├── .dockerignore ├── .gitignore ├── .npmignore ├── .vscode ├── launch.json ├── settings.json └── tasks.json ├── Dockerfile ├── README.md ├── assets ├── a.svg ├── c.svg ├── g.svg └── t.svg ├── bin └── biocad ├── biocad ├── BiocadApp.ts ├── BiocadProject.ts ├── BiocadTerms.ts ├── DropOverlay.ts ├── DropReceiver.ts ├── Headless.ts ├── IdentifiedChain.ts ├── InitUData.ts ├── ProjectTabs.ts ├── Repository.ts ├── browser.ts ├── cad │ ├── DepictionTreeView.ts │ ├── ImageRenderer.ts │ ├── LayoutThumbnail.ts │ ├── RelayoutDialog.ts │ ├── RenderContext.ts │ ├── SVGDefs.ts │ ├── ScrollbarWidget.ts │ ├── createInteraction.ts │ ├── detail-preset │ │ ├── DetailPreset.ts │ │ ├── DetailPreset1.ts │ │ ├── DetailPreset2.ts │ │ ├── DetailPreset5.ts │ │ └── levelToPreset.ts │ ├── drag-op │ │ ├── DOp.ts │ │ ├── DOpEnterParent.ts │ │ ├── DOpEnterSibling.ts │ │ ├── DOpEnterWorkspace.ts │ │ ├── DOpMoveInBackbone.ts │ │ ├── DOpMoveInParent.ts │ │ ├── DOpMoveInWorkspace.ts │ │ └── DOpTwoBlackboxesMakeConstraint.ts │ ├── drawDegradationBin.ts │ ├── layout-editor │ │ ├── LayoutEditor.ts │ │ ├── LayoutEditorContextMenu.ts │ │ ├── LayoutEditorDebugLog.ts │ │ ├── LayoutEditorOverlay.ts │ │ ├── LayoutEditorToolbar.ts │ │ └── LayoutEditorView.ts │ ├── layout-instruction │ │ ├── Instruction.ts │ │ ├── InstructionSet.ts │ │ ├── MarginInstruction.ts │ │ ├── PinInstruction.ts │ │ ├── ReplaceInstruction.ts │ │ └── WhitelistInstruction.ts │ ├── layout │ │ ├── BackboneDepiction.ts │ │ ├── CircularBackboneDepiction.ts │ │ ├── ComponentDepiction.ts │ │ ├── ComponentDisplayList.ts │ │ ├── Depiction.ts │ │ ├── DepictionPOD.ts │ │ ├── DepictionRefByChain.ts │ │ ├── DepictionRefByUid.ts │ │ ├── FeatureLocationDepiction.ts │ │ ├── InteractionDepiction.ts │ │ ├── LabelDepiction.ts │ │ ├── Layout.ts │ │ ├── LayoutPOD.ts │ │ ├── LocationableDepiction.ts │ │ ├── MappingDepiction.ts │ │ └── configurator │ │ │ ├── configurate.ts │ │ │ ├── configurateBackbone.ts │ │ │ ├── configurateComponent.ts │ │ │ ├── configurateFeatureLocation.ts │ │ │ ├── configurateLabel.ts │ │ │ └── strategy │ │ │ ├── backboneStrategy.ts │ │ │ ├── binPack.ts │ │ │ ├── binPackStrategy.ts │ │ │ ├── circularStrategy.ts │ │ │ └── tileHorizontalStrategy.ts │ ├── renderHandles.ts │ └── renderPlasmid.ts ├── dialog │ ├── BrowseSBHDialog.ts │ ├── CreateComponentDialog.ts │ ├── InspectComponentDialog.ts │ ├── InspectComponentThumbnailView.ts │ ├── OntologyTermSelectorDialog.ts │ ├── PopupMessageDialog.ts │ └── TestDialog.ts ├── droppable │ ├── Droppable.ts │ └── SBOLDroppable.ts ├── glyph │ └── Glyph.ts ├── mode │ ├── circuit │ │ ├── CircuitMode.ts │ │ ├── CircuitView.ts │ │ ├── CircuitViewLeftSidebar.ts │ │ ├── CircuitViewRightSidebar.ts │ │ ├── Inspector.ts │ │ └── PartsListView.ts │ ├── headless │ │ ├── HeadlessMode.ts │ │ └── HeadlessView.ts │ ├── library │ │ ├── LibraryMode.ts │ │ ├── LibraryTree.ts │ │ ├── LibraryView.ts │ │ ├── LibraryViewLeftSidebar.ts │ │ ├── LibraryViewPartScroller.ts │ │ ├── PartSummaryView.ts │ │ └── SVGScrollerWidget.ts │ ├── loadsave │ │ ├── LoadSaveMode.ts │ │ └── LoadSaveView.ts │ ├── repository │ │ ├── RepoCollectionMembersView.ts │ │ ├── RepoComponentSeqView.ts │ │ ├── RepoComponentVisualView.ts │ │ ├── RepoMode.ts │ │ ├── RepoTree.ts │ │ ├── RepoView.ts │ │ └── RepoViewLeftSidebar.ts │ ├── sequence │ │ ├── ComponentBrowser.ts │ │ ├── CreateAnnotationDialog.ts │ │ ├── IdentifiedLinearRange.ts │ │ ├── SequenceAnalyzer.ts │ │ ├── SequenceEditor.ts │ │ ├── SequenceEditorBody.ts │ │ ├── SequenceEditorContextMenu.ts │ │ ├── SequenceEditorLine.ts │ │ ├── SequenceEditorOverlay.ts │ │ ├── SequenceEditorRenderState.ts │ │ ├── SequenceEditorToolbar.ts │ │ ├── SequenceMode.ts │ │ ├── SequenceTransform.ts │ │ ├── SequenceView.ts │ │ ├── SequenceViewSidebar.ts │ │ ├── SequenceWizard.ts │ │ ├── renderAnnotations.ts │ │ ├── renderDefs.ts │ │ ├── renderElements.ts │ │ └── renderLineNumbers.ts │ ├── setup │ │ ├── EditURIPrefixDialog.ts │ │ ├── RemoveURIPrefixDialog.ts │ │ ├── SetupCurrentDocumentView.ts │ │ ├── SetupMode.ts │ │ └── SetupViewSidebar.ts │ ├── simulator │ │ ├── SimulatorMode.ts │ │ └── SimulatorView.ts │ └── source │ │ ├── EncodingSelector.ts │ │ ├── SourceMode.ts │ │ └── SourceView.ts ├── projectbar │ └── BiocadProjectbar.ts ├── property │ ├── PropertyAccessor.ts │ ├── PropertyAccessorStrand.ts │ ├── PropertyAccessorString.ts │ ├── PropertyAccessorURI.ts │ ├── PropertyAccessorURISet.ts │ ├── PropertyEditor.ts │ ├── PropertyEditorCombo.ts │ ├── PropertyEditorDebug.ts │ ├── PropertyEditorInteractionParticipants.ts │ ├── PropertyEditorOneline.ts │ ├── PropertyEditorSubComponent.ts │ └── PropertyEditorTermSet.ts ├── stateless-ui │ ├── renderCDRoleEditor.ts │ ├── renderCDStrandChooser.ts │ └── renderCDTypeChooser.ts ├── topbar │ └── BiocadTopbar.ts ├── util │ ├── SBOLConverterValidator.ts │ ├── copySBOL.ts │ ├── drawArrow.ts │ ├── generateTitle.ts │ ├── getNameFromRole.ts │ ├── measureText.ts │ ├── nameToDisplayId.ts │ ├── separateInteractionParticipations.ts │ └── sortByDepth.ts ├── version.ts └── view │ ├── BrowseSBHView.ts │ ├── CytoscapeRDFWidget.ts │ └── OntologyTreeView.ts ├── cli ├── dom.js └── main.ts ├── configs ├── default.ts └── headless.ts ├── custom.d.ts ├── data ├── cdTypes.ts ├── colors.ts ├── describeSOUri.ts ├── detailLevels.ts ├── gene-ontology.js ├── palettes.ts ├── parts.ts ├── roles.ts ├── sequence-ontology.js ├── soTrie.js └── systems-biology-ontology.js ├── deploy.sh ├── glyph_definitions ├── Aptamer.svg ├── AssemblyScar.svg ├── BluntRestrictionSite.svg ├── CDS.svg ├── ChromosomalLocus3.svg ├── ChromosomalLocus5.svg ├── CircularPlasmid3.svg ├── CircularPlasmid5.svg ├── Composite.svg ├── DNACleavageSite.svg ├── DNALocation.svg ├── DNAStabilityElement.svg ├── DNAStopSite.svg ├── DoubleStrandedNucleicAcid.svg ├── EngineeredRegion.svg ├── Insulator.svg ├── Macromolecule.svg ├── NoGlyph.svg ├── NonCodingRNA.svg ├── NucleicAcidOneStrand.svg ├── OmittedDetail.svg ├── Operator.svg ├── OriginOfReplication.svg ├── OriginOfTransfer.svg ├── OverhangSite3.svg ├── OverhangSite5.svg ├── PolyASite.svg ├── PolypeptideRegion.svg ├── Primer.svg ├── Promoter.svg ├── Protein.svg ├── ProteinCleavageSite.svg ├── ProteinLocation.svg ├── ProteinLocationAlternate.svg ├── ProteinStabilityElement.svg ├── RNACleavageSite.svg ├── RNALocation.svg ├── RNALocationAlternate.svg ├── RNAStabilityElement.svg ├── RNAStopSite.svg ├── RecombinationSite.svg ├── RibosomeEntrySite.svg ├── Signature.svg ├── SimpleChemical.svg ├── SingleStrandedNucleicAcid.svg ├── Spacer.svg ├── SpecificRecombinationSite.svg ├── StickyEndRestrictionEnzymeCleavageSite3.svg ├── StickyEndRestrictionEnzymeCleavageSite5.svg ├── Terminator.svg └── Unspecified.svg ├── index.html ├── index.ts ├── less.txt ├── less ├── balloon.less ├── biocad-circuit-view-minimap.less ├── biocad-palette.less ├── biocad-sequence-view.less ├── biocad-setup.less ├── biocad.less └── pictureframe.less ├── 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