeqIterator::GetChunkForVersion(), CBamRefSeqInfo::GetChunkGraphRange(), CSNPDbSeqIterator::GetEntry(), SBamIndexRefIndex::GetLimitRange(), GetProteinName(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadRanges(), CAlnWriter::ProcessSeqId(), SAnnotObject_Key::Reset(), TMaskedQueryRegions::RestrictToSeqInt(), s_ExtractSeqidsAndRanges(), s_SeqLocToTotalRangesInfoMapByStrand(), SCompartmentData::SCompartmentData(), CVDBGraphSeqIterator::SeqTableIsSmaller(), CBlobSplitterImpl::SetLoc(), SAnnotObject_Key::SetMultiple(), CSGFeatureJob::x_CalcIntervals(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CSNPDbFeatIterator::x_Excluded(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CID2SNPProcessor_Impl::x_LoadChunk(), CBamRefSeqInfo::x_LoadRangesCov(), CBamRefSeqInfo::x_LoadRangesStat(), CWGSSeqIterator::x_NormalizeSeqRange(), CLinearSelHandler::x_OnChangeSelRange(), CTextSelHandler::x_OnChangeSelRange(), CLinearSelHandler::x_OnStartSel(), CTextSelHandler::x_OnStartSel(), CBlastOptionsBuilder::x_ProcessOneOption(), and x_RoundRange().
◆ size() ◆ swap() ◆ Valid() ◆ m_FirstFromtemplate<class Position >
◆ m_Flagstemplate<class Position >
◆ m_Fromtemplate<class Position >
Definition at line 381 of file range.hpp.
◆ m_Lengthtemplate<class Position >
◆ m_LevelIter ◆ m_Range ◆ m_SecondFromtemplate<class Position >
◆ m_SelectIter ◆ m_SelectIterEnd ◆ m_SelectMapDefinition at line 535 of file rangemap.hpp.
Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::begin(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::clear(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::CRangeMapBase(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::empty(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::end(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::find(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::insertLevel(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::size(), and CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::swap().
◆ m_ToOpentemplate<class Position >
Definition at line 381 of file range.hpp.
◆ CRangeMap< mapped_type, position_type > ◆ CRangeMapBase< typename TTraits::TMapTraits > ◆ CRangeMultimap< mapped_type, position_type >RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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