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GUI Object Utility Classes and Modules

Utility and support routines for the GUI framework. More...

Utility and support routines for the GUI framework.

These routines make use of the object manager and associated tools.

Definition at line 119 of file utils.hpp.

Definition at line 51 of file nonasn_track_data.hpp.

get all GIs for a given NA accession

Definition at line 176 of file na_utils.hpp.

flags controlling feature retrieval

Definition at line 145 of file utils.hpp.

flags controlling use of annotation selectors

Definition at line 152 of file utils.hpp.

Definition at line 61 of file alignment_smear.hpp.

flags for classifying annotation names.

unnamed annotation

all named annotations

all annotations

any given named annots

Definition at line 131 of file utils.hpp.

flags controlling BLAST track default visibility

Definition at line 484 of file utils.hpp.

eutils databases that can be used

try both nucleotide and protein databases, merge results

Definition at line 126 of file na_utils.hpp.

Definition at line 88 of file annot_info.hpp.

source of obtained NA metadata were internal caches hit, partially hit or totally missed during some cached operations

Definition at line 134 of file na_utils.hpp.

Definition at line 143 of file na_utils.hpp.

Add this one alignment to my smear.

Definition at line 338 of file alignment_smear.cpp.

References CDensityMap< CntType >::AddRange(), CSparseAln::CreateSegmentIterator(), IAlnSegmentIterator::eSkipGaps, CSparseAln::GetAlnRange(), IAlnSegment::GetAlnRange(), CSparseAln::GetAnchor(), CRange_Base::GetFrom(), CSparseAln::GetNumRows(), CRange_Base::GetTo(), CAlignmentSmear::m_AccumGap, CAlignmentSmear::m_AccumSeg, and row.

Add this one alignment to my smear.

Definition at line 96 of file utils.hpp.

Definition at line 78 of file alignment_glyph.cpp.

References eNa_strand_minus, eNa_strand_plus, IScoringAlignment::GetAnchor(), IScoringAlignment::GetBaseWidth(), IAlnGraphicDataSource::GetSeqId(), IAlnGraphicDataSource::GetSeqStart(), IAlnGraphicDataSource::GetSeqStop(), IAlnGraphicDataSource::IsNegativeStrand(), CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Location, CRef< C, Locker >::Reset(), and CAlignGlyph::x_IsPWAlign().

check that a given seq-id can potentially have placements (to weed out cases like local ids)

Definition at line 1089 of file utils.cpp.

References CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gi, CSeq_id::eAcc_refseq_contig, CSeq_id::eAcc_refseq_genome, CSeq_id::eAcc_refseq_genomic, CSeq_id::eAcc_refseq_mrna, CSeq_id::eAcc_refseq_mrna_predicted, CSeq_id::eAcc_refseq_ncrna, CSeq_id::eAcc_refseq_ncrna_predicted, CSeq_id::eAcc_refseq_prot, CSeq_id::eAcc_refseq_prot_predicted, CSeq_id::eAcc_refseq_unreserved, CSeq_id::eAcc_refseq_wgs_intermed, CSeq_id::eAcc_refseq_wgs_nuc, CSeq_id::eAcc_refseq_wgs_prot, CSeq_id::eAcc_type_mask, and info.

Referenced by CSeqUtils::GetAccessionPlacementsMsec().

Definition at line 121 of file annot_info.hpp.

Definition at line 41 of file feat_label.cpp.

Definition at line 81 of file utils.hpp.

Ctor with target sequence id.

Only the named annotations associated with the target sequence will be returned. However, the target sequence is ignored if the requested NAAs are explicitly listed.

Definition at line 556 of file utils.cpp.

References CPacked_seqint::AddInterval(), CPacked_seqint_Base::Get(), ITERATE, CPacked_seqint_Base::Set(), CSeq_loc::SetInt(), and CSeq_loc::SetPacked_int().

Referenced by CViewGraphic::GetSearchLoc(), CCrossAlignView::GetSelection(), CDotMatrixView::GetSelection(), CMultiAlignView::GetSelection(), CSeqTextView::GetSelection(), and CViewGraphic::GetSelection().

help methods for creating HTML text

Definition at line 979 of file utils.cpp.

Definition at line 967 of file alignment_glyph.cpp.

References abs, CGlRect< T >::Bottom(), IRender::Color4f(), IRender::ColorC(), ctx, IRender::Disable(), CRenderingContext::DrawSelection(), CRenderingContext::DrawTriangle(), CAlignGlyph::e3_Prime, CAlignGlyph::e5_Prime, IAlnExplorer::eLeft, COpenRange< Position >::Empty(), IRender::Enable(), IAlnGraphicDataSource::ePartial_3prime, IAlnGraphicDataSource::ePartial_5prime, IAlnExplorer::eRight, Error(), CAlignmentConfig::eTails_Hide, CAlignmentConfig::eTails_ShowGlyph, CAlignmentConfig::eTails_ShowSequence, IAlnGraphicDataSource::GetAlnPosFromSeqPos(), IAlnGraphicDataSource::GetAlnRangeWithTails(), IScoringAlignment::GetAnchor(), CAlignGlyph::GetBarHeight(), IScoringAlignment::GetBaseWidth(), CRange_Base::GetFrom(), GetGl(), CRenderingContext::GetGlPane(), CException::GetMsg(), IScoringAlignment::GetNumRows(), IAlnGraphicDataSource::GetPartialFlags(), IAlnGraphicDataSource::GetQuery(), CRenderingContext::GetScale(), CGlPane::GetScaleY(), IAlnGraphicDataSource::GetSeqStart(), IAlnGraphicDataSource::GetSeqStop(), COpenRange< Position >::GetToOpen(), IAlnGraphicDataSource::GetUnalignedTails(), CRenderingContext::IntersectVisible(), IAlnGraphicDataSource::IsNegativeStrand(), CAlignGlyph::IsSimplified(), LOG_POST, CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_DisableTooltipsCaching, CAlignGlyph::m_FadeFactor, CAlignGlyph::m_Score, CAlignmentConfig::m_UnalignedSequence, CAlignmentConfig::m_UnalignedTailsMode, row, CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), swap(), Warning(), CRenderingContext::WillSeqLetterFit(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawGaps(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawIntronsAndInternalUnalignedRegions(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CAlignGlyph::x_DrawNoScoreAlign(), CAlignGlyph::x_DrawSimplified(), CAlignGlyph::x_DrawStrandIndicators(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawTailSequences(), CAlignGlyph::x_DrawUnalignedRowSequence(), CAlignGlyph::x_GetOverrideColor(), CAlignGlyph::x_RenderAveragableScores(), CAlignGlyph::x_RenderNonAveragableScores(), CAlignGlyph::x_ShowScore(), and CAlignGlyph::x_ShowUnalignedTails().

Referenced by CAlignGlyph::x_DrawPWAlign().

Convert feature subtypes to track subtypes.

If the feature subtype list contains 'gene' feature, all gene, RNA, cdregion and exon feature subtypes will be combined into one track subtype: gene_model. If the feature type is variation_ref, the track type will be dbVar. If the feature tyep is variation, the track type will be dbSNP. For anything else, track type will be just treated as a feature track subtype.

Definition at line 206 of file na_utils.cpp.

References CSeqFeatData_Base::e_Gene, set< Key, Compare >::end(), set< Key, Compare >::erase(), set< Key, Compare >::find(), CSeqFeatData::GetFeatList(), CFeatList::GetStoragekey(), set< Key, Compare >::insert(), CDataTrackUtils::IsGeneModelFeature(), ITERATE, and kSnpSubtypeStr.

Referenced by CNAUtils::GetNATrackInfo().

same, with a timeout in milliseconds

Definition at line 1135 of file utils.cpp.

References CSeqUtils::CanHavePlacements(), eGetId_ForceGi, eSerial_AsnText, flags, CSeq_id_Handle::GetGi(), GetId(), GetLinksURL(), GetSeqIdString(), NcbiMsToTimeout(), CObjectIStream::Open(), and s_GetAlnMapplingLocs().

Referenced by CSeqUtils::GetAccessionPlacements().

get a is_source_assembly_query string from AlignDb annotation suffixed after a second '#'

get a is_source_assembly_query string fro AlignDb annotation suffixed after a second '#'

Definition at line 878 of file utils.cpp.

References CSeqUtils::IsAlignDb(), NStr::Split(), and string.

Inline methods.

Definition at line 249 of file alignment_glyph.hpp.

References CAlignGlyph::m_AlnMgr.

Referenced by CSGAlignmentDS::CalculateAlignmentScore(), CMatePairGlyph::CMatePairGlyph(), CSGAlignmentDS::GetAlignType(), CSGAlignmentDS::InitAlignQualityScore(), CSGAlignmentDS::InitAlignScore(), CSGAlignmentDS::InitAlignScoreCache(), CAlignGlyph::LessBySeqPos(), CAlignmentTrack::x_AddAlignmentLayout(), CSGAlignmentJob::x_CreateFeatGlyph(), CAlignmentTrack::x_GetAlignGlyphType(), and CSGAlignmentJob::x_LoadAlignmentFeats().

Get alignment type.

The alignment types include:

• nucleotide: nucleotide-to-nucleotide alignment
• protein: protein-to-protein alignment
• mixed: protein-to-nucleotide alignment

Definition at line 77 of file na_utils.cpp.

References CSeq_align::CheckNumRows(), CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, fAlign_DNA, fAlign_Invalid, fAlign_Mixed, fAlign_Protein, CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), CSeq_align::GetSeq_id(), kEmptyStr, and row.

Referenced by CNAUtils::GetNATrackInfo().

Get a list of NAAs associated with the target sequence.

It returns only the named annotation names only (no meta-data). If the target sequence is not set, it returns nothing.

Parameters

naas data structure for returned NA names. context is a viewer context that predefines a set of NAAs applied only under the given viewer context. Maybe, we can remove it when TMS is fully integrated.

Definition at line 529 of file na_utils.cpp.

References context, CNAUtils::x_GetNAAs(), and CNAUtils::x_GetNAIds().

create a annotation selector for collecting annotation names only.

Parameters

Definition at line 266 of file utils.cpp.

References SAnnotSelector::AddNamedAnnots(), SAnnotSelector::AddUnnamedAnnots(), CSeqUtils::eAnnot_All, CSeqUtils::eAnnot_Named, CSeqUtils::eAnnot_Other, CSeqUtils::eAnnot_Unnamed, SAnnotSelector::ExcludeUnnamedAnnots(), CSeqUtils::GetAnnotSelector(), SAnnotSelector::IncludeNamedAnnotAccession(), CSeqUtils::IsExtendedNAA(), CSeqUtils::IsNAA(), ITERATE, CSeqUtils::NameTypeStrToValue(), SAnnotSelector::SetCollectNames(), and NStr::StartsWith().

request an annotation selector for a given type

Definition at line 168 of file utils.cpp.

References SAnnotSelector::ExcludeNamedAnnots(), CSeqUtils::fAnnot_UnsetDepth, CSeqUtils::fAnnot_UnsetNamed, flags, CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetKeys(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), SAnnotSelector::IncludeNamedAnnotAccession(), ITERATE, NULL, SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetExcludeExternal(), SAnnotSelector::SetOverlapTotalRange(), and SAnnotSelector::SetResolveAll().

Referenced by CAlignmentSmear::AddAnnot(), CLinkUtils::AddDbxrefLinksForSNP(), CSGAlignmentDS::CalcAlnStat(), CBinsTrack::CBinsTrack(), CFeatureTrack::CFeatureTrack(), CGeneModelTrack::CGeneModelTrack(), CGraphTrack::CGraphTrack(), CHapmapTrack::CHapmapTrack(), Convert_Seq_loc_Seq_align(), Convert_Seq_loc_Seq_annot(), Convert_Seq_loc_Seq_feat(), Convert_Seq_loc_Seq_graph(), CSubAnnotationPanel::Create5ColFeatTable(), CVarTrackFactory::CreateTracks(), CFeatureTrackFactory::CreateTracks(), CGraphTrackFactory::CreateTracks(), CSeqTableGraphTrackFactory::CreateTracks(), CSequenceTrackFactory::CreateTracks(), CAlignmentTrackFactory::CreateTracks(), CGeneModelFactory::CreateTracks(), CSeqTextJob::CSeqTextJob(), CGBObjectLoader::Execute(), NSearchFeatPanel::GatherFeatures(), CSGAlignmentDS::GetAlignmentCost(), CSGAlignmentJob::GetAlignType(), CEpigenomicsDS::GetAnnotNames(), CSGSnpDS::GetAnnotNames(), CSeqUtils::GetAnnotSelector(), CSeqTextPaneConfig::GetCaseFeature(), CSGAlignmentDS::GetDataLoader(), NSnpAnnot::GetFeat_CI(), CSeqTextDataSourceInterval::GetFeatureData(), CSeqTextDataSource::GetFeaturesAtPosition(), CSeqTextDataSourceInterval::GetFeaturesAtPosition(), CSGFeatureDS::GetFilters(), NSnpAnnot::GetGraph_CI(), CSGAlignmentDS::GetGraphCost(), CGuiObjectInfoVariation::GetLinks(), CSeqTextDataSourceInterval::GetSubtypesForAlternatingExons(), CSeqTextDataSourceInterval::GetToolTipForPosition(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), CLDBlockDS::GetTrackNames(), CSeqTextDataSourceInterval::GetVariations(), CFeatTableDS::Init(), CAlnVecMultiDataSource::Init(), CAlnMultiDSBuilder::Init(), CHitMatrixDSBuilder::Init(), CSGAlignmentDS::InitAlignType(), CSGAlignmentDS::LoadAlignFeats(), CSGAlignmentDS::LoadAlignments(), CSGAlignmentDS::LoadCoverageGraph(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CEpigenomicsDS::LoadData(), CSeqTextDataSourceInterval::RenderFeatureExtras(), CAlignTabExportJob::Run(), C5ColExportJob::Run(), CFlatFileExportJob::Run(), CFeatCompareJob_Align::Run(), CFeatCompareJob_Location::Run(), CTestBMApp::Run(), s_Create5ColFeatTable(), s_GetAnnotSelector(), s_GetMappedFeat(), s_Render_SeqFeat(), CSeqTextPaneConfig::SetCaseFeature(), CSnpJob::x_FetchFtable(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CSGAlignmentJob::x_GetAlignments(), CDensityMapDS::x_GetAnnotSelector(), x_GetAnnotSelector(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CwxAnnotConfigDlg::x_InitAnnotList(), CLDBlockJob::x_Load(), CSGAlnQualityScore::x_RetrieveQualityMap(), CFlatFeatureRetrieveJob::x_Run(), CFeatureSearchJob::x_SearchFeatures(), CFeatureSearchJob::x_SearchForSNP(), CAlignTabExportPage2::x_StartAlignNamesJob(), CFeatureGraph::x_StartJob(), CAlignTabExportPage2::x_StartNAAlignNamesJob(), and x_ToBlastVec().

get all assembly accessions corresponding to a GI

Definition at line 1561 of file utils.cpp.

References xml::node_set::begin(), set< Key, Compare >::clear(), CSeqUtils::CreateIdStr(), xml::node_set::end(), Error(), xml::node::get_content(), xml::document::get_root_node(), CSeqUtils::GetAssmIds_GI(), CException::GetMsg(), set< Key, Compare >::insert(), kAssmDb, kRetMax, LOG_POST, xml::node::run_xpath_query(), CEutilsClient::SetMaxReturn(), and CEutilsClient::Summary().

get all assembly ids associated with a gi where this gi is a chromosome

Note

transplanted from w_loaders/assm_info.cpp because this is needed for GetChrGI()

Parameters

gi GI to try to match to a chromosome in any assembly gc_ids

• will be reset and filled with list of assemblies where the given GI is a chromosome
• will become empty if there is no assembly where this GI is a chromosome

Definition at line 1365 of file utils.cpp.

References xml::node_set::begin(), CSeqUtils::CreateIdStr(), CSeqUtils::ELinkQuery(), ctll::empty(), xml::node_set::end(), Error(), xml::node::get_content(), xml::document::get_root_node(), CException::GetMsg(), GI_TO, kAssmDb, kNucDb, kRetMax, LOG_POST, xml::node::run_xpath_query(), CEutilsClient::SetMaxReturn(), and CEutilsClient::Summary().

Referenced by CSeqUtils::GetChrGI().

Referenced by CCitationsPanel::CreateControls(), CreateEditorForObject(), CCmdPromoteCDS::Execute(), CMacroBioData_FeatIterBase::GetBioseqHandle(), CMacroBioData_FeatIntervalIter::GetBioseqHandle(), s_GetAccession(), CMacroFunction_RemoveBothPartials::s_RemoveBothPartials(), CMacroFunction_SetBothPartials::s_SetBothEndsPartial(), CGenericPropsPanel::x_IsRefSeq(), and CIdentifiersPanel::x_UpdateXrefDescriptions().

Derive the CDS feature mapping information based on its parent RNA feature mapping info.

Definition at line 2037 of file utils.cpp.

References CSeq_id::Assign(), CSeq_feat_Base::CanGetProduct(), CSeq_loc::CompareSubLoc(), done, eExtreme_Biological, eNa_strand_minus, eNa_strand_plus, CSeqFeatData::eSubtype_cdregion, SAnnotSelector::ExcludeNamedAnnots(), CSeq_loc::fMerge_AbuttingOnly, CPacked_seqint_Base::Get(), CScope::GetBioseqHandle(), CRange_Base::GetFrom(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetMappedFeature(), CSeq_loc_Base::GetPacked_int(), CSeq_feat_Base::GetProduct(), CMappedFeat::GetProduct(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetTotalRange(), COpenRange< TSeqPos >::GetWhole(), SAnnotSelector::IncludeFeatSubtype(), int, CSeq_feat_Base::IsSetExcept(), ITERATE, CSeq_id::Match(), CSeq_loc::Merge(), NULL, r1, r2, s_AdjustToAnnotatedCDS(), SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetExactDepth(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_loc::SetPacked_int(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveDepth(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().

Referenced by CSeqUtils::GetMappingInfo(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), and CSGFeatureJob::x_CreateFeature1().

Collect all column header names for a given seq-table.

The header name is from either field-name or field-id.

Definition at line 165 of file na_utils.cpp.

References CSeqTable_column_info_Base::CanGetField_id(), CSeqTable_column_info_Base::CanGetField_name(), CEnumeratedTypeValues::FindName(), CSeq_table_Base::GetColumns(), CSeq_annot_Base::GetData(), CSeqTable_column_info_Base::GetField_id(), CSeqTable_column_info_Base::GetField_name(), CSeq_annot_Base::C_Data::GetSeq_table(), set< Key, Compare >::insert(), CSeq_annot::IsSeq_table(), and ITERATE.

Referenced by CNAUtils::GetNATrackInfo().

Retrieve mapped-up sequences.

Help method for retrieving upper level sequences for a given gi.

Parameters

gi the source sequence gi

Definition at line 1069 of file utils.cpp.

References Error(), eSerial_AsnText, flags, GetLinksURL(), CException::GetMsg(), LOG_POST, NStr::NumericToString(), CObjectIStream::Open(), s_GetAlnMapplingLocs(), STimeoutTag::sec, and STimeoutTag::usec.

Get html active areas.

This function is for CGI mode only. By default, it does nothing.

Reimplemented from CSeqGlyph.

Definition at line 155 of file alignment_glyph.cpp.

References CHTMLActiveArea::fNoCaching, IScoringAlignment::GetNumRows(), CAlignGlyph::GetSignature(), CSeqGlyph::GetVisible(), IAlnGraphicDataSource::IsNegativeStrand(), CAlignGlyph::m_AlnMgr, CAlignGlyph::m_DisableTooltipsCaching, CHTMLActiveArea::m_Flags, CHTMLActiveArea::m_PositiveStrand, CHTMLActiveArea::m_Signature, and CSeqGlyph::x_InitHTMLActiveArea().

Definition at line 2880 of file utils.cpp.

References CGencollIdMapper::SIdSpec::Alias, CGencollIdMapperAdapter::CGencollIdMapperAdapter(), CGC_TypedSeqId_Base::e_Genbank, CGC_SeqIdAlias::e_Public, CGC_TypedSeqId_Base::e_Refseq, eGC_SequenceRole_top_level, CGC_Assembly::IsRefSeq(), CGencollIdMapper::SIdSpec::Role, and CGencollIdMapper::SIdSpec::TypedChoice.

Referenced by CBamUIDataSource::AddDataLoader(), SCoverageData::GetMapper(), CVcfLoadingJob::x_CreateProjectItems(), CVcfRefSequencesPanel::x_FillList(), and CBamUILoadManager::x_GetBamRefSeqs().

Retrieve locations on mapped-up sequences Help method for retrieving upper level sequences for a given loc.

Parameters

loc source location (expected to be a pnt or int)

Returns

list of locations represented as intervals

Definition at line 1161 of file utils.cpp.

References CSeq_align::CheckNumRows(), Error(), eSerial_AsnText, fHTTP_AutoReconnect, CRange_Base::GetFrom(), CSeq_id_Base::GetGi(), GetLinksURL(), CException::GetMsg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align_Base::C_Segs::GetStd(), CRange_Base::GetTo(), INVALID_GI, CSeq_id_Base::IsGi(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, LOG_POST, NStr::NumericToString(), CObjectIStream::Open(), STimeoutTag::sec, swap(), and STimeoutTag::usec.

Definition at line 85 of file utils.hpp.

Definition at line 83 of file utils.hpp.

Definition at line 2282 of file utils.cpp.

References CSeqFeatData_Base::e_Cdregion, eNa_strand_minus, CSeqFeatData::eSubtype_V_segment, CSeqFeatData_Base::GetCdregion(), CSeqUtils::GetCdsMappingInfoFromRna(), CSeq_feat_Base::GetData(), CSeqUtils::GetFeatLocation(), CCdregion_Base::GetFrame(), CSeq_loc::GetId(), CMappedFeat::GetLocation(), CMappedFeat::GetMappedFeature(), CSeqUtils::GetMappingInfoFromLocation(), CSeqUtils::GetMrnaForCds(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CSeqUtils::GetRnaMappingInfo(), CBioseq_Handle::GetScope(), GetStrand(), CSeqFeatData::GetSubtype(), info, NStr::IntToString(), CSeqFeatData_Base::IsRna(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::IsSetProduct(), offset, and CSeqFeatData_Base::Which().

Referenced by CGuiObjectInfoSeq_feat::x_GetProductSequence().

Do data track discovery for a given NA.

This method relies on NA meta-data to do data discovery completely or partially depending on the annotation type. For example, for seq-table, it will need to look at the data to report the column names. For alignment, it will need to check the alignment type: protein or nucleotide.

Definition at line 607 of file na_utils.cpp.

References CNAUtils::GetNAMetaData().

Referenced by CNAUtils::GetNATrackInfo().

Do data track discovery for a given NA with meta-data.

See also

void GetNATrackInfo(TTrackInfoList& track_info, const string& naa) const;

Definition at line 616 of file na_utils.cpp.

References SAnnotSelector::AddNamedAnnots(), set< Key, Compare >::begin(), data, CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_Seq_table, map_checker< Container >::empty(), set< Key, Compare >::empty(), map_checker< Container >::end(), CDataTrackUtils::FeatSubtypes2TrackSubtypes(), map_checker< Container >::find(), ftable, CDataTrackUtils::GetAlignType(), CDataTrackUtils::GetColumnHeader(), CSeq_annot_Handle::GetCompleteSeq_annot(), CSeq_annot_Base::GetData(), CSeq_table_Base::GetFeat_subtype(), CSeq_annot_Base::C_Data::GetSeq_table(), CDataTrackUtils::GetSeqTableSubtype(), COpenRange< TSeqPos >::GetWhole(), SAnnotSelector::IncludeAnnotType(), SAnnotSelector::IncludeNamedAnnotAccession(), info, set< Key, Compare >::insert(), CSeq_table_Base::IsSetFeat_subtype(), ITERATE, CNAUtils::m_BioseqHandle, CNAUtils::m_Scope, CNAUtils::m_TargetSeq, s_GetFeatSubtypeStr(), CSeq_annot_Base::C_Data::SelectionName(), SAnnotSelector::SetCollectNames(), and SAnnotSelector::SetMaxSize().

Implemented in CVcfTrackData.

return signature for this glyph.

Implements IObjectBasedGlyph.

Definition at line 212 of file alignment_glyph.cpp.

References CSeq_loc::Assign(), CObjFingerprint::GetAlignSignature(), IScoringAlignment::GetAnchor(), CAlignGlyph::GetLocation(), CAlignGlyph::GetObject(), CAlignGlyph::GetOrigAlignment(), CRenderingContext::GetScope(), IAlnGraphicDataSource::GetSeqId(), CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, CAlignGlyph::m_Location, CAlignGlyph::m_OrigSeqAlign, CSeq_loc::SetId(), and CAlignGlyph::x_IsSRA().

Referenced by CAlignGlyph::GetHTMLActiveAreas().

Referenced by CMacroEditorContext::CMacroEditorContext(), CAECRFrame::CreateControls(), CCorrectIntervalOrder::Init(), CRemoveFeaturesDlg::Init(), CRemoveGeneXrefs::Init(), CSuppressGenes::Init(), CFeatureTypePanel::ListPresentFeaturesFirst(), CAdjustFeaturesForGaps::PopulateFeatureList(), CMacroFeatsOnSeqPanel::x_GetFeatureChoices(), CAddFeatureBetweenDlg::x_ListFeatures(), CBulkOtherAddPanel::x_ListFeatures(), and CAlignOtherAddPanel::x_ListFeatures().

Definition at line 1189 of file alignment_glyph.cpp.

References CLabel::eContent, CLabel::eDescription, CLabel::eDescriptionBrief, CLabel::eType, CLabel::eUserTypeAndContent, CLabel::GetLabel(), IScoringAlignment::GetNumRows(), CAlignGlyph::GetOrigAlignment(), CRenderingContext::GetScope(), CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, CAlignGlyph::m_OrigAnchor, CAlignGlyph::m_OrigSeqAlign, row, NStr::UIntToString(), and CAlignGlyph::x_IsPWAlign().

Referenced by CAlignGlyph::x_DrawPWAlign(), and CAlignGlyph::x_UpdateBoundingBox().

Get the tooltip if available.

The x and y are in 'world' coord system which is the coord. system for the uppermost layout object.

Reimplemented from CSeqGlyph.

Definition at line 118 of file alignment_glyph.cpp.

References ITooltipFormatter::AddRow(), CAlignGlyph::GetAlignment(), CRef< C, Locker >::GetPointer(), CRenderingContext::GetScale(), CRenderingContext::GetScope(), CSeqGlyph::GetVisible(), CRenderingContext::IsFlippedStrand(), CAlignGlyph::IsLastRow(), CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, CAlignGlyph::m_OrigAnchor, NULL, CGuiObjectInfoSeq_align::SetAnchorRow(), CGuiObjectInfoSeq_align::SetDataSource(), CGuiObjectInfoSeq_align::SetFlippedStrands(), CGuiObjectInfoSeq_align::SetScale(), and CGlPoint< T >::X().

Definition at line 2596 of file utils.cpp.

References CScope::eMissing_Null, GetBioseqForSeqFeat(), GetDefaultTopLevelSeqEntry(), CConstRef< C, Locker >::GetPointer(), GetSeqEntryForPubdesc(), GetSeqEntryForSeqdesc(), CBioseq_Handle::GetTopLevelEntry(), CBioseq_set_Handle::GetTopLevelEntry(), SConstScopedObject::object, and SConstScopedObject::scope.

Referenced by CEditingBtnsPanel::EditSequence(), CSequenceEditingEventHandler::EditSequence(), CSelectFeatures::GetMainObject(), CSUCDataGenerator::GetSUCResults(), CBulkCmdDlg::GetTopLevelSeqEntryAndProcessor(), CValidatePanel::GetTopSeqAndSeqSubmit(), CEditObjViewDlgModal::InitWidget(), IsEditable(), CAddFeatureBetweenDlg::OnApplyButton(), CEditingBtnsPanel::OnDataChange(), CUnculTaxTool::OnRefreshBtn(), CSelectTargetDlg::OnSelTargetAcceptClick(), CDiscrepancyPanel::OpenEditor(), CRemoveSet::remove_sets_from_set(), s_Create5ColFeatTable(), CGuiCoreHelper::Sync(), CTableViewWithTextViewNav::x_EditObject(), CSuspectProductRulesEditor::x_SetUpTSEandUnDoManager(), and CSequenceEditingEventHandler::x_SetUpTSEandUnDoManager().

Get data track information from a seq-annot.

Definition at line 79 of file feat_label.cpp.

Definition at line 48 of file pw_alignment.cpp.

Get the commonly used symbol representing a unnnamed annotation.

Definition at line 534 of file utils.hpp.

Referenced by CTrackConfigManager::AdjustTrackOrder(), CGraphGlyph::CGraphGlyph(), CGeneModelFactory::CreateTracks(), CSGFeatureJob::GetAnnotNames(), CSGSegmentSmearJob::GetAnnotNames(), CSGAlignmentJob::GetAnnotNames(), CSGSeqGraphJob::GetAnnotNames(), CEpigenomicsDS::GetAnnotNames(), CSGFeatureJob::GetAnnotNames_var(), CHistParamsManager::GetHistParams(), CSGSeqGraphJob::GetSeqtableAnnots(), CHistParamsManager::HasSettings(), CHistParamsManager::IsTempSettings(), CSeqUtils::IsUnnamed(), CTempTrackProxy::SaveToRegistry(), CSGAnnotJob::x_AddGraphObject(), CHistParamsManager::x_AddSettings(), CBatchFeatJob::x_LoadFeatProducts(), CSGSeqGraphJob::x_LoadSeqTable(), and CAlignTabExportPage2::x_StartAlignNamesJob().

Query if this glyph is clickable.

Mainly for chaging mouse cursor for clickable glyph. By default, it returns false. If a glyph is clickable, but there is no need to change mouse cursor due to any other reason, such as there is already other visual hint, then don't need to override this function.

Reimplemented from CSeqGlyph.

Definition at line 182 of file alignment_glyph.cpp.

check if a given annotation is an extended NAA (named accession[.version][number], as used in e.g.

SNP2) when isSctrict == false, regular NAs are now included into this as well i.e. the result of calling this is now the same as IsNAA

Definition at line 851 of file utils.cpp.

References s_IsExtendedNAA().

Referenced by CSnpTrackFactory::CreateTracks(), CSeqUtils::GetAnnotSelector(), NSnpAnnot::GetGraph_CI(), CSnpTrackFactory::GetMatchedAnnots(), CTempTrackProxy::IsExtendedNA(), CSeqUtils::IsNAA(), s_ConvertMetaData(), CSeqUtils::SetAnnot(), and CSnpJob::x_FetchGraphs().

Does feature belong to gene model track Gene, RNA, cdregion, exon, C_region, and VDJ segments.

Definition at line 190 of file na_utils.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, CSeqFeatData::eSubtype_C_region, CSeqFeatData::eSubtype_D_segment, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_J_segment, CSeqFeatData::eSubtype_misc_RNA, and CSeqFeatData::eSubtype_V_segment.

Referenced by CDataTrackUtils::FeatSubtypes2TrackSubtypes(), CTrackConfigManager::ValidFeatureTrack(), CAlignmentTrack::x_AddAlignFeatLayout(), and CSGAlignmentJob::x_LoadAlignmentFeats().

check if a given annotation is a named annotation accession[.version][number] when isSctrict == false, includes extended NAs since it is considered no harm to relax the rules for all NAs

Definition at line 797 of file utils.cpp.

References CSeqUtils::IsExtendedNAA(), and s_IsNAA().

Referenced by CObjFingerprint::GetAlignSignature(), CSGSegmentSmearJob::GetAnnotNames(), CSeqUtils::GetAnnotSelector(), CObjFingerprint::GetFeatSignature(), CObjFingerprint::GetGraphSignature(), CObjFingerprint::GetHistogramSignature(), ILayoutTrackFactory::GetMatchedAnnots(), CAllOtherFeaturesTrackFactory::GetSettings(), CVarTrack::InitHTMLActiveArea(), CTempTrackProxy::IsNA(), CTrackConfigManager::OnShownList(), CObjFingerprint::ParseSignature(), CTrackInitializationJob::Run(), CSnpJob::s_AdjustAnnotName(), CSeqUtils::SetAnnot(), CHapmapJob::x_Load(), and CGenBankLoadOptionPanel::x_ProccessText().

Definition at line 1476 of file utils.cpp.

References CSeq_id::AsFastaString(), CSeq_id::eAcc_refseq_chromosome, map_checker< Container >::end(), Error(), map_checker< Container >::find(), CScope::GetBioseqHandle(), GetGiForId(), CSeq_id::IdentifyAccession(), info, CGencollSvc::isGenCollSequence(), LOG_POST, m_TopLevels, m_TopLevelsLock, CSeqUtils::Match(), s_GetAssemblySeqIds(), and ZERO_GI.

Link features into a hierarchical list.

This function will transform a linear, feature-order-sorted list of CLinkedFeature into a hierarchically arranged list in which genes are linked to mRNAs, mRNAs to CDSs, etc.

Parameters

mode 0:eFeatId_ignore, 1:eFeatId_by_type, 2:eFeatId_always

Definition at line 453 of file utils.cpp.

References ISeqTaskProgressCallback::AddTaskCompleted(), NON_CONST_ITERATE, ISeqTaskProgressCallback::SetTaskCompleted(), ISeqTaskProgressCallback::SetTaskName(), ISeqTaskProgressCallback::SetTaskTotal(), and ISeqTaskProgressCallback::StopRequested().

Referenced by CGeneModelFeatJob::GetFilters(), CGeneModelFeatJob::x_CreateFeaturesWithFilter(), CGeneModelFeatJob::x_Execute(), CSGFeatureJob::x_LinkFeatures(), and CSGAlignmentJob::x_LoadAlignmentFeats().

create an annotation name for a remote file pipeline, appending sSuffix

Definition at line 808 of file utils.cpp.

check to see if two seq-ids are identical.

If provided with a scope, this function will use the synonyms available through a scope to check for identicality. Note that this may require network access, and may be slow.

Referenced by CVisibleRange::Clamp(), CQueryFuncPromoteEq::Evaluate(), CQueryFuncPromoteIn::Evaluate(), CProjectView::GetReflectionInfo(), CSeqUtils::isTopLevel(), CVisibleRange::Match(), CAlnMultiWidget::SetSelectedIds(), CTaxTreeBrowser::SetSelectedUids(), and CComponentSearchJob::x_DoSearch().

Create a new seq-loc with a unique seq-id from a "mixed" loc.

"Mixed" means mixed seq-ids, e.g. a seq-loc with multi seq-ids.

Definition at line 662 of file utils.cpp.

References CPacked_seqint::AddInterval(), COpenRange< Position >::Empty(), CPacked_seqint_Base::Get(), CRange_Base::GetFrom(), CBioseq_Handle::GetSeqId(), CRange_Base::GetTo(), CBioseq_Handle::IsSynonym(), CPacked_seqint_Base::Set(), CSeq_loc::SetInt(), and CSeq_loc::SetPacked_int().

Referenced by CSeqUtils::GetFeatLocation(), CSGFeatureJob::x_CreateCrossOriginGlyphs(), CSGFeatureJob::x_CreateFeature1(), and CGuiObjectInfoSeq_feat::x_GetFeatLocation().

Definition at line 141 of file utils.cpp.

References CSeqUtils::eAnnot_Other.

Referenced by CTrackConfigManager::AdjustTrackOrder(), CAlignmentTrackFactory::CreateTracks(), NSearchFeatPanel::GatherFeatures(), CSeqUtils::GetAnnotSelector(), NSnpAnnot::GetFeat_CI(), CSnpJob::s_AdjustAnnotName(), CFeatureTrack::SetAnnot(), CGeneModelTrack::SetAnnot(), CGraphTrack::SetAnnot(), CSeqUtils::SetAnnot(), NSearchFeatPanel::CTrackFeatSubtype::Track(), CSnpJob::x_FetchFtable(), and CSnpJob::x_FetchGraphs().

Check if need to show tooltip.

If the tooltip retrieval is trivial, the derived glyph may decide to fill out the tooltip (info object) in this call.

Reimplemented from CSeqGlyph.

Definition at line 112 of file alignment_glyph.cpp.

Read attributes stream into the table.

Definition at line 62 of file biotree_attr_reader.cpp.

References CNcbiTable< TValue, TRow, TColumn >::AddColumn(), CNcbiTable< TValue, TRow, TColumn >::AddRow(), CStreamLineReader::AtEOF(), CBioTreeAttrReader::CheckLineReader(), CNcbiTable< TValue, TRow, TColumn >::Cols(), ERR_POST, NStr::fSplit_Tokenize, CNcbiTable< TValue, TRow, TColumn >::GetCell(), CStreamLineReader::GetLineNumber(), i, ITERATE, l(), LOG_POST, NCBI_THROW2, row, NStr::Split(), CBioTreeAttrReader::TableValueDecode(), and Warning().

Referenced by CPhyloTreeWidget::OnLoadAttributes().

Construct a bioseq to fit a given location.

If the location is of type 'whole', then a duplicate of the original will be returned; otherwise, a new bioseq will be constructed to cover just the region indicated in the seq-loc

Definition at line 601 of file utils.cpp.

References CSerialObject::Assign(), CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eRepr_raw, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_loc::GetLabel(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqId(), CSeqVector::IsProtein(), CSeq_loc_Base::IsWhole(), CSeqportUtil::Pack(), CRef< C, Locker >::Release(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeqdesc_Base::SetTitle(), and CSeqVector::size().

help function for setting up an annotation.

Definition at line 321 of file utils.cpp.

References CSeqUtils::eAnnot_All, CSeqUtils::eAnnot_Named, CSeqUtils::eAnnot_Other, CSeqUtils::eAnnot_Unnamed, CSeqUtils::IsExtendedNAA(), CSeqUtils::IsNAA(), and CSeqUtils::NameTypeStrToValue().

Referenced by CSGAlignmentDS::CalcAlnStat(), CSGAlignmentDS::GetAlignmentCost(), CSGFeatureDS::GetFilters(), CSGAlignmentDS::GetGraphCost(), CSGAlignmentDS::LoadAlignments(), CSGAlignmentDS::LoadCoverageGraph(), CEpigenomicsDS::LoadData(), and CAlignTabExportJob::Run().

help function for setting selector resolve depth.

Parameters

sel target annotation selector adaptive adaptive selector if true, otherwise, exact selector depth resolve depth. For adaptive selector, it resolves all if depth < 0, otherwie resolve up to the specified depth. For exact selector, depth is the exact the resovle depth (>=0).

Definition at line 406 of file utils.cpp.

References depth, CSeqUtils::GetMaxSearchSegments(), CSeqUtils::GetMaxSearchSegmentsAction(), CSeqUtils::GetMaxSearchTime(), and CSeqUtils::GetSelectorRegistry().

Referenced by CSGAlignmentDS::CalcAlnStat(), CFeatureTrack::GenerateAsn1(), CGeneModelTrack::GenerateAsn1(), CSGAlignmentDS::GetAlignmentCost(), CEpigenomicsDS::GetAnnotNames(), CSGFeatureDS::GetAnnotNames(), CSGSegmentMapDS::GetAnnotNames(), CSGAlignmentDS::GetAnnotNames(), CSGGraphDS::GetAnnotNames(), CSGSnpDS::GetAnnotNames(), CSGFeatureDS::GetAnnotNames_var(), CSeqUtils::GetAnnotSelector(), NSnpAnnot::GetFeat_CI(), NSnpAnnot::GetGraph_CI(), CSGAlignmentDS::GetGraphCost(), CSGGraphDS::GetSeqtableAnnots(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), CLDBlockDS::GetTrackNames(), CSGAlignmentDS::LoadAlignments(), CSGAlignmentDS::LoadCoverageGraph(), CEpigenomicsDS::LoadData(), CSGFeatureDS::LoadGeneModelFeatures(), CSGGraphDS::LoadSeqGraphs(), CAlignTabExportJob::Run(), CSnpJob::x_FetchFtable(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CHapmapJob::x_Load(), CLDBlockJob::x_Load(), and CAlignTabExportPage2::x_StartAlignNamesJob().

Definition at line 2386 of file alignment_glyph.cpp.

References IScoringAlignment::CreateSegmentIterator(), IAlnExplorer::eLeft, COpenRange< Position >::Empty(), IAlnExplorer::eRight, Error(), IAlnSegmentIterator::eSkipGaps, IAlnGraphicDataSource::GetAlnPosFromSeqPos(), IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), IScoringAlignment::GetBaseWidth(), CRange_Base::GetFrom(), IAlnSegment::GetRange(), IScoringAlignment::GetSeqPosFromAlnPos(), IAlnGraphicDataSource::GetSeqStart(), IAlnGraphicDataSource::GetSeqStop(), CRange_Base::GetTo(), CRenderingContext::IntersectVisible(), IAlnSegment::IsAligned(), IAlnSegment::IsIndel(), CAlignGlyph::IsSimplified(), kMinSegDistance, LOG_POST, CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, max(), r(), row, CRenderingContext::SeqToScreen(), and swap().

Referenced by CAlignGlyph::x_DrawMultiAlign(), and CAlignGlyph::x_UpdateBoundingBox().

The default renderer for this layout object.

Implements CSeqGlyph.

Definition at line 1249 of file alignment_glyph.cpp.

References CAlignGlyph::ApplyFading(), CSeqGlyph::GetBottom(), CRenderingContext::GetGlPane(), CSeqGlyph::GetTop(), CSeqGlyph::GetVisible(), CGlPane::GetVisibleRect(), CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawPWAlign(), and CAlignGlyph::x_IsPWAlign().

Definition at line 1673 of file alignment_glyph.cpp.

References IRender::Color3f(), IRender::ColorC(), CSeqManip::Complement(), IScoringAlignment::CreateSegmentIterator(), CRenderingContext::DrawDisk2(), CRenderingContext::DrawLineStrip(), CSeqUtil::e_Iupacaa, CSeqUtil::e_Iupacna, CBioseq_Handle::eCoding_Iupac, IAlnExplorer::eLeft, eMaxRowLimit, COpenRange< Position >::Empty(), CAlignGlyph::eOne2One, CAlignGlyph::eOne2Three, IAlnExplorer::eRight, IAlnSegmentIterator::eSkipGaps, CAlignGlyph::eThree2One, IScoringMethod::fForeground, CSeqTranslator::fIs5PrimePartial, IAlnGraphicDataSource::GetAlnPosFromSeqPos(), IAlnSegment::GetAlnRange(), IScoringAlignment::GetAlnSeqString(), IScoringAlignment::GetAnchor(), CAlignGlyph::GetBarHeight(), IScoringAlignment::GetBaseWidth(), IAlnGraphicDataSource::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CRange_Base::GetFrom(), IAlnGraphicDataSource::GetGenCode(), GetGl(), CSeqGlyph::GetLeft(), IAlnSegment::GetRange(), CSeqGlyph::GetRight(), CSeqVector::GetSeqData(), IScoringAlignment::GetSeqPosFromAlnPos(), IAlnGraphicDataSource::GetSeqStart(), IAlnGraphicDataSource::GetSeqStop(), CBioseq_Handle::GetSeqVector(), CSeqGlyph::GetTearline(), CRange_Base::GetTo(), CSeqGlyph::GetWidth(), CRenderingContext::IntersectVisible(), CBioseq_Handle::IsAa(), CRenderingContext::IsFlippedStrand(), CAlignGlyph::IsLastRow(), IAlnGraphicDataSource::IsNegativeStrand(), kPWAlignPackLevel, CRgbaColor::Lighten(), CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_LabelFont, CAlignGlyph::m_Score, CAlignmentConfig::m_SeqFont, CAlignmentConfig::m_ShowIdenticalBases, match(), min(), msg(), NULL, r(), CSeqManip::Reverse(), CSeqManip::ReverseComplement(), row, CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), COpenRange< Position >::Set(), CRgbaColor::SetAlpha(), CRange_Base::SetFrom(), CGenetic_code::SetId(), swap(), IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), and CSeqTranslator::Translate().

Referenced by CAlignGlyph::DrawPWAlignElem(), and CAlignGlyph::x_DrawMultiAlign().

Definition at line 248 of file alignment_glyph.cpp.

References IRender::ColorC(), IScoringAlignment::CreateSegmentIterator(), ctx, IRender::Disable(), CRenderingContext::DrawLine(), IAlnSegmentIterator::eAllSegments, IAlnGraphicDataSource::eCigar_N, COpenRange< Position >::Empty(), IAlnSegment::fIndel, IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), IAlnGraphicDataSource::GetCigarAtAlnPos(), CRange_Base::GetFrom(), GetGl(), IScoringAlignment::GetNumRows(), IAlnSegment::GetRange(), IScoringAlignment::GetSeqPosFromAlnPos(), CRange_Base::GetTo(), IAlnSegment::GetType(), IRender::LineWidth(), CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_Gap, CAlignmentConfig::m_Intron, row, CRenderingContext::SeqToScreen(), and swap().

Referenced by CAlignGlyph::DrawPWAlignElem().

Definition at line 322 of file alignment_glyph.cpp.

References IRender::ColorC(), CompressLength(), IScoringAlignment::CreateSegmentIterator(), ctx, IRender::Disable(), CRenderingContext::DrawLine(), CRenderingContext::DrawTriangle(), IAlnSegmentIterator::eAllSegments, IAlnExplorer::eBackwards, IAlnExplorer::eForward, COpenRange< Position >::Empty(), CAlignmentConfig::eNormal, IAlnExplorer::eRight, IAlnSegment::fAligned, IAlnSegment::fIndel, IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), CRange_Base::GetFrom(), GetGl(), COpenRange< Position >::GetLength(), IScoringAlignment::GetNumRows(), IAlnSegment::GetRange(), CRenderingContext::GetScale(), IScoringAlignment::GetSeqPosFromAlnPos(), CRange_Base::GetTo(), IAlnSegment::GetType(), int, CRgbaColor::Interpolate(), IAlnGraphicDataSource::IsNegativeStrand(), len, CRgbaColor::Lighten(), CAlignGlyph::m_AlnMgr, CAlignmentConfig::m_CompactMode, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_DisableTooltipsCaching, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_Insertion, max(), min(), row, CRenderingContext::ScreenToSeq(), and CRenderingContext::SeqToScreen().

Referenced by CAlignGlyph::DrawPWAlignElem().

Definition at line 505 of file alignment_glyph.cpp.

References IRender::ColorC(), IScoringAlignment::CreateSegmentIterator(), ctx, CRenderingContext::DrawStippledLine(), IAlnSegmentIterator::eAllSegments, IAlnExplorer::eLeft, COpenRange< Position >::Empty(), IAlnExplorer::eRight, IAlnSegment::fUnaligned, NStr::fWithCommas, IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), CRange_Base::GetFrom(), GetGl(), CRenderingContext::GetGlPane(), COpenRange< Position >::GetLength(), IScoringAlignment::GetNumRows(), IAlnSegment::GetRange(), IScoringAlignment::GetSeqPosFromAlnPos(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), IAlnSegment::GetType(), CGlPane::GetViewport(), CRenderingContext::GetViewWidth(), i, CRenderingContext::IntersectVisible(), NStr::IntToString(), CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_DisableTooltipsCaching, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_Label, CAlignmentConfig::m_LabelFont, round(), row, CRenderingContext::ScreenToSeq(), CRange_Base::SetFrom(), swap(), IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), and CGlRect< T >::Width().

Referenced by CAlignGlyph::x_DrawIntronsAndInternalUnalignedRegions().

Definition at line 1436 of file alignment_glyph.cpp.

References IRender::Color4f(), IRender::ColorC(), CompressLength(), IScoringAlignment::CreateSegmentIterator(), IRender::Disable(), CRenderingContext::Draw3DQuad(), CRenderingContext::DrawLine(), CRenderingContext::DrawLine_NoAA(), CRenderingContext::DrawSelection(), IAlnSegmentIterator::eAllSegments, IAlnExplorer::eLeft, COpenRange< Position >::Empty(), CAlignmentConfig::ePos_Above, CAlignmentConfig::ePos_Side, IAlnExplorer::eRight, Error(), IAlnSegment::fIndel, IAlnGraphicDataSource::GetAlnPosFromSeqPos(), IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), CAlignGlyph::GetBarHeight(), IScoringAlignment::GetBaseWidth(), CRange_Base::GetFrom(), GetGl(), COpenRange< Position >::GetLength(), CSeqGlyph::GetModelRect(), CException::GetMsg(), IScoringAlignment::GetNumRows(), IAlnSegment::GetRange(), IAlnGraphicDataSource::GetSeqAlnRange(), IScoringAlignment::GetSeqPosFromAlnPos(), IAlnGraphicDataSource::GetSeqStart(), IAlnGraphicDataSource::GetSeqStop(), CRange_Base::GetTo(), IAlnSegment::GetType(), COpenRange< Position >::IntersectionWith(), CRenderingContext::IntersectVisible(), CRenderingContext::IsFlippedStrand(), CRenderingContext::IsHorizontal(), IAlnGraphicDataSource::IsNegativeStrand(), CSeqGlyph::IsSelected(), ITERATE, kAlignRowSpace, kLabelSpace_v, len, IRender::LineWidth(), LOG_POST, CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_FG, CAlignmentConfig::m_Insertion, CAlignmentConfig::m_LabelFont, CAlignmentConfig::m_LabelPos, CAlignGlyph::m_Score, CAlignmentConfig::m_SeqFont, CAlignmentConfig::m_SeqMismatch, CAlignmentConfig::m_Sequence, max(), row, CRenderingContext::ScreenToSeq(), COpenRange< Position >::Set(), swap(), IRender::TextHeight(), CRenderingContext::TextOut(), CGlRect< T >::Top(), Warning(), CRenderingContext::WillLabelFit(), CRenderingContext::WillSeqLetterFit(), CAlignGlyph::x_CalcIntervals(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawMultiAlignLabel(), CAlignGlyph::x_GetOverrideColor(), CAlignGlyph::x_RenderAveragableScores(), CAlignGlyph::x_RenderNonAveragableScores(), CAlignGlyph::x_ShowLabel(), and CAlignGlyph::x_ShowScore().

Referenced by CAlignGlyph::x_Draw().

Definition at line 1632 of file alignment_glyph.cpp.

References IRender::ColorC(), CRenderingContext::DrawBackground(), CLabel::eContent, CAlignmentConfig::ePos_Above, IScoringAlignment::GetAnchor(), CRange_Base::GetFrom(), GetGl(), CLabel::GetLabel(), CSeqGlyph::GetLeft(), COpenRange< Position >::GetLength(), CRenderingContext::GetScope(), CRenderingContext::GetSelLabelColor(), IAlnGraphicDataSource::GetSeqId(), CRange_Base::GetTo(), CRenderingContext::IntersectVisible(), IAlnGraphicDataSource::IsNegativeStrand(), CSeqGlyph::IsSelected(), label, CAlignGlyph::m_AlnMgr, CAlignmentConfig::m_BG, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_Label, CAlignmentConfig::m_LabelFont, CAlignmentConfig::m_LabelPos, row, CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), and CGlTextureFont::Truncate().

Referenced by CAlignGlyph::x_DrawMultiAlign().

Definition at line 850 of file alignment_glyph.cpp.

References IRender::ColorC(), ctx, CRenderingContext::DrawLine(), CSeq_align_Base::C_Segs::e_Spliced, eNa_strand_minus, CSpliced_exon_Base::GetAcceptor_before_exon(), CSplice_site_Base::GetBases(), CSpliced_exon_Base::GetDonor_after_exon(), CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), GetGl(), CSpliced_seg::GetSeqStrand(), IsConsensusSplice(), CSpliced_exon_Base::IsSetAcceptor_before_exon(), CSpliced_exon_Base::IsSetDonor_after_exon(), ITERATE, kEmptyStr, IRender::LineWidth(), CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_NonConsensus, CAlignGlyph::m_OrigAnchor, and CAlignGlyph::m_SeqAlign.

Referenced by CAlignGlyph::DrawPWAlignElem().

Definition at line 1372 of file alignment_glyph.cpp.

References IRender::ColorC(), CRenderingContext::DrawBackground(), CAlignGlyph::DrawPWAlignElem(), CLabel::eDefault, CAlignmentConfig::ePos_Above, CSeqGlyph::GetBottom(), CRange_Base::GetFrom(), GetGl(), CSeqGlyph::GetLeft(), COpenRange< Position >::GetLength(), CSeqGlyph::GetModelRect(), CSeqGlyph::GetRight(), CRenderingContext::GetSelLabelColor(), CAlignGlyph::GetTitle(), CRange_Base::GetTo(), CRenderingContext::IntersectVisible(), IAlnGraphicDataSource::IsNegativeStrand(), CSeqGlyph::IsSelected(), label, CAlignGlyph::m_AlnMgr, CAlignmentConfig::m_BG, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_FG, CAlignmentConfig::m_Label, CAlignmentConfig::m_LabelFont, CAlignmentConfig::m_LabelPos, CAlignmentConfig::m_SeqMismatch, CAlignmentConfig::m_Sequence, CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), CGlRect< T >::Top(), CGlTextureFont::Truncate(), and CAlignGlyph::x_ShowLabel().

Referenced by CAlignGlyph::x_Draw().

Definition at line 932 of file alignment_glyph.cpp.

References color, IRender::ColorC(), ctx, CRenderingContext::Draw3DQuad(), CRenderingContext::DrawQuad(), CSeq_align::eScore_IdentityCount, CSeq_align::eScore_PercentIdentity, GetGl(), int, CRgbaColor::Interpolate(), IAlnGraphicDataSource::IsRegular(), CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignGlyph::m_SeqAlign, CAlignGlyph::m_ShowScore, and CAlignGlyph::x_DrawStrandIndicators().

Referenced by CAlignGlyph::DrawPWAlignElem().

Definition at line 913 of file alignment_glyph.cpp.

References IRender::Color4f(), ctx, CRenderingContext::DrawGreaterLessSign(), CAlignmentConfig::eExtremeCompact, GetGl(), CAlignmentConfig::m_CompactMode, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CRenderingContext::SeqToScreen(), and CRenderingContext::WillSeqLetterFit().

Referenced by CAlignGlyph::DrawPWAlignElem(), and CAlignGlyph::x_DrawSimplified().

Definition at line 615 of file alignment_glyph.cpp.

References IRender::ColorC(), ctx, CRenderingContext::DrawUnalignedTail(), CAlignGlyph::e3_Prime, CAlignGlyph::e5_Prime, CAlignmentConfig::eTails_ShowSequence, NStr::fWithCommas, IScoringAlignment::GetAnchor(), IAlnGraphicDataSource::GetBioseqHandle(), CRange_Base::GetFrom(), GetGl(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), IAlnGraphicDataSource::GetUnalignedTails(), NStr::IntToString(), CGuiObjectInfoSeq_align::IsPolyA(), kCompactLabelSpace_h, kCompactTailGlyphLen, kLabelSpace_h, kTailGlyphLen, CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, CAlignmentConfig::m_Label, CAlignmentConfig::m_LabelFont, CAlignmentConfig::m_TailColor, CAlignmentConfig::m_UnalignedTailsMode, CRenderingContext::ScreenToSeq(), ncbi::grid::netcache::search::fields::size, IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), CAlignGlyph::x_ConvertAlnTaillRngToSeqRng(), and CAlignGlyph::x_GetAlnTailRange().

Referenced by CAlignGlyph::DrawPWAlignElem(), and CAlignGlyph::x_DrawTailSequences().

Definition at line 710 of file alignment_glyph.cpp.

References IRender::Color4d(), ctx, COpenRange< Position >::Empty(), CRgbaColor::GetBlue(), CRange_Base::GetFrom(), GetGl(), CRgbaColor::GetGreen(), CRgbaColor::GetRed(), CRenderingContext::GetScale(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), CRenderingContext::IntersectVisible(), CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, IRender::PolygonMode(), IRender::PopMatrix(), IRender::PushMatrix(), IRender::Rectd(), IRender::Scalef(), CRenderingContext::SeqToScreenX(), and CAlignGlyph::x_GetAlnTailRange().

Referenced by CAlignGlyph::x_DrawTailSequences().

Definition at line 733 of file alignment_glyph.cpp.

References IRender::ColorC(), CSeqManip::Complement(), ctx, CSeqUtil::e_Iupacaa, CSeqUtil::e_Iupacna, CBioseq_Handle::eCoding_Iupac, COpenRange< Position >::Empty(), CAlignGlyph::eOne2One, CAlignGlyph::eOne2Three, CAlignGlyph::eThree2One, CSeqTranslator::fDefault, IScoringAlignment::GetAnchor(), IAlnGraphicDataSource::GetBioseqHandle(), CRange_Base::GetFrom(), IAlnGraphicDataSource::GetGenCode(), GetGl(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CRange_Base::GetTo(), CRenderingContext::IntersectVisible(), CBioseq_Handle::IsAa(), CRenderingContext::IsFlippedStrand(), kPWAlignPackLevel, CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignmentConfig::m_SeqFont, CSeqManip::Reverse(), CSeqManip::ReverseComplement(), CRenderingContext::ScreenToSeq(), CRange_Base::SetFrom(), CGenetic_code::SetId(), CRange_Base::SetTo(), swap(), IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), CSeqTranslator::Translate(), CAlignGlyph::x_ConvertAlnTaillRngToSeqRng(), and CAlignGlyph::x_GetAlnTailRange().

Referenced by CAlignGlyph::DrawPWAlignElem().

get all GIs for a given uid this needs a given database where to search for GIs

Parameters

if isIncremental == true, the newly found GIs are appended to gis, not erasing it

Definition at line 1096 of file na_utils.cpp.

References xml::node::begin(), set< Key, Compare >::clear(), CNAUtils::EEDB_Undef, CSeqUtils::ELinkQuery(), ctll::empty(), map_checker< Container >::end(), xml::node::end(), Error(), CNAUtils::EUidsSource_Cache, CNAUtils::EUidsSource_Eutils, CNAUtils::EUidsSource_Mixed, map_checker< Container >::find(), xml::node::get_content(), xml::node::get_name(), xml::document::get_root_node(), CException::GetMsg(), set< Key, Compare >::insert(), xml::node::is_text(), ITERATE, LOG_POST, NCBI_ASSERT, s_EEDBToString(), s_MakeUidtoGiCacheKey(), CNAUtils::sm_UidtoGiCache, and ct::sort().

Referenced by CNAUtils::GetAllGIs(), CNAUtils::x_GetAllGIs(), and CNAUtils::x_NAIdMatchesGI().

get all available NA uids for a given gi.

Definition at line 804 of file na_utils.cpp.

References CStopWatch::AsSmartString(), CSeqUtils::ELinkQuery(), Error(), CTimeSpan::eSSP_Millisecond, first(), CException::GetMsg(), i, info, LOG_POST, CNAUtils::m_SeqDB, CNAUtils::m_SeqIdHandle, s_EEDBToString(), CStopWatch::Start(), CStopWatch::Stop(), and sw.

Referenced by CNAUtils::x_GetNAIds().

get all available NA ids applied to a viewer context for a given gi.

Definition at line 831 of file na_utils.cpp.

References xml::node_set::begin(), context, count, CSeqUtils::ELinkQuery(), xml::node_set::empty(), Error(), CSeqUtils::ESearchQuery(), xml::node::get_content(), xml::document::get_root_node(), CException::GetMsg(), LOG_POST, CNAUtils::m_SeqDB, CNAUtils::m_SeqIdHandle, xml::node::run_xpath_query(), and s_EEDBToString().

Referenced by CNAUtils::x_GetNAIds().

Definition at line 462 of file alignment_smear.cpp.

References CUser_field_Base::CanGetData(), CUser_field_Base::CanGetLabel(), CUser_object_Base::CanGetType(), CUser_field_Base::C_Data::e_Bool, CUser_field_Base::C_Data::e_Int, CAnnotdesc_Base::e_Name, CObject_id_Base::e_Str, CAnnotdesc_Base::e_User, CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::GetLabel(), CAnnotdesc_Base::GetName(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CAnnotdesc_Base::GetUser(), ITERATE, label, s_BlastFieldKey(), s_HistFieldKey(), CObject_id_Base::Which(), CUser_field_Base::C_Data::Which(), and CAnnotdesc_Base::Which().

Referenced by CAlignmentSmear::SeparateStrands().

get all assembly ids associated with a gi.

Retrieve Entrez links for a given NA.

Definition at line 1467 of file na_utils.cpp.

References xml::node_set::begin(), CSeqUtils::CreateIdStr(), data, CSeqUtils::ELinkQuery(), CAnnotMetaData::ELinksStatus_Absent, CAnnotMetaData::ELinksStatus_Present, xml::node_set::end(), Error(), xml::node::find(), xml::node::get_content(), xml::document::get_root_node(), CException::GetMsg(), LOG_POST, NON_CONST_ITERATE, and xml::node::run_xpath_query().

Referenced by CNAUtils::x_GetNAMetaData().

get an id for a given NAA string returns false if no id is found

Definition at line 1262 of file na_utils.cpp.

References map_checker< Container >::end(), Error(), CNAUtils::EUidsSource_Cache, CNAUtils::EUidsSource_Eutils, CNAUtils::EUidsSource_Mixed, map_checker< Container >::find(), CException::GetMsg(), kRetMax, LOG_POST, NCBI_ASSERT, CEutilsClient::Search(), CEutilsClient::SetMaxReturn(), and CNAUtils::sm_NAAtoUidCache.

Referenced by CNAUtils::GetAllGIs(), and CNAUtils::x_SearchNAIds().

Retrieve NA meta data for a list of NA uids.

Definition at line 883 of file na_utils.cpp.

References CStopWatch::AsSmartString(), data, CAnnotMetaData::ELinksStatus_Undef, CNAUtils::EMetaDataSource_Cache, CNAUtils::EMetaDataSource_EmptyRequest, CNAUtils::EMetaDataSource_Eutils, CNAUtils::EMetaDataSource_Mixed, map_checker< Container >::end(), NStr::Equal(), CTimeSpan::eSSP_Millisecond, map_checker< Container >::find(), first(), xml::node::get_content(), i, info, ITERATE, CNAUtils::m_MaxNAMeta, NON_CONST_ITERATE, NStr::NumericToString(), CNAUtils::sm_UidtoMetaDataCache, CStopWatch::Start(), CStopWatch::Stop(), sw, CNAUtils::x_GetNAEntrezLinks(), and CNAUtils::x_ParseNAMetaData().

Referenced by CNAUtils::GetAllNAMetaData(), and CNAUtils::GetNAMetaData().

Definition at line 2564 of file alignment_glyph.cpp.

References CAlignmentConfig::eTails_ShowGlyph, CAlignmentConfig::eTails_ShowSequence, CAlignGlyph::GetBarHeight(), kCompactLabelSpace_h, kCompactTailGlyphLen, kLabelSpace_h, kTailGlyphLen, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignmentConfig::m_UnalignedTailsMode, CRenderingContext::ScreenToSeq(), and CAlignGlyph::x_GetTailLabelWidth().

Referenced by CAlignGlyph::x_UpdateBoundingBox().

Initialize some internal states.

Definition at line 769 of file na_utils.cpp.

References CNAUtils::EEDB_Nucleotide, CNAUtils::EEDB_Protein, eGetId_ForceGi, CSeq_id_Handle::GetGi(), GetId(), kRetMax, CNAUtils::m_BioseqHandle, CNAUtils::m_Gi, CNAUtils::m_MaxNAMeta, CNAUtils::m_Scope, CNAUtils::m_SeqDB, CNAUtils::m_SeqIdHandle, CNAUtils::m_TargetSeq, and ZERO_GI.

Referenced by CNAUtils::CNAUtils().

Definition at line 2604 of file alignment_glyph.cpp.

References CSeq_id::AsFastaString(), eGetId_Canonical, IScoringAlignment::GetAnchor(), GetId(), CRenderingContext::GetScope(), IAlnGraphicDataSource::GetSeqId(), CSeq_id_Handle::GetSeqId(), CSeqUtils::IsVDBAccession(), CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, and CAlignGlyph::m_OrigSeqAlign.

Referenced by CAlignGlyph::GetSignature().

Parse the meta-data xml DocSum.

Definition at line 1317 of file na_utils.cpp.

References data, CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_Seq_table, set< Key, Compare >::end(), NStr::Equal(), set< Key, Compare >::find(), ftable, xml::document::get_root_node(), i, set< Key, Compare >::insert(), ITERATE, kEmptyStr, label, NULL, NStr::Replace(), and CSeq_annot_Base::C_Data::SelectionName().

Referenced by CNAUtils::x_GetNAMetaData().

Definition at line 2214 of file alignment_glyph.cpp.

References abs, IRender::Begin(), color, IRender::Color4d(), IScoringAlignment::CreateSegmentIterator(), IAlnSegmentIterator::eAllSegments, IAlnExplorer::eBackwards, IAlnExplorer::eForward, COpenRange< Position >::Empty(), IRender::End(), IScoringMethod::fBackground, IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), IAlnScoreIterator::GetAttr(), IScoringAlignment::GetBaseWidth(), IAlnScoreIterator::GetFrom(), CRange_Base::GetFrom(), GetGl(), CRenderingContext::GetGlPane(), CRenderingContext::GetScale(), CGlPane::GetScaleY(), IScoringAlignment::GetSeqPosFromAlnPos(), IAlnScoreIterator::GetTo(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), i, CRgbaColor::Interpolate(), IAlnSegment::IsAligned(), IAlnSegment::IsGap(), IAlnSegment::IsIndel(), len, IRender::LineWidth(), CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, SScPix2::m_GapLen, SScPix2::m_GapScore, SScPix2::m_Init, CAlignmentConfig::m_Insertion, SScPix2::m_IntLen, SScPix2::m_IntScore, SScPix2::m_MinScore, CAlignGlyph::m_Score, max(), min(), IRender::PolygonMode(), IRender::PopMatrix(), IRender::PushMatrix(), r(), IRender::Rectd(), row, IRender::Scalef(), CRenderingContext::SeqToScreen(), CRenderingContext::SeqToScreenXInModelUnit(), CRange_Base::SetFrom(), CRange_Base::SetTo(), swap(), and IRender::Vertex2d().

Referenced by CAlignGlyph::DrawPWAlignElem(), and CAlignGlyph::x_DrawMultiAlign().

Definition at line 2046 of file alignment_glyph.cpp.

References IRender::Begin(), color, IRender::ColorC(), IScoringAlignment::CreateSegmentIterator(), IRender::End(), IAlnSegmentIterator::eSkipGaps, IScoringMethod::fBackground, FSetPixMaxCoverage(), IAlnSegment::GetAlnRange(), IScoringAlignment::GetAnchor(), IAlnScoreIterator::GetAttr(), IScoringAlignment::GetBaseWidth(), IAlnScoreIterator::GetFrom(), CRange_Base::GetFrom(), GetGl(), CRenderingContext::GetScale(), IScoringAlignment::GetSeqPosFromAlnPos(), IAlnScoreIterator::GetTo(), COpenRange< Position >::GetToOpen(), i, IAlnSegment::IsGap(), CAlignGlyph::m_AlnMgr, CSeqGlyph::m_Context, CAlignGlyph::m_FadeFactor, SScPix::m_Gap, SScPix::m_MaxCoverage, CAlignGlyph::m_Score, SScPix::m_Score, IRender::PopMatrix(), IRender::PushMatrix(), r(), IRender::Rectd(), row, IRender::Scalef(), CRenderingContext::SeqToScreenX(), swap(), and IRender::Vertex2d().

Referenced by CAlignGlyph::DrawPWAlignElem(), and CAlignGlyph::x_DrawMultiAlign().

Definition at line 2461 of file alignment_glyph.cpp.

References CAlignmentConfig::ePos_Above, CAlignmentConfig::ePos_NoLabel, CAlignGlyph::GetRange(), CRenderingContext::IntersectVisible(), CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignmentConfig::m_LabelPos, CAlignmentConfig::m_ShowLabel, r(), and CRenderingContext::WillLabelFit().

Referenced by CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawPWAlign(), and CAlignGlyph::x_UpdateBoundingBox().

Definition at line 2485 of file alignment_glyph.cpp.

References IAlnGraphicDataSource::ePolyA_No, CAlignmentConfig::eTails_Hide, IAlnGraphicDataSource::HasPolyATail(), CRenderingContext::IsOverviewMode(), kTailGlyphLen, CAlignGlyph::m_AlnMgr, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_SeqAlign, CAlignmentConfig::m_ShowUnalignedTailsForTrans2GenomicAln, CAlignmentConfig::m_UnalignedTailsMode, and CAlignGlyph::x_IsPWAlign().

Referenced by CAlignGlyph::DrawPWAlignElem(), and CAlignGlyph::x_UpdateBoundingBox().

Update the bounding box assuming children's sizes are fixed if any.

Implements CSeqGlyph.

Definition at line 1270 of file alignment_glyph.cpp.

References CLabel::eContent, CLabel::eDefault, CAlignmentConfig::eNormal, CAlignmentConfig::ePos_Above, IScoringAlignment::GetAnchor(), CAlignGlyph::GetBarHeight(), IScoringAlignment::GetBaseWidth(), CRange_Base::GetFrom(), GetGl(), CSeqGlyph::GetHeight(), CLabel::GetLabel(), CSeqGlyph::GetLeft(), GetLength(), COpenRange< Position >::GetLength(), IScoringAlignment::GetNumRows(), CAlignGlyph::GetRange(), CRenderingContext::GetScope(), IAlnGraphicDataSource::GetSeqId(), CAlignGlyph::GetTitle(), IAlnGraphicDataSource::GetUnalignedTails(), CSeqGlyph::GetWidth(), IAlnGraphicDataSource::IsNegativeStrand(), CAlignGlyph::IsSimplified(), kAlignRowSpace, kLabelSpace_h, kLabelSpace_v, label, CAlignGlyph::m_AlnMgr, CAlignmentConfig::m_CompactMode, CAlignGlyph::m_Config, CSeqGlyph::m_Context, CAlignGlyph::m_Intervals, CAlignmentConfig::m_LabelFont, CAlignmentConfig::m_LabelPos, max(), row, CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), CSeqGlyph::SetHeight(), CSeqGlyph::SetLeft(), CSeqGlyph::SetWidth(), IRender::TextHeight(), IRender::TextWidth(), CAlignGlyph::x_CalcIntervals(), CAlignGlyph::x_GetTailWidth(), CAlignGlyph::x_IsPWAlign(), CAlignGlyph::x_ShowLabel(), and CAlignGlyph::x_ShowUnalignedTails().

Definition at line 99 of file nonasn_track_data.hpp.

Definition at line 83 of file nonasn_track_data.hpp.

Definition at line 116 of file utils.hpp.

pointer to the actual alignment information.

Definition at line 217 of file alignment_glyph.hpp.

Referenced by CAlignGlyph::CAlignGlyph(), CAlignGlyph::DrawPWAlignElem(), CAlignGlyph::GetAlignMgr(), CAlignGlyph::GetAlnAnchorPair(), CAlignGlyph::GetHTMLActiveAreas(), CAlignGlyph::GetSignature(), CAlignGlyph::GetTitle(), CAlignGlyph::GetTooltip(), CAlignGlyph::IsNegative(), CAlignGlyph::IsSimplified(), CAlignGlyph::LessBySeqPos(), CAlignGlyph::x_CalcIntervals(), CAlignGlyph::x_ConvertAlnTaillRngToSeqRng(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawGaps(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CAlignGlyph::x_DrawPWAlign(), CAlignGlyph::x_DrawSimplified(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawTailSequences(), CAlignGlyph::x_DrawUnalignedRowSequence(), CAlignGlyph::x_IsPWAlign(), CAlignGlyph::x_IsSRA(), CAlignGlyph::x_RenderAveragableScores(), CAlignGlyph::x_RenderNonAveragableScores(), CAlignGlyph::x_ShowUnalignedTails(), and CAlignGlyph::x_UpdateBoundingBox().

annot type, such as ftable, seq-table, align

Definition at line 70 of file annot_info.hpp.

Definition at line 228 of file alignment_glyph.hpp.

Referenced by CAlignGlyph::DrawPWAlignElem(), CAlignGlyph::GetBarHeight(), CAlignGlyph::SetConfig(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawGaps(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CAlignGlyph::x_DrawPWAlign(), CAlignGlyph::x_DrawStrandIndicators(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawTailSequences(), CAlignGlyph::x_DrawUnalignedRowSequence(), CAlignGlyph::x_GetTailLabelWidth(), CAlignGlyph::x_GetTailWidth(), CAlignGlyph::x_RenderAveragableScores(), CAlignGlyph::x_ShowLabel(), CAlignGlyph::x_ShowUnalignedTails(), and CAlignGlyph::x_UpdateBoundingBox().

data indentifier.

Different data source may have different data id format. For example, for SADB, it will be NA accession. For ID or other user local data, it will be just annotation name. And for cSRA, it will be just cSRA file path.

Definition at line 66 of file annot_info.hpp.

data source such as ID, SADB, cSRA and SRA

Definition at line 67 of file annot_info.hpp.

Definition at line 241 of file alignment_glyph.hpp.

Referenced by CAlignGlyph::ApplyFading(), CAlignGlyph::DrawPWAlignElem(), CAlignGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawGaps(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CAlignGlyph::x_DrawNoScoreAlign(), CAlignGlyph::x_DrawPWAlign(), CAlignGlyph::x_DrawSimplified(), CAlignGlyph::x_DrawStrandIndicators(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawTailSequences(), CAlignGlyph::x_DrawUnalignedBar(), CAlignGlyph::x_GetOverrideColor(), CAlignGlyph::x_RenderAveragableScores(), and CAlignGlyph::x_RenderNonAveragableScores().

Definition at line 100 of file utils.hpp.

annotation id. It may only apply to NAs from SADB

Definition at line 101 of file annot_info.hpp.

The target sequence associating with the NAAs.

This is optional. If it is set, we only look at the NAAs associated with the target sequence. If it is not set, all requested/found NAAs will be returned. However, the target sequence may be ignored for some cases, such as searching meta-data for a speicfic NA.

Definition at line 305 of file na_utils.hpp.

Referenced by CNAUtils::GetNATrackInfo(), CNAUtils::x_Init(), and CNAUtils::x_NAIdMatchesGI().

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