SharedGCContentModel

Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Provided by the gccontent plugin. View source.

Members a composed model contributes are listed here too, so these tables are the whole surface.

Properties

Member	Description	Defined by
configuration `configuration: ConfigurationReference(configSchema)`		SharedGCContentModel
type `type: types.literal('LinearWiggleDisplay')`		LinearWiggleDisplay
id `id: ElementId`		BaseDisplay
layout `layout: types.stripDefault(types.frozen<S[]>(), [])`		TreeSidebarMixin
clusterTree `clusterTree: types.stripDefault(types.maybe(types.string), undefined)`		TreeSidebarMixin
clusterProvenance `clusterProvenance: types.stripDefault( types.maybe(types.frozen<ClusterProvenance>()), undefined, )`	What `clusterTree` was computed from — the locus and the settings. Set only for a tree this app computed; a supplied phylogeny (maf's `.nh`) leaves it undefined. Persisted with the tree so it survives a session snapshot, which is the case that most needs it: a shared link otherwise hands over a dendrogram with no way to learn its locus.	TreeSidebarMixin
subtreeFilter `subtreeFilter: types.stripDefault( types.maybe(types.array(types.string)), undefined, )`		TreeSidebarMixin
runClustering `runClustering: types.maybe(types.boolean)`	Transient declarative launch spec, the same idea as `LinearGenomeView`'s `init`: a session or config sets this true and the real clustering RPC runs once automatically, with no dialog, as soon as the display reports itself ready. `setupRunClusteringAutorun` clears it afterwards, so a saved session never re-triggers. Lives here rather than on each display because it is the trigger for a run whose output — `clusterTree`, `clusterProvenance`, `layout` — is this mixin's state. Three displays declared it identically, each with its own wrapper module that existed to code-split the clustering code and, along the way, hand-wrote the same six-member duck type of the display. Splitting inside the `run` callback does the same job and loads on a run rather than on every attach. What each run actually is stays per display, in that callback.	TreeSidebarMixin
clusterRegion `clusterRegion: types.maybe(types.string)`	Where that run reads from, as a locstring (whitespace-separated for several). Clustering is region-scoped, so running it over the visible window feeds the estimator whatever happens to be on screen; naming the locus instead lets a session cluster on the signal and then show it against its context — otherwise a zoom the user has to perform in the right order. Cleared with `runClustering`, since it is that flag's argument and a locus left standing describes a run that is not coming.	TreeSidebarMixin
sortRowsBy `sortRowsBy: types.maybe(types.frozen<RowSortSpec>())`	Transient declarative launch spec, the same idea as `runClustering`: set `{refName, pos}` to order the rows once by the value each carries at that genomic column — the session-expressible form of the right-click "Sort rows by ... here". `setupRowSortAutorun` applies it once the region containing it has loaded and then clears it, so the resulting `layout` persists but a saved session never re-sorts. Clustering orders rows by the whole region in view, and `layout` states an order outright. This spec ranks rows at one position, so a figure can open a cohort ranked at a candidate locus with the surrounding context still on screen. Each display defines the value at the column in its `sortRows` callback.	TreeSidebarMixin

Volatiles

Member	Description	Defined by
error `error: undefined as unknown`		BaseDisplay
statusMessage `statusMessage: undefined as string \| undefined`		BaseDisplay
statusProgress `statusProgress: undefined as number \| undefined`	determinate progress fraction [0,1] for the current status, or undefined when the in-flight phase is indeterminate. Set alongside `statusMessage` by `setStatusMessage`; a display that never shows a bar simply leaves it undefined.	BaseDisplay
scrollTop `scrollTop: 0`		TrackHeightMixin
loadedRegions `loadedRegions: regionDataMap<LoadedRegion>('loadedRegions')`	The per-region store, keyed by `displayedRegionIndex`: what a fetch asked for (the span), what it was issued under (`fetchInputs`) and what it brought back (`payload`), written as one record by `ctx.commitRegion`. A display's own `rpcDataMap` was the payload column of this map held separately, and every hook that existed to keep the two in step — `clearDisplaySpecificData`, a `regionHasData` that answered `rpcDataMap.has(idx)`, a hand-rolled prune — was that separation's cost. A display reads the payload back through `regionPayloads`.	MultiRegionDisplayMixin
forceLoadTrack `forceLoadTrack: false`	The force-load button's track-wide approval. Volatile so it never reaches a saved session; the `forceLoad` config slot is the durable form.	RegionTooLargeMixin
byteEstimate `byteEstimate: undefined as ByteEstimate \| undefined`	The last byte measurement: bytes, the span they were taken at, and whether zooming has been shown not to shrink them. Survives `clearAllRpcData`; dropped on chromosome navigation and on a tier swap.	RegionTooLargeMixin
gateMeasuredViewportKey `gateMeasuredViewportKey: undefined as unknown`	The `gateViewport` key the gate last asked the adapter about, on either axis — the viewport AND the settings it asked under. Separate from `byteEstimate` because a density refusal measures no bytes.	RegionTooLargeMixin
canvasDrawn `canvasDrawn: false`	flips true on first paint; read by test selectors to detect render	RenderLifecycleMixin
paintCount `paintCount: 0`	bumped after every frame the backend painted, so a consumer that reads this display's canvas — the circular view's ring, which copies the strip into a texture — knows when the pixels moved	RenderLifecycleMixin
currentRenderingBackend `currentRenderingBackend: undefined`	current backend reference, updated on context-loss recovery. Typed `unknown` (not generic `B`) on purpose: this mixin is composed by every display via a non-generic factory, so the per-display backend type `B` isn't known here — it's supplied at `attachRenderingBackend<B>` and narrowed with `as B` inside the autoruns. Don't "fix" the cast.	RenderLifecycleMixin
renderTick `renderTick: 0`	counter the render autorun observes; bumped to force a re-render	RenderLifecycleMixin
autorunsInstalled `autorunsInstalled: false`	guards attachRenderingBackend so the autorun pair spawns once per instance	RenderLifecycleMixin
renderError `renderError: undefined`	the render-backend (GPU/Canvas2D init or context-loss) error, or undefined. Single source of truth for the render-error terminal state: `useRenderingBackend` writes it from the canvas-init mechanism so the model — not React-local hook state — owns every terminal state. Read by `displayPhase` (whose `renderError` term outranks `loading`, suppressing the scrim) and by `DisplayChrome` (shows the retry overlay).	RenderLifecycleMixin
activeSignal `activeSignal: undefined as AbortSignal \| undefined`	signal of the in-flight fetch, or undefined when idle	FetchMixin
fetchGeneration `fetchGeneration: 0`	bumps at every fetch end; autoruns read it to re-evaluate, and it doubles as the staleness epoch inside runFetch	FetchMixin
reloadCounter `reloadCounter: 0`	Bumped by `reload()` and read unconditionally by the fetch autoruns, so a user retry re-runs the body even where nothing else moved — after an error every other fetch input is unchanged. It is also the half that survives a `reload()` override that forgets to invalidate, which is the dead Retry button `makeRetryContractCheck` reports. Declared here because this is the one mixin every fetch foundation composes, the same argument that put `fetchInert` below; the comparative family carried its own until ADR-105.	FetchMixin
statusWindow `statusWindow: createStatusWindow(writeStatus(self))`	This display's status field, and the only thing that writes it: one throttle window, one slot per concurrent operation, so N parallel per-region fetches thin to one stream between them rather than N and a second operation cannot end the first one's label (ADR-081). Lent whole to `createAbortRotation` by a display that also runs a bare-autorun fetch — see `StatusReporter`.	FetchMixin
fetchCanceled `fetchCanceled: false`	true after the user explicitly cancels a load (the loading overlay's cancel button → `cancelFetchByUser`). A durable, blocking state — unlike `cancelFetch`, it does not retrigger the fetch autoruns — so the load stays stopped until the user retries (`reload`) or the viewport changes. Any new fetch clears it (`runFetch` resets it at the start).	FetchMixin
fetchRotation `fetchRotation: createAbortRotation(self, { statusWindow: self.statusWindow, })`	The latest-wins machine this mixin is a wrapper around, and not a second one: `createAbortRotation` owns abort rotation, the `isCurrent` guard, the status slot and the supersede-versus-end rule (ADR-080, ADR-081), for every fetch in the codebase that has one. `runFetch` adds the observable bookkeeping a display needs on top — `isLoading`, `error`, `fetchGeneration`, `fetchCanceled` — and nothing else. It was two implementations of that machine until 2026-08-20, which is how they came to disagree about whether a completed fetch releases its signal. A display's primary fetch is this wrapper; a second concurrent fetch on the same node holds a rotation of its own, which is why the primitive is the thing that exists and this is the thing built on it (ADR-054 §1, the one section ADR-105 keeps). It is lent this display's `statusWindow`, so the fetch takes a slot on the one field rather than opening a second window over it — the whole point of `StatusReporter`.	FetchMixin
storedHoveredFeature `storedHoveredFeature: undefined as T \| undefined`		StoredHoverMixin
dismissedLegendSections `dismissedLegendSections: [] as string[]`	Ids of the scales whose section the reader closed on its own; cleared when the whole legend is shown again. Volatile where `showLegend` is config: which sections a reader collapsed in one sitting is not how the track is configured.	LegendMixin
hoveredTreeNode `hoveredTreeNode: undefined as HoveredTreeNode \| undefined`		TreeSidebarMixin
treeCanvas `treeCanvas: null as HTMLCanvasElement \| null`		TreeSidebarMixin
mouseoverCanvas `mouseoverCanvas: null as HTMLCanvasElement \| null`		TreeSidebarMixin
contextMenuInfo `contextMenuInfo: undefined as Info \| undefined`		ContextMenuMixin

Getters

Member	Description	Defined by
windowSize `number`		SharedGCContentModel
windowDelta `number`		SharedGCContentModel
gcMode `"content" \| "skew"`		SharedGCContentModel
adapterConfig `{…} \| { windowSize: number; windowDelta: number; gcMode: string; type: string; sequenceAdapter: { type: string; }; }`	The parent track's adapter with the display's GC parameters applied, wrapped in a `GCContentAdapter` where the track names a bare sequence adapter — see `gcAdapterConfig`.	SharedGCContentModel
defaultScoreDomain `[number \| undefined, number \| undefined]`	Overrides ScoreScaleMixin's autoscale-both-ends default. GC content is a fraction of the bases in a window, so [0,1] is the quantity's own range and pins the axis across loci. Skew is deliberately left autoscaling. Its range is [-1,1] and fixing it there would be just as correct, and useless: real skew sits within roughly ±0.3, so a [-1,1] axis squashes the sign flip at the replication origin — the entire thing the track is read for — into a flat line. Bounded and worth pinning are two different properties.	SharedGCContentModel
isDensityMode `boolean`		LinearWiggleDisplay
colorSetting `ColorSetting`	The `color` object as written, `value` undefined while nothing names a colour and the layout decides (`effectiveColor`).	LinearWiggleDisplay
colorScaleChoices `string[]`	The scales this display's colour paints, for the Edit as JSON box.	LinearWiggleDisplay
colorMembers `string[]`	The members this display's colour object declares, for the Edit as JSON box.	LinearWiggleDisplay
channelSpecExamples `{ spec: string; description: string; }[]`		LinearWiggleDisplay
facet `FacetSetting \| undefined`	The `facet` object as written, or undefined while every source shares one plot. `source` is the only field the config admits here.	LinearWiggleDisplay
isFaceted `boolean`	Whether each source takes a row of its own, which is the whole of what the facet decides here: the tree sidebar, the row labels, the separators, the clustering menu and the row-order sort all hang off it.	LinearWiggleDisplay
rowDomain `string[]`	`TreeSidebarMixin`'s hook, overridden: this display declares no `domain` slot of its own, because the row order is the facet's — one word for one idea, and `domain` on a wiggle display is already the score axis.	LinearWiggleDisplay
isOverlay `boolean`	Every source in one plot box. The complement of the facet, named for what is drawn rather than for the setting that is off.	LinearWiggleDisplay
sourcesWithoutLayout `SourceInfo[]`		LinearWiggleDisplay
editableSources `SourceInfo[]`		LinearWiggleDisplay
clusterableSources `SourceInfo[]`	The rows a clustering run acts on: `editableSources` narrowed to the focused clade, and deliberately NOT the decorated `sources` below — `clusteredCladeLayout` writes what it is handed into `layout`, where a synthesized palette color has no business. Under no subtree filter this is `editableSources` itself.	LinearWiggleDisplay
sharesOnePlot `boolean`	Whether several plots share one box, which is the one thing the layout decides about colour: overlaid sources need a palette entry each to be told apart, where a lone plot has nothing to be told apart from and is the pos/neg picture a quantitative track has always drawn.	LinearWiggleDisplay
effectiveColor `ColorSetting`	The colour actually painted: what the config says, or the picture the layout asks for where it says nothing. A resolved getter rather than a `defaultValue`, because the default moves with the layout and a slot default cannot.	LinearWiggleDisplay
colorEncoding `string \| FieldColorEncoding \| undefined`	`effectiveColor` as it paints, through the one resolver every display's colour object goes through.	LinearWiggleDisplay
notices `string[]`	What `colorSetting`'s slots say together that it cannot paint as written, for the corner notice.	LinearWiggleDisplay
wiggleColor `ResolvedWiggleColor`	`colorEncoding` as the encoder and both backends take it.	LinearWiggleDisplay
legendColor `string`	The one colour the circular view's key names this track by (`CircularLegendSource`), which a ring of this display answers where it draws no ramp. The positive side, which is the whole plot wherever nothing parts.	LinearWiggleDisplay
channelSpec `ChannelSpec`	`ChannelSpecHost`'s hook: the two settings the Edit as JSON box writes, as written rather than as resolved, so a round trip through the box changes nothing on its own.	LinearWiggleDisplay
sources `SourceInfo[]`		LinearWiggleDisplay
scoreRuleValues `number[]`	Overrides WiggleCommonMixin's empty base, so the axis reaches a rule of `scales.y.rules` even where the visible data does not. Empty in density, where no rule is drawn: the domain is spent on the colour ramp there, so widening it stretches the ramp over a range nothing on screen reaches.	LinearWiggleDisplay
numSources `number`		LinearWiggleDisplay
autoscaleSourceNames `Set<string>`		LinearWiggleDisplay
legendItems `LegendItem[]`	The source key's rows — one per (group, color) pair, colors resolved. `colorScales` and `overlayLegendApplies` both read this one list, so what is drawn and what was counted before deciding to draw cannot disagree. See `buildLegendItems`.	LinearWiggleDisplay
effectiveRowHeight `number`	Resolved per-row height. This display is always fit-to-display-height — there is no pinned-height setting and so no `rowHeight` sentinel to resolve — but it carries the same name every row display exposes its resolved height under (see agent-docs/reference/ROW_HEIGHT_AND_FIT), which is also what tree-sidebar's `TreeDrawingModel` reads.	LinearWiggleDisplay
numRows `number`	Rows actually drawn: overlay collapses every source onto one shared plot. Read by the render state and by everything that repeats itself per row (scalebars, cross hatches), so they can't disagree about how many rows exist.	LinearWiggleDisplay
plotGeometry `{ yTop: number; plotHeight: number; numRows: number; tickHeight: number; }`	One row takes the scalebar-label gutter at top and bottom, so its end labels are never clipped; a stack of rows gives that up, because the axis is drawn per row and maximum density is the point. `ticks`, the render height, the on-screen canvas and the SVG clip all read this, so a tick stays on the data it labels.	LinearWiggleDisplay
scoreRampApplies `boolean`	Only density spends color on the score, and only when every row shares the one ramp: a source with its own color is drawn on its own pos side (see buildSourceRenderData), so a single bar would describe none of them.	LinearWiggleDisplay
valueScales `ValueScale[]`	The one scale every row shares, ruling a band per row stacked down the track, past the dendrogram where one is shown. Density rows each in their own colour map the scale to colour rather than to y, so they rule no band and the chrome captions the domain instead; under the one ramp the ramp is the key and carries the domain itself.	LinearWiggleDisplay
showRowSeparators `boolean`		LinearWiggleDisplay
overlayLegendApplies `boolean`	Whether the source color key applies at all. Gates the menu checkbox, which has to stay visible while the legend is toggled off. Four questions in order, each with its own guard below: 1. Is there anything to key? One source names itself by the track name. 2. Does anything ELSE on the frame name the colors? Overlay collapses every source onto one plot, so nothing does and the key is the only identification there has ever been — but it still has to pass (3): overlay's row palette is `set1`, which wraps every nine sources (`sourcesLogic.ts`), so 40 ungrouped overlay rows would draw a 40-row key in nine repeating colors. A multi-row track names its rows beside them — but only while they carry text (`rowLabelsCarryText`, asked of the drawing side rather than restated) AND is drawing them at all — `showRowLabels` off means nothing beside the rows names anything, so the key is once again the only identification there is. Below that `SvgRowLabels` drops to an unlabelled swatch, and a per-cell density track at 0.14 px a row is then a stripe of nine colors with nothing saying what any of them is; that is the case this was widened for ("we need to make it so density can show legend also ideally because the left side labels are too small to see"). `showTree` is deliberately no part of this: the labels are `WiggleRowLabels`' own and draw whether or not a dendrogram does, so reading it here drew a key restating labels still on screen. 3. Is the key worth its rows? Short enough to read, and made of more than one color — both `legendIsReadable`, shared with the other display that has to decide. Asked of `legendItems`, the very list that gets drawn, so a key can't be counted in one form and rendered in another. Every mode answers it, overlay included.	LinearWiggleDisplay
thresholdColorScale `ColorScale \| undefined`	The key a threshold with a declared cut draws: one row per interval, labelled by the span it covers. A threshold cutting at the `origin` draws none, because the axis already shows where the origin is and a `< 0` / `≥ 0` key on every bigWig says nothing a reader did not ask for. Density draws none either: there the ramp is the key.	LinearWiggleDisplay
prefersOffset `boolean`	Offset the track label above the plot so the left y-axis stays pinned to the content edge instead of dodging right of the label, and so a stack of rows is not hidden behind it. One density plot draws no left axis (just a top score legend), so there let the label overlap.	LinearWiggleDisplay
colorScales `ColorScale[]`	`LegendMixin`'s hook: the density ramp where one describes every row, then the source key where it is worth its rows. A row's `value` is the group or subtrack `focusLegendEntry` narrows to.	LinearWiggleDisplay
hierarchy `ClusterHierarchyNode \| undefined`	The positioned dendrogram, or undefined in an overlay mode: overlay collapses every source onto one row, so a tree spreading its leaves over the full height would align to nothing. This is the single gate — the on-screen sidebar, the SVG export, `spatialIndex` (subtree hover), and `treeSidebarRightEdge` (the tooltip/crosshair dead zone the sidebar reserves) all read it, so none of them can keep drawing or reserving space on their own. A subtree filter set in a row mode still applies and is still clearable from the track menu and WiggleHint.	LinearWiggleDisplay
spatialIndex `TreeSpatialIndex \| undefined`		LinearWiggleDisplay
parentTrack `AbstractTrackModel`		BaseDisplay
RenderingComponent `FC<…>`		BaseDisplay
DisplayBlurb `FC<{ model: ModelInstanceTypeProps<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; type: ISimpleType<string>; }> & { ...; } & { ...; } & IStateTreeNode<...>; }> \| null`		BaseDisplay
isMinimized `boolean`	Returns true if the parent track is minimized. Used to skip expensive operations like autoruns when track is not visible.	BaseDisplay
hoveredFeature `unknown`	Overridable hook (default `undefined`): what the pointer is currently over, for readers outside the display. `LinearGenomeViewContainer` publishes it to `session.hovered`, the view-wide "what is the user pointing at" channel a plugin can subscribe to. Declared here because a cross-display consumer can only read a name the base declares — the same reason `FetchMixin.fetchInert` is a hook rather than a getter each display invents. The container used to read `featureUnderMouse`, which only the wiggle, alignments and Manhattan families spelled that way — canvas said `hoveredFeature`, variants `hoveredGenotype` — so the channel carried a hover from a third of the display types and nothing said which. It also asked only `displays[0]` of each track. `unknown` because the payload genuinely differs — a read, a wiggle bin, a SNP, a genotype cell — and `session.hovered` is typed to match ("can be anything; code that wants to deal with this should examine it"). Narrow it in the override.	BaseDisplay
featureNoun `string`	Overridable hook (default `'feature'`): the SINGULAR word for one of the things this display draws, as a menu row or a chip says it — "Hide this read", "Showing 3 variants". Declared here for the same reason as `hoveredFeature` above: it is read across the display boundary, by chrome that has no idea which display it is drawing for (`SoloSelectionChip`, alignments' group-label overlay), and a name only the base declares is a name every such consumer can rely on. Two displays declared it independently and one of those declarations WAS this default. A control keeps the generic word; content takes this one. "Variant height" reads as a different setting from "Feature height" when it is the same one, so the shared menus stay on "feature" however the display answers here, and the noun varies where it names what the user is looking at — "Showing 3 variants", "Hide this read". A display drawing something the generic word already fits is right to leave this alone. Distinct from the per-hit noun a context menu takes off the clicked item's own `type` ("mRNA", "gene"); that names one annotation, this names what the track holds. The hit noun falls back to this.	BaseDisplay
featureWidgetType `{ type: string; id: string; }`	The widget `openFeatureWidget` opens for one of this display's features. Displays may override it. The default is the generic feature widget, for displays drawing plain features. Displays whose features are a specific kind (a read, a variant, a synteny block) override it, including the `id`: two displays naming one id share the drawer panel, which suits two displays showing the same kind of feature.	BaseDisplay
height `number`		TrackHeightMixin
resizing `boolean`	True for the duration of a height drag on this track, whichever handle is running it. A display whose row geometry is a function of the track height restretches every row per animation frame, and can use this to sit an expensive per-frame layer out of the drag (MAF's dense per-base letter overlay is a Canvas2D pass that scales with rows x columns). The flag itself is the track's (`BaseTrackModel`), so the view brackets a drag without needing the active display to have opted into this mixin. This getter reads it so that a display that did opt in has `self.resizing`.	TrackHeightMixin
scrollContentHeight `number`	Overridable hook: the height of the content that scrolls, in px.	TrackHeightMixin
scrollViewportHeight `number`	Overridable hook: the height of the window it scrolls behind, in px.	TrackHeightMixin
scrollableHeight `number`	How far the content scrolls. A sub-pixel overflow is 0: a fit mode that divides the viewport across n rows multiplies back to a few ULPs over it, and an extent of 1e-14px still draws a scrollbar and holds the wheel away from the page.	TrackHeightMixin
host `RegionHost`	The containing LinearGenomeView, typed once for every display in this family — see `containingHost` for the cast it owns and why both foundations still declare the name.	MultiRegionDisplayMixin
canvasWidthPx `number`	The CSS width of this display's on-screen canvas, in px — and the `canvasWidth` its `renderState` must carry, since the two have to agree or the bp→px mapping is scaled against a box it doesn't fill. `trackWidthPx`, not `view.width`: `TrackRenderingContainer` insets the rendering component by the 2px track outline under `contain: strict`, so a `view.width`-wide canvas overhangs its own container and the browser clips the overhang away. It renders almost identically, which is why MAF drifted onto `view.width` uncaught. A getter rather than a note on each display, because the choice was being made by copying a neighbour out of four plausible view getters — `width` (the viewport), this one, and `totalWidthPx` / `totalWidthPxWithoutBorders` (the content width, which the global family's heatmaps legitimately want: a different question, not a different answer). `no-restricted-syntax` bans the underlying read everywhere but this line, since a second spelling agrees until it doesn't. SVG export is the one exception: the export shell has no outline, so `renderSvg` overrides `canvasWidth` with the shell's own width (see `LgvSvgBodyProps`).	MultiRegionDisplayMixin
settledSubPixelBinBp `number`	Genomic bp one cell of a per-base pass stands for at the settled zoom: `subPixelBinBp` off the host's debounced `coarseBpPerPx`, and 1 until the view initializes. A per-base encode or fetch reads this rather than the live zoom so a wheel tick does not redo every region.	MultiRegionDisplayMixin
canRender `boolean`	Overrides `RenderLifecycleMixin`'s default-true hook with the LGV precondition both foundations share — see `foundationCanRender`.	MultiRegionDisplayMixin
rendersCanvas `boolean`	Fills `RenderLifecycleMixin`'s hook off `fetchInert`, as `GlobalFetchMixin` does: a display that will never fetch here shows a placeholder where its canvas would be.	MultiRegionDisplayMixin
trackVisibleRegions `VisibleRegion[]`	The visible blocks on the track's own assemblies, the ones this display fetches and is judged against. A view of several genomes leaves a single-genome track's other regions blank.	MultiRegionDisplayMixin
viewportWithinLoadedData `boolean`	true when every visible block lies within an already-fetched region — i.e. the viewport shows data we actually loaded, not the stale fringe left after a zoom-out/pan. Drives the loading overlay through the pre-refetch debounce. Spatial only, and it stays that way. Whether the data held for a block is still what a fetch would bring back is `isCacheValid`, which `dataCurrent` conjoins for the export gate. The scrim reads this getter and `dataSuperseded`, never `isCacheValid`: a phase that went `loading` on a moved `fetchInputs` would raise the overlay into every zoom.	MultiRegionDisplayMixin
viewportEmpty `boolean`	No content block is on screen, so this display has nothing to fetch and nothing to paint — see `viewportEmpty.ts` for the one viewport that reaches it, how narrow that is, and why the state still has to be terminal rather than a permanent scrim. Both foundations declare it over that one expression, the same way they each declare `host` and `paintInert`.	MultiRegionDisplayMixin
fetchSuspended `boolean`	Overridable hook (default false), read by the fetch plan: the display is drawing something in the features' place and wants no fetch while it does. `DensityTierMixin` says it while the band is up and the gate is not blocking, so a track forced to `density` never downloads the features it will not draw, while a refused viewport keeps its measurement pass and the gate can still release. Not `fetchInert`: that one suppresses the scrim and ends the export wait, and a display saying this still has its stand-in to load. On this foundation alone, because only this family's plan reads it.	MultiRegionDisplayMixin
layoutReady `boolean`	Overridable hook (default false): whether a searchable feature layout currently exists. Any display defining a feature-lookup method (`searchFeatureByID`) must override it, so callers can tell "laid out, but off-display" from "no layout exists yet" — a distinction only the display can make. See packages/display-kit/CLAUDE.md §"Four readiness axes".	MultiRegionDisplayMixin
dataSuperseded `boolean`	Overridable hook (default false): the held data is loaded and covers the viewport, but a fetch input has moved past it, so the data is about to be refetched. A display says so here rather than overriding `dataCurrent`, for the reason `FetchMixin.fetchInert` is a hook: an override has to restate the freshness terms and then misses the next one added. Both answers a display gives about being finished read it — the export gate through `dataCurrent`, the loading scrim through `displayPhase`. The export gate is the sharper case: `awaitSvgReady` samples freshness once, and an export that samples it inside this window renders the data that is about to be replaced. GWAS's LD auto-index is that case: adopting the top hit as the index SNP is an `rpcProps` change, so the very load that produced the top hit is what it invalidates — and `SettingsInvalidate` lands a tick after the write, so until it does not even `staleSettingsDrawn` has seen it. The window is NOT invisible on screen, which this used to say while `displayPhase` took a spatial-only argument: alignments' per-base wall spends the debounce plus the RPC painting a 1 px stripe every 8 px, with nothing in the key having moved yet. The input need not have settled yet. Alignments counts the debounce window ahead of its per-base bin, where the bin the data was fetched under has not moved and the clear is inevitable rather than committed. That is the half of the window an export lands in, since a reader zooms and then reaches for the menu. What may NOT go in is a change that could still be taken back: this fails hung, not stale. So state the live-vs-settled half as a value compare and leave the stamp alone. The settled half — the stamp a fetch committed under against the `zoomFetchArgs` a fetch now would send — is the foundation's already, through the `isCacheValid` term in `dataCurrent`, and an override restating it buys nothing: a second derivation misses the field the args gain next, latches this true, and every export of the display then waits out `awaitSvgReady`'s backstop instead of failing.	MultiRegionDisplayMixin
renderBlocks `RenderBlock[]`	Shared cached view for every LGV-based GPU display. A single displayedRegion may produce multiple render blocks (shared GPU buffer, different scissor clips on screen). Plugins that want to suppress rendering in certain states (e.g. no domain yet) can override this getter to return [] — the autorun lifecycle will then issue an empty-blocks render that clears the canvas.	MultiRegionDisplayMixin
fetchInputs `FetchInputs`	What a fetch issued right now would stamp on a region: the settings tier (`FetchMixin.settingsFetchInputs`, the tier `staleSettingsDrawn` compares alone) and the zoom tier (the display's `zoomFetchArgs()` object). `fetchRegions` captures it before the RPC goes out and stamps it beside the loaded region; `isCacheValid` compares against it.	MultiRegionDisplayMixin
regionPayloads `ReadonlyMap<number, unknown>`	The store's payloads, keyed by `displayedRegionIndex`. A display narrows this once — `get rpcDataMap() { return self.regionPayloads as ReadonlyMap<number, MyResult> }` — and every reader it already had goes on reading a map. MST makes a `.views()` getter a computed, so the Map is built once per store change and handed back by reference after that — which is what keeps `installUpload`'s diff a reference compare per key and a frame that changed no data free of it. While something observes it: MobX suspends an unobserved computed and rebuilds on every read, so a display whose only reader is a pointer handler needs the keep-alive canvas and Manhattan both install (display-kit/CLAUDE.md §"A hit test's index needs an observer"). The render lifecycle's upload autorun is that reader for every display that draws.	MultiRegionDisplayMixin
hasRegionData `boolean`	A fetch has landed: at least one region's payload is in the store. The render callback's first-paint gate reads this, so an empty frame before any data cannot flip `canvasDrawn`; an empty but loaded region counts, and paints its empty frame.	MultiRegionDisplayMixin
staleSettingsDrawn `boolean`	A visible block's held data was fetched under a settings or adapter key that has since moved: drawn, and wrong for the current settings, until the refetch `isCacheValid` already owes lands. The loading scrim's third staleness term, beside spatial coverage and `dataSuperseded` — the one that used to come from `SettingsInvalidate` emptying the coverage map, and the reason it no longer has to. False on a zoom by construction: it compares the stamp's `settings` tier alone, so a moved zoom tier raises no scrim. That is the whole distance from the declined fold, which compared the whole key and put the overlay 250 ms into every zoom.	MultiRegionDisplayMixin
dataCurrent `boolean`	This family's answer to the shared freshness question every display foundation must answer (`dataCurrent`): the held data corresponds to what is on screen right now. Four terms — spatial coverage of every visible block, `loadedRegions.size` to rule out the vacuously-true empty viewport, `isCacheValid` per block, and the display's own `dataSuperseded`. Regions stream in one at a time, so a multi-region/whole-genome export waits on this getter to be complete; waiting on the first datum to arrive would export a partial set. `isCacheValid` belongs here and not in the scrim. Coverage answers "is the data here", never "is it what a fetch now would bring back", so a zoom that moves `fetchInputs` leaves every held region covered and stale at once — and an export sampling `svgReady` across that window painted bins the worker computed for the previous zoom. `displayPhase` takes `dataSuperseded` but NOT this term: folding a moved `fetchInputs` into the phase raises the loading scrim into every zoom, which is the trade this does not take. The term cannot latch, and the reason is structural rather than a case list: a block reaches `fetchNeeded` unless `planRegionFetch` finds it ungated, covered AND cache-valid, and it reads that last term tracked. The `&&` short-circuits ahead of it drop its observables only where the block is fetched anyway, so the key move that closes this gate is the same read, in the same dependency set, that wakes the refetch reopening it.	MultiRegionDisplayMixin
loadedAssembly `(ModelInstanceTypeProps<…> & { error: unknown; loadingP: Promise<…> \| undefined; ... 10 more ...; refNameMismatches: Map<…>; } & ... 13 more ... & IStateTreeNode<...>) \| undefined`	The assembly the data in hand came from, once it can answer about refNames — `undefined` before that. Read off the first LOADED region rather than the view's displayed ones, and defined here for that reason: a display holding fetched data is asking about the assembly THAT data is on, and the view's regions can already have moved on. The `initialized` gate is why this returns the assembly rather than its name. `getCanonicalRefName2` and `refNameToIndex` answer WRONGLY rather than throwing before the aliases land — identity, and a miss — so a caller that skips the gate gets a plausible answer and no signal. Returning `undefined` until the aliases load forces the caller to write its fallback.	MultiRegionDisplayMixin
phaseViewportCurrent `boolean`	The loading scrim's staleness argument: what is drawn answers for what is on screen. Spatial coverage, `dataSuperseded` and `staleSettingsDrawn`; NOT `isCacheValid`, which is `dataCurrent`'s and would scrim every zoom. `displayPhase` reads it, and so does a stand-in phase (`coarseTierDisplayPhase`) — one predicate, so a term added here reaches both.	MultiRegionDisplayMixin
svgReady `boolean`	true once an off-screen (SVG) export can safely read this display's data. Policy single-sourced in `computeSvgReady`; this family supplies only the freshness half, which `foundationSvgReady` reads as `dataCurrent` or the vacuous currency of `viewportEmpty`. Off-screen renderers gate on it via `awaitSvgReady(model)` instead of inlining the condition.	MultiRegionDisplayMixin
paintInert `boolean`	Fills `RenderLifecycleMixin`'s `paintInert` hook — see there for why a failed fetch has to read as finished to the consumers outside the display, and `foundationPaintInert` for the second such state and why both fetch families answer it through one function. Overridable, as the hook is: a display with a third inert state of its own says so here.	MultiRegionDisplayMixin
paintSuperseded `boolean`	Fills `RenderLifecycleMixin`'s hook with `staleSettingsDrawn`, so `painted` — and `data-display-drawn` through it — reads pending over a canvas painted under the previous settings until the refetch lands. `clearAllRpcData` used to reset `canvasDrawn` for the same effect; the hook says it without blanking anything.	MultiRegionDisplayMixin
displayPhase `DisplayPhase`	The display's mutually-exclusive visual state, mapped in `foundationDisplayPhase` — every foundation calls it and supplies only its staleness argument, so a term added to `computeActivityPhase` reaches all three without being wired three times. This family's argument is `phaseViewportCurrent`: spatial coverage AND `dataSuperseded` (data a settled fetch-input change is drawing wrong right now — alignments zooming perBaseLetter from 16 bp/px to 1 stays inside the loaded region and reported `ready` over a wall drawn as a 1 px stripe every 8 px) AND `staleSettingsDrawn`. A thunk, so a suppressed or already-loading display doesn't subscribe to viewport churn. A subclass customizes this through `fetchInert` (FetchMixin), never by overriding the getter — see that hook.	MultiRegionDisplayMixin
gateEnabled `boolean`	The opt-in. Overridden with a literal `true` by gated displays, and `check-gated-adapter-budgets` insists on a literal: this mixin returns early on it in an autorun and in `commitFetchBytes`.	RegionTooLargeMixin
byteGateAdapterConfig `Record<string, unknown>`	The adapter config the gate measures — the one at `byteGateAdapterPath`. Overridable for a display whose adapter config is synthesized rather than read off the track.	RegionTooLargeMixin
configuredFetchSizeLimit `number \| undefined`	The display's `fetchSizeLimit` slot, from `regionTooLargeConfigSchemaFields`. `number \| undefined`, because `getConf` answers `undefined` for a slot a composing display's schema never declared and typing it `number` hid the whole failure — `resolveByteLimit` falls back closed, and says why.	RegionTooLargeMixin
densityTooLarge `boolean`	The density axis's verdict, and the whole of that axis's opt-in: `CanvasFeatureGateMixin` overrides it beside the measurement that fills it, and a byte-only display leaves it false.	RegionTooLargeMixin
byteGateAdapterPath `ByteGateAdapterPath`	Where on the track config the measured adapter sits. A tiered display overrides this one hook (MAF: `['adapter', 'summaryAdapter']` while `showSummary`), and both the measurement and the budget follow it.	RegionTooLargeMixin
adapterFetchSizeLimit `number \| undefined`	The measured adapter's own `fetchSizeLimit` slot, read off the live track config rather than the `adapterConfig` snapshot, which omits slots at their default.	RegionTooLargeMixin
configForceLoad `boolean`	The declarative `forceLoad` slot.	RegionTooLargeMixin
gateViewport `GateViewport \| undefined`	What a measurement taken now would be about: the span on screen, and a key for the stretch of genome it covers and the settings it would be taken under. Undefined until the view is measured, and the mixin's only read of the view. Captured before the fetch's round trip, never at commit, so the stamp names the settings the worker actually counted under. The settings term is `settingsFetchInputs`, the axis every family invalidates data on. It belongs in the measurement because the worker's density probe counts ADMITTED features (`densityGate`'s `admit`), so a filter admitting almost nothing is a different measurement of the same viewport — and while staleness was viewport-only, the main thread never went back to ask. The byte axis is an index read no `rpcProps` field can move; the rule is one rule rather than one per axis.	RegionTooLargeMixin
aboveForceLoadFloor `boolean`	Whether the span on screen is at or above `AUTO_FORCE_LOAD_BP`, the one comparison against that constant. False on an unmeasured view.	RegionTooLargeMixin
gateExempt `boolean`	Nothing may gate on either axis: the `forceLoad` slot or the button.	RegionTooLargeMixin
estimatedFetchBytes `number \| undefined`	The stored estimate's bytes; undefined when nothing has been measured.	RegionTooLargeMixin
gateMeasurementStale `boolean`	Whether the last measurement still describes what a fetch issued now would ask: the viewport on screen, under the settings on screen. True before any measurement. The triple's third term, the adapter tier, is not here — a tier swap drops the measurement outright (`ClearByteEstimateOnNavOrTierSwap`) rather than marking it stale.	RegionTooLargeMixin
gateByteLimit `number`	The byte budget: the adapter's limit, else the display's, doubled below `AUTO_FORCE_LOAD_BP`. Read only through `resolvedByteLimit()`.	RegionTooLargeMixin
gateActive `boolean`	Whether the gate may act right now, on any axis: opted in, not exempt, view measured. The view is read last, so an ungated display never touches it.	RegionTooLargeMixin
densityGateActive `boolean`	Whether the density axis may act: `gateActive`, and the span is above the floor — the one axis the floor applies to. Whether it has anything to say is `densityTooLarge`.	RegionTooLargeMixin
tooLargeStatus `RegionTooLargeStatus`	The verdict and its banner text, from the stored estimate against `resolvedByteLimit()` and the density axis when it may act.	RegionTooLargeMixin
regionTooLarge `boolean`		RegionTooLargeMixin
regionTooLargeReason `string`	Banner text for the axis that tripped; empty when not too large.	RegionTooLargeMixin
zoomCanReleaseGate `boolean`	Whether "zoom in to see features" is honest advice. Density always releases on zoom; bytes only if the last zoom-in moved the estimate.	RegionTooLargeMixin
gateSkipsMeasuredViewport `boolean`	The skip both fetch skeletons apply: the banner is up and its measurement already describes the viewport on screen.	RegionTooLargeMixin
painted `boolean`	The first-paint answer every consumer outside the display should read, `canvasDrawn` being only the raw flag: a display that is deliberately not painting a canvas has finished, and reporting it unfinished leaves every waiter on it waiting forever. The two `rendersCanvas: false` states each had three of their four consumers wired by hand — the loading scrim (`rendersCanvas` / `fetchInert`) and the SVG export (`fetchInert`) — while the fourth, `data-display-drawn`, went on publishing `"false"` forever off the raw flag. That attribute is what `PENDING_DISPLAYS` (`@jbrowse/browser-test-utils`) selects on, so a zoomed-out reference sequence track made every `waitForDisplaysDone` on the page run to its full timeout, and that wait swallows its own timeout without reporting it. `fetchInert` on the comparative side has the same problem: the forgotten reader is the one outside the display, so the display has to publish one name for it. `paintInert` is the third term and the same argument once more, for the state where a display would paint a canvas and never gets to — a fetch that failed before first paint. `paintSuperseded` is the fourth, and the one that subtracts: a canvas painted from data a settings change has made wrong is drawn and not finished. See both hooks.	RenderLifecycleMixin
isLoading `boolean`	true while a fetch is active	FetchMixin
isLoadingOrCanceled `boolean`	`isLoading` widened to cover a user-canceled load: what a hover gate wants, since neither state has a frame on screen that a hit describes. Not a phase input — `computeActivityPhase` reads the two apart, because a cancel is finished (`canceled`) where a fetch is not (`loading`).	FetchMixin
fetchInert `boolean`	Overridable hook (default false): the states where this display deliberately never fetches, so it holds no data and none is coming. Sequence sets it past base resolution ("Zoom in to see sequence"); LD sets it with the triangle toggled off. One hook has three readers. A display that gains such a state declares it once, which covers the reader it would otherwise forget, always the one outside the display: - the phase (`computeActivityPhase`), which otherwise parks a scrim over the placeholder, or a canceled overlay once Cancel is clicked; - the SVG export (`computeSvgReady`'s `extraTerminal`), whose `awaitSvgReady` is an unbounded `when`, so one such display hangs the whole view's export; - the retry contract check (`makeRetryContractCheck`), which would otherwise report a dead Retry on a display correctly declining to load anything. `fetchInert` replaces three hooks: `loadingSuppressed`, `svgReadyExtraTerminal` on each of the two foundations, and `fetchInert` on the comparative family, which had already collapsed them. Both LGV displays that override it returned one expression for all three, and the global family hard-coded one of the three to `false` for a while, so LD could express only half its state. All three fetch families declare it here since the comparative one composed this mixin (ADR-105), so the retry check reads one field everywhere. ADR-082. A hook rather than a `displayPhase` override, because overriding the getter means restating the whole loading condition. Sequence held a verbatim copy of the other terms that way, and a copy misses any term added to the condition later. `fetchInert` lives here because this is the one mixin all three display foundations compose. Same argument, one level down, that put `rendersCanvas` on `RenderLifecycleMixin` beside `canvasDrawn`.	FetchMixin
awaitingPrerequisite `boolean`	Overridable hook (default false), read only by the retry contract check (`makeRetryContractCheck`): "this run declined because a prerequisite fetch in another autorun has not landed, and its arrival wakes this one again". It defers the retry verdict to that later run rather than waiving it, so a display cannot spend its retry on a decline it called preliminary. Two displays set it, one per fetch foundation, so it lives beside `fetchInert` rather than on either: HiC's contacts fetch declines until `CoreGetInfo` lands, and `MultiSampleVariantBaseModel`'s `fetchNeeded` declines until `sourcesBase` does. Both have a `reload()` that wakes the prerequisite's autorun as well as their own. It has to be strictly narrower than the gate it explains. One that restates the gate's negation makes every decline a deferred one. No run is then ever judged, which exempts the display from the check. HiC does this deliberately, because its gate and its prerequisite are one condition; what covers its retry instead is `LinearHicDisplay/infoFetchFailure.test.ts`. Not for a display deliberately not fetching at all — that is `fetchInert` above, which the loading scrim and the export read too.	FetchMixin
awaitingDependentData `boolean`	Overridable hook (default false), read by `computeActivityPhase`: a load this display depends on beyond its primary fetch has not landed for the first time, so the frame the primary fetch calls current is still missing something. Multi-way synteny sets it until its lane genes and lane links first arrive, so an export or a capture never lands between the ortholog fetch and the gene models that fill the lanes. A hook rather than a `displayPhase` override, for the reason `fetchInert` is one: that display carried the override, restating the foundation's two arguments verbatim to append one term, and a copy like that misses any term added to the foundation later. Not `dataSuperseded`, which holds the export through every later refetch too: a display saying this wants the scrim on the first landing only, since later lane fetches redraw over lanes already on screen.	FetchMixin
settingsFetchInputs `unknown`	The settings axis every fetch family invalidates on: this display's `rpcProps()` payload and its adapter config, as one value compared structurally. The per-region family watches it from `SettingsInvalidate` and stamps it on each region, the keyed families fold it into `currentFetchKey`, and the byte gate measures under it — one getter, so no two can come to invalidate on different axes. `undefined` inside the payload is a real state and a class instance compares by its own fields, which a serialized key could not say; `makeSettingsFetchInputs` has why.	FetchMixin
resolution `number`	Points per pixel the fetch asks for, clamped to what the Resolution menu offers: the slot is reachable from a track config, which runs no setter, and `0` there divides by zero inside the adapter.	WiggleCommonMixin
rpcDataMap `ReadonlyMap<number, WiggleDataResult>`	The fetched scores, keyed by displayedRegionIndex — the foundation's per-region store, narrowed.	WiggleCommonMixin
origin `number`	The value bars grow from, which a colour scale also reads where its own domain says nothing.	WiggleCommonMixin
lineWidth `number`		WiggleCommonMixin
maxGapMultiple `number`	Interpolated-line gap threshold, as a multiple of the track's own mean point spacing (see gapBreakLimit). 0 keeps one connected line.	WiggleCommonMixin
summaryScoreMode `string`		WiggleCommonMixin
renderingType `string`		WiggleCommonMixin
minimalTicks `boolean`		WiggleCommonMixin
hasResolution `boolean`	Asked of the display's OWN adapter, which for the GC display is the synthesized GCContentAdapter rather than the track's raw sequence adapter — the two diverged when the adapter config moved onto the shared model. It answers the same today, since only BigWigAdapter and MultiWiggleAdapter declare the capability, and the display's adapter is the honest subject: the resolution slot it gates is passed to whatever this display fetches from.	WiggleCommonMixin
effectiveSummaryScoreMode `string`	The summary mode actually drawn. Density has no whiskers presentation — `sourceLayers` falls back to the average scores — so the autoscale domain reads this rather than the raw slot; otherwise the color ramp spans the whisker extremes while the plot paints averages, and the score legend reports a range nothing on screen reaches. Single-wiggle defaults to whiskers, so plain "plot type → Density" hit this.	WiggleCommonMixin
domain `[number, number] \| undefined`	The autoscaled domain over the sources visible in the settled blocks. `undefined` until the view and the data are ready, which is not the `[0, 1]` a caller falls back to — see `visibleStatsDomain`.	WiggleCommonMixin
scoreField `string`	The feature field the worker plots on the score axis, `score` by default. A fetch input: every composing display carries it in its `rpcProps()`, since the field is read where the features are.	ScoreFieldConfigMixin
scatterPointSize `number`		WiggleScoreConfigMixin
displayCrossHatches `boolean`	The configured cross-hatch setting the menu toggles; `showCrossHatches` is what draws.	WiggleScoreConfigMixin
showCrossHatches `boolean`	Whether the score-axis cross hatches draw: never in density mode, which has no height axis to rule and no toggle in its menu.	WiggleScoreConfigMixin
scaleType `string`		ScoreScaleMixin
scaleTypeChoices `string[]`	The scale types this display's own enum admits, which is what the scale-type radio offers; a display with one draws no radio.	ScoreScaleMixin
autoscaleType `string \| undefined`	`undefined` on a display whose domain consults no autoscale mode.	ScoreScaleMixin
numStdDev `number`		ScoreScaleMixin
numQuantile `number`		ScoreScaleMixin
symlogConstant `number`	Raw slot; `0` means "derive from the domain". Resolve it with `resolveSymlogConstant` once the domain is known.	ScoreScaleMixin
manualMinScore `number \| undefined`	The lower bound the config pins, `undefined` where it pins none.	ScoreScaleMixin
manualMaxScore `number \| undefined`	The upper bound the config pins, `undefined` where it pins none.	ScoreScaleMixin
scaleTitle `string \| undefined`	`scales.y.title` as written: `undefined` while unset, which leaves the caption to the display, and the empty string for an axis the author wants bare. Also `undefined` on a display whose scale declares no title.	ScoreScaleMixin
scoreRulesDrawn `boolean`	Whether this display draws `scales.y.rules`, which is whether the score menu offers the reference lines: its scale declares them, and a scale it places y through rules a band for them to cross, which a density plot's colour-mapped rows and a colour ramp do not.	ScoreScaleMixin
scoreRules `ValueScaleRule[]`	`scales.y.rules`, read off the live nodes: a snapshot strips a slot at its default, and a rule at 0 is one. Empty on a display whose scale declares no rules.	ScoreScaleMixin
minScoreBound `number \| undefined`	Resolved lower bound; `undefined` means autoscale this end.	ScoreAxisMixin
maxScoreBound `number \| undefined`	Resolved upper bound; `undefined` means autoscale this end.	ScoreAxisMixin
hasManualScoreBounds `boolean`	Whether the user has pinned either end, which is a different question from whether either end resolved to a number: `defaultScoreDomain` fills the unset ends in, so a GC content track answers yes to the second with nothing configured. The score menu asks this one — it gates the "Clear manual min/max" row, and a Clear that writes the nothing already there is a row that does nothing and never goes away.	ScoreAxisMixin
axes `YAxis[]`	The axes, one per declared scale whose domain resolved: where each tick lands in the band's own pixel space, through `computeYTicks` unless the scale brought its own ladder, and where each of the scale's `rules` inside the domain lands in that same box, through the scale type the renderer places its values by.	ScoreAxisMixin
showLegend `boolean`	Whether the legend is drawn.	LegendMixin
legendTop `number`	Overridable hook (default 0): px the on-screen key is pushed down from its own inset. A display that already draws a control of its own in that corner — Hi-C's resolution box — answers that control's height; the chrome adds its own axis captions on top. The export draws no controls, so it does not read this.	LegendMixin
legendSpec `LegendSpec`	The key, derived from `colorScales` less the sections the reader dismissed. `DisplayChrome` renders it on screen and `renderDisplaySvg` flattens it for the export, so the two describe one set of colors.	LegendMixin
hasLegendKey `boolean`	Whether the display has a key at all. The "Show legend" row is offered only when it does. Overridable for a display whose key is only waiting for data: a scale that stays empty until a region lands must not remove the toggle in the meantime.	LegendMixin
showTree `boolean`	Whether the dendrogram sidebar is drawn.	TreeSidebarMixin
showBranchLength `boolean`	Whether tree nodes are positioned by branch length (dendrogram) or evenly by topology (cladogram).	TreeSidebarMixin
showRowLabels `boolean`	Whether each row's name is drawn over the left of the plot.	TreeSidebarMixin
treeAreaWidth `number`	Width in px of the sidebar the dendrogram draws in. On the config rather than the display snapshot for the same reason `height` is: the config node outlives the display instance, so a dragged width survives unticking and reticking the track.	TreeSidebarMixin
parsedTree `HierarchyNode<NewickNode> \| undefined`		TreeSidebarMixin
root `HierarchyNode<NewickNode> \| undefined`		TreeSidebarMixin
treeHasBranchLengths `boolean`		TreeSidebarMixin
rowOrderIsCustom `boolean`	Whether the rows have been arranged away from the order they arrived in — what "Reset row order" is offered on: a written `layout`.	TreeSidebarMixin

Methods

Member	Description	Defined by
rpcProps `() => { windowSize: number; windowDelta: number; gcMode: "content" \| "skew"; summaryScoreMode: string; resolution: number; scoreField: string; }`	The three GC parameters are fetch inputs: `adapterConfig` folds them into the `GCContentAdapter` config, so each changes what the worker computes. `adapterConfig` is a structural arg and deliberately not a cache key, so listing them here is the only thing that invalidates the loaded regions. They ride along in the payload too; the worker ignores them and reads the adapter. They used to live outside `rpcProps()`, with each setter calling `reload()` by hand — which covered the track menu and nothing else.	SharedGCContentModel
trackMenuItems `() => (MenuDivider \| MenuSubHeader \| NormalMenuItem \| CheckboxMenuItem \| RadioMenuItem \| SubMenuItem \| CustomMenuItem \| { ...; } \| { ...; })[]`		SharedGCContentModel
channelSpecProblems `(spec: ChannelSpec) => string[]`	A wiggle colours per signal and keeps no runtime filter list, so a spec naming `filter` is refused rather than silently dropped.	LinearWiggleDisplay
gpuProps `() => {…}`	The row list is this display's own: the encoder places each payload source by its position here, so a filter or a reorder re-uploads bytes already in hand. The colour rides here and not in `rpcProps`: the worker ships one set of score arrays and the main thread colours each instance by its side of the cut, so a new colour re-encodes and refetches nothing.	LinearWiggleDisplay
contextMenuItems `() => MenuItem[]`	Right-click menu, built from the column the click landed on. The position is captured here rather than read inside the onClick, because `closeContextMenu` runs first when an item is clicked.	LinearWiggleDisplay
renderingProps `() => { displayModel: ModelInstanceTypeProps<{ id: IOptionalIType<…>; type: ISimpleType<string>; }> & { ...; } & { ...; } & { ...; } & IStateTreeNode<...>; }`	props passed to the renderer's React "Rendering" component. these are client-side only and never sent to the worker. includes displayModel and callbacks	BaseDisplay
regionHasData `(displayedRegionIndex: number) => boolean`	Overridable hook: whether the display can draw what this region is marked loaded over, at the zoom the view has. The default answers off the store — an entry a fetch committed carries what it stored — and off the payload's `zoomRange` where the adapter declared one (`BaseFeatureDataAdapter.getZoomRange`): a BigWig tier answers a band of zooms, and the region reads as stale when the view leaves it. A payload carrying no range answers at every zoom. What survives an override is the question the store cannot answer: which of several held payloads answers. MAF caches a summary tier and a detail tier side by side under one `displayedRegionIndex`, so crossing the threshold inside an already-loaded region changes which map has to answer. The multi-row display's override survives for the auto-partition reconciliation (`regionHasPinnedData`). A view, not an action, so the reads it makes register as dependencies of `FetchVisibleRegions`.	MultiRegionDisplayMixin
isCacheValid `(displayedRegionIndex: number) => boolean`	Whether the data held for a region still answers the current view. Not a hook a display fills: a display states its rule as `zoomFetchArgs` (what a fetch now would send the worker) and `regionHasData` (does what the last one stored still answer), and this compares the whole input set against the one the region was fetched under.	MultiRegionDisplayMixin
resolvedByteLimit `() => number \| undefined`	The budget the worker enforces and the banner compares against — the one spelling of that pair. Undefined when the gate may not act.	RegionTooLargeMixin
gateFetchState `() => GateFetchState`	The gate as it stands for a fetch about to be issued. Calling it is the capture, which is why it is a method.	RegionTooLargeMixin
svgLegendWidth `() => number`	Overridable hook (default 0): the width the LGV export reserves beside the plot for this legend. A display whose plot fills its band — the contact matrix, the LD triangle — answers `svgLegendGutterWidth(self)` so the key does not cover it.	LegendMixin
willClearTree `(next: S[]) => boolean`		TreeSidebarMixin

Actions

Member	Description	Defined by
setGCContentParams `({ windowSize, windowDelta, }: { windowSize?: number \| undefined; windowDelta?: number \| undefined; }) => void`	Either parameter alone; the other keeps its current value. Both menus change one of the two, and spelling that as "write both, carrying the other across" put `windowDelta: self.windowDelta` in four call sites — which is also where the clamp below would have had to be repeated.	SharedGCContentModel
setGCMode `(mode: "content" \| "skew") => void`		SharedGCContentModel
startRenderingBackend `(backend: WiggleRenderingBackend) => void`		LinearWiggleDisplay
setShowRowSeparators `(arg: boolean) => void`		LinearWiggleDisplay
setColor `(color?: string \| Partial<ColorSetting> \| undefined) => void`	The whole colour object at once, since a scale and the slots it reads are one setting; `undefined` returns to the layout's own picture.	LinearWiggleDisplay
setFaceted `(on: boolean) => void`	The layout half of a Plot type leaf — `Multi-row` or `Overlapping`, each holding the five plot names. Writes the field alone: an order declared in `facet.domain` survives a trip through the shared plot and comes back with the rows. Writing the object whole would not — `rowDomain` reads the order back through `facet`, which is undefined while the sources share a plot.	LinearWiggleDisplay
focusLegendEntry `(_scaleId: string, label: string) => void`	`LegendMixin`'s hook: narrow the rows to the subtracks one key row stands for — what clicking that swatch does. A key row is a group where the subtrack has one and the subtrack itself otherwise (`buildLegendItems`), so this matches the same way.	LinearWiggleDisplay
openChannelSpecDialog `(seed?: ChannelSpec \| undefined) => void`	The Edit color... row: the colour object, and the facet beside it, as JSON.	LinearWiggleDisplay
sortRowsByScoreAt `(refName: string, pos: number) => boolean`	Rank the rows by each source's score at one genomic base. Reads the region data already in hand — no refetch, no RPC — and writes the order through `layout`, the same channel clustering and the arrangement dialog write, so "Reset row order" undoes all three. Named by coordinate rather than by loaded-region index because both entry points are: the right-click hit resolves to one, and a session's `sortRowsBy` carries one across a reload. Resolving that region and refusing the two cases where a sort would only cost a `layout` write are `sortRowsAtColumn`'s, shared with the multi-row feature display's twin, and so is the returned "did it sort" the declarative entry point reads to decide whether to keep its trigger for a later fetch.	LinearWiggleDisplay
fetchNeeded `(needed: IndexedRegion[]) => Promise<void>`		LinearWiggleDisplay
renderSvg `(opts?: ExportSvgDisplayOptions \| undefined) => Promise<ReactElement<unknown, string \| JSXElementConstructor<any>> \| Iterable<...> \| AwaitedReactNode>`		LinearWiggleDisplay
setStatusMessage `(status?: RpcStatus \| undefined) => void`		BaseDisplay
setError `(error?: unknown) => void`		BaseDisplay
clearHoveredFeature `() => void`	Overridable hook (default no-op): drop whatever `hoveredFeature` reports. The writing twin of that getter, and what `installClearHoverOnViewportChange` calls. A display that STORES its hover owes an override; one that derives it from the live pointer (MAF, Hi-C, LD) owes nothing, and the default costs it nothing. Declared here so the clear can be installed for every display rather than remembered per display — forgetting it is the failure ARCHITECTURE.md's stored-hover section is about, and it used to be six closures at six call sites, which is six chances to omit one.	BaseDisplay
reload `() => void`	base display reload does nothing, see specialized displays for details	BaseDisplay
applyDisplaySettings `(settings: Record<string, unknown>, options?: { allowSetters?: boolean \| undefined; } \| undefined) => { applied: string[]; unapplied: UnappliedSetting[]; failed: { ...; }[]; }`	Apply a set of display settings to the live display, and report which were applied. Each key runs through the display config schema's `preProcessSnapshot` (shorthand expansions and legacy-key migrations, as `showTrackGeneric` applies to a session spec's inline track keys), then writes the matching config slot. A key naming a sub-schema (`facet`, `color`) replaces the whole object, its string shorthand lifted by that schema, and `null` clears it. Keys that are not slots come back in `unapplied` as `{ key, reason }`, so a caller can tell a misspelling from a key that has an action instead of a slot. `allowSetters` also routes a non-slot key to a single-argument action named `set<Key>`. It is off by default because session specs, share links and embeds pass untyped JSON here, and a default fallback would let them call internal setters (`setError`, `setScrollTop`, ...) and call multi-argument setters with one argument. A caller that wants a specific action can call it directly. A key whose write threw is reported in `failed`. Only `failed` means the caller passed a bad value. `unapplied` needs the caller's own context to read: `showTrackGeneric` spreads the same settings into the display's snapshot, so a declared prop (`resolution`) has already landed by the time it reports here, while the restyle path spreads nothing and every entry there did nothing. A per-key error does not abort the remaining keys. A caller mid-`showTrack` has already pushed the track, and one rejected value should not leave it half-configured.	BaseDisplay
setScrollTop `(scrollTop: number) => void`		TrackHeightMixin
setHeight `(displayHeight: number) => number`		TrackHeightMixin
resizeHeight `(distance: number) => number`		TrackHeightMixin
expandToContentHeight `() => number`	Grow the track by the content it is hiding, for the resize handle's double click. Goes through `resizeHeight` so grow mode's override leaves grow first.	TrackHeightMixin
setLoadedRegion `(displayedRegionIndex: number, region: Region, payload: {} \| undefined, fetchInputs?: FetchInputs) => void`	The raw write behind `ctx.commitRegion`, and not what a fetch should call. A display naming its span itself is the bug this family spent a release fixing, and the context gives a fetch no way to express it — see RegionFetchContext. Direct callers are tests staging an already-loaded display. The payload is named on every call, `undefined` included: this write replaces the whole record, so a re-stamp that left it off dropped the data a test had staged one line earlier, and the failure surfaced as a reader throwing three layers away. A test stages a claim with nothing behind it by saying so. An action so callers after an async boundary stay in MST strict mode. Stamps the region with the fetch key its data came back under. `fetchRegions` passes the key it captured before issuing the RPC; the default reads it now, which is right for a caller holding the region already and wrong for anything resuming after an await, where the viewport may have moved under the fetch.	MultiRegionDisplayMixin
evictRegionStore `(keep: ReadonlySet<number>) => void`	The store's bound. Drops the entries a fetch can no longer be about: an index outside the view's buffered viewport, once the store is over `MAX_STORED_REGIONS`, oldest first. One rule for every display, where canvas hand-rolled `pruneRpcDataMapToVisible` (prune to the buffer on every fetch) and every other display had no bound at all beyond `displayedRegions.length`. That count is the contig count, so a fragmented assembly was effectively unbounded. The cap lets a pan back onto a recently-visited region draw immediately, which the prune-to-buffer rule did not.	MultiRegionDisplayMixin
dropLoadedRegion `(displayedRegionIndex: number) => void`	Forget one region — for a display pruning what has scrolled off screen.	MultiRegionDisplayMixin
clearDisplaySpecificData `() => void`	Overridable hook (no-op base): drop what this display holds beside the store — a second store of its own, a verdict about the viewport that was just dropped. Called by `clearAllRpcData`, which runs on a displayed-regions change, on a viewport move past an error or a cancel, and on `reload()`.	MultiRegionDisplayMixin
clearSettingsBakedData `() => void`	Overridable hook (no-op base): drop what this display holds that is wrong under a changed setting rather than merely stale — a payload whose shape the setting decides. Called by `invalidateSettings`, where `clearDisplaySpecificData` is deliberately not: bins, reads and features fetched under the previous setting draw honestly under the scrim `staleSettingsDrawn` raises until the refetch lands, the way canvas has kept its features since ADR-006 and every display does since 2026-09. The variant matrix overrides it, for a structural reason: it holds one payload for every visible region and the row set is a setting, so there is no per-region replacement to wait for.	MultiRegionDisplayMixin
clearAllRpcData `() => void`	full reset: cancels fetch, clears error, loadedRegions, display-specific data, and the canvas-drawn flag. The too-large gate is derived (a pure function of the cached estimate × viewport), so it needs no explicit clear here — the fetch autorun re-measures at the new viewport and the verdict follows.	MultiRegionDisplayMixin
invalidateSettings `() => void`	`SettingsInvalidate`'s reset: the half of `clearAllRpcData` a settings change still needs now that the settings and adapter axes are in `fetchInputs`. The in-flight fetch is superseded now rather than when its payload lands stamped stale, a blocking error or cancel is cleared so the plan is not `blocked`, and the display drops its settings-baked data. `loadedRegions` and the canvas-drawn flag stay: every held region already reads `!isCacheValid`, so the plan refetches it, and until that lands the data stays on screen under the scrim `staleSettingsDrawn` raises.	MultiRegionDisplayMixin
fetchRegions `(needed: IndexedRegion[], work: (ctx: RegionFetchContext) => Promise<void>) => Promise<void>`	Run a per-region fetch. The work callback calls `ctx.commitRegion` as it stores each region's payload, which is what marks it loaded — see RegionFetchContext for why this function no longer does that itself. Its only callers are the three helpers in `fetchEachRegion.ts`, which make that call for every display in the family; a display reaching past them owns both `ctx.isStale()` guards and the commit by hand, and none does. The fetch key is captured here, at issue, and carried into every commit — never re-read after the await. `ctx.isStale()` trips on a newer fetch or a cancel, not on a viewport that moved under a fetch that is still current, so a key read at commit time would stamp this data with a zoom it was not fetched at.	MultiRegionDisplayMixin
afterAttach `() => void`	installs the fetch-lifecycle autoruns (DisplayedRegionsChange, FetchVisibleRegions, SettingsInvalidate, ClearBlockingStateOnViewportChange)	MultiRegionDisplayMixin
clearByteEstimate `() => void`	Drops the estimate and the viewport stamp. `forceLoadTrack` survives: it is a track-wide approval.	RegionTooLargeMixin
setForceLoadTrack `(flag: boolean) => void`		RegionTooLargeMixin
commitFetchBytes `(perRegionBytes: (number \| undefined)[], issued: GateFetchState, partial?: boolean) => void`	The byte axis of a finished fetch, called by the fetch runners with the `gateFetchState()` they captured at issue. Commits the per-region max; an empty batch, or an ungated display, commits nothing.	RegionTooLargeMixin
forceLoad `() => void`	The banner's button: exempt the track on both axes and refetch.	RegionTooLargeMixin
markCanvasDrawn `() => void`		RenderLifecycleMixin
resetCanvasDrawn `() => void`		RenderLifecycleMixin
stopRenderingBackend `() => void`		RenderLifecycleMixin
renderNow `() => void`		RenderLifecycleMixin
setRenderError `(error: unknown) => void`	set/clear the render-backend error. Called by `useRenderingBackend`: with the error when the canvas factory rejects (or context-loss re-init fails), and with `undefined` on successful (re)init and on retry.	RenderLifecycleMixin
attachRenderingBackend `<B>(backend: B, setup: () => RenderingBackendCallbacks<B>) => void`	attach a GPU/Canvas2D backend and install the upload + render autorun pair. Idempotent: re-calling swaps the backend and does not run `setup` again, so the callbacks and everything they close over are the first call's.	RenderLifecycleMixin
stopActiveFetch `() => void`	Abort the in-flight fetch (if any) and retire its slot. The shared preamble of both cancel paths; the difference between them is only what they do to `fetchCanceled` / `fetchGeneration` afterward.	FetchMixin
openStatusStream `(isCurrent: () => boolean) => StatusStream`	Open one operation's slot on the display's status field: an RPC `statusCallback` throttled through the display-wide window and guarded so a callback that fires after the node is torn down (RPCs resolve their status stream asynchronously) is a safe no-op, plus the `clear` that retires the slot when the operation ends. Every operation on the display opens one, and the two come back together because an operation that never retires keeps reporting status for a phase that is over. The viewport fetch (`runFetch`), the clustering run and a lent `createAbortRotation` are three of them on one field; before ADR-081 each blanked the field outright and the last one to finish overwrote the status of the other two. `isCurrent` is required and has no "node is alive" default, because a live node is not enough: a superseded fetch is on a live node, and its late status repainting the overlay of the fetch that replaced it is the failure this guards. `runFetch` passes `!isStale()`, and every display gets that through `ctx.statusCallback` unasked; a caller outside a fetch (the clustering autorun) passes its own run's flag. Defaulting to `isAlive` made the loose answer the easy one and five displays took it. `runFetch`'s own slot is opened by the rotation; this is for an operation outside any fetch, the tree sidebar's clustering run.	FetchMixin
cancelFetch `() => void`	cancel any in-flight fetch and bump fetchGeneration (always bumps, so callers can retrigger fetch autoruns even when nothing was in flight). This is the internal reset `clearAllRpcData` runs — it clears any user-cancel flag so the retrigger actually re-fetches.	FetchMixin
cancelFetchByUser `() => void`	User-initiated cancel from the loading overlay. Stops the in-flight fetch and lands in a durable `fetchCanceled` state. Unlike `cancelFetch`, it does NOT bump fetchGeneration — so the fetch autoruns don't immediately restart the load. The user retries via `reload` (the overlay's retry button), or it clears on the next viewport change.	FetchMixin
beforeDestroy `() => void`	Abort an in-flight fetch on teardown. Without this, a display destroyed mid-fetch (track/view closed while loading) never signals the worker to abort the now-useless work, and its in-flight HTTP reads keep downloading. MST auto-chains lifecycle hooks, so a composing display can still define its own beforeDestroy.	FetchMixin
beginFetch `(signal: AbortSignal) => void`	The `onBegin` half of a fetch's bookkeeping: publish the in-flight signal (`isLoading`) and clear the durable user-cancel — a load starting is the single clear point that covers every retrigger path (reload, viewport change, settings invalidate). An action of its own for the same reason `endFetch` is: `installFetch`'s lifecycle callbacks run outside any MST flow this mixin owns.	FetchMixin
endFetch `(current: boolean) => void`	The `finally` half of `runFetch`'s bookkeeping, an action of its own because `runFetchOnce`'s `finally` resumes on a microtask the flow does not own — a direct volatile write there is outside the action context, which is the one thing hoisting the sequence into a shared function costs. The stale branch is a superseded fetch, which must not clear the loading flag the run that replaced it just set.	FetchMixin
runFetch `(work: (ctx: FetchContext) => Promise<void>) => Promise<void>`	Run a cancel-safe fetch (cancels any prior). The work callback gets a FetchContext with a signal to forward to the RPC and an isStale() check to short-circuit commits once the user has moved on. The MST-flow wrapper over the shared `runFetchOnce` sequence, and only the wrapper: the begin/clear/run/commit/error/end order, and the rules that keep a superseded run from writing back, are the same function every other fetch in the tree runs. What this adds is the observable bookkeeping a display needs — `isLoading` through `activeSignal`, `fetchGeneration`, the user-cancel clear — and the flow itself, which is an action, so `work`'s synchronous prefix runs untracked wherever a fetch autorun calls this.	FetchMixin
setRpcData `(displayedRegionIndex: number, data: WiggleDataResult, region: Region) => void`	Stage a region as fetched, with this mixin's payload shape — so a test stands up a loaded display in one call. Production goes through `ctx.commitRegion`.	WiggleCommonMixin
selectFeature `(feat: WiggleHoveredFeature) => void`		WiggleCommonMixin
setResolution `(res: number) => void`		WiggleCommonMixin
setOrigin `(val?: number \| undefined) => void`		WiggleCommonMixin
setRenderingType `(type: string) => void`		WiggleCommonMixin
setSummaryScoreMode `(val: string) => void`		WiggleCommonMixin
setLineWidth `(val?: number \| undefined) => void`		WiggleCommonMixin
toggleCrossHatches `() => void`		WiggleScoreConfigMixin
setScatterPointSize `(val?: number \| undefined) => void`		WiggleScoreConfigMixin
setScaleType `(scaleType: string) => void`		ScoreScaleMixin
setAutoscale `(val?: string \| undefined) => void`		ScoreScaleMixin
setMinScore `(val?: number \| undefined) => void`		ScoreScaleMixin
setMaxScore `(val?: number \| undefined) => void`		ScoreScaleMixin
setScoreRules `(rules: (number \| ValueScaleRule)[]) => void`	Replaces `scales.y.rules` whole, each entry in a form the config takes: a number, or `{ value, color, label }`.	ScoreScaleMixin
setHoveredFeature `(hit?: T \| undefined) => void`		StoredHoverMixin
setShowLegend `(arg: boolean) => void`	Writes the slot, and showing the legend again restores the sections closed inside it.	LegendMixin
dismissLegendSection `(id: string) => void`	Close one section of the legend, leaving the others up.	LegendMixin
setShowTree `(arg: boolean) => void`		TreeSidebarMixin
setShowBranchLength `(arg: boolean) => void`		TreeSidebarMixin
setShowRowLabels `(arg: boolean) => void`		TreeSidebarMixin
setLayout `(layout: S[]) => void`		TreeSidebarMixin
clearLayout `() => void`		TreeSidebarMixin
setClusterTree `(tree?: string \| undefined) => void`		TreeSidebarMixin
setLayoutAndClusterTree `(layout: S[], tree?: string \| undefined, provenance?: ClusterProvenance \| undefined) => void`		TreeSidebarMixin
setTreeAreaWidth `(width: number) => void`		TreeSidebarMixin
setSubtreeFilter `(names?: string[] \| undefined) => void`		TreeSidebarMixin
setRunClustering `(arg?: boolean \| undefined) => void`		TreeSidebarMixin
setClusterRegion `(arg?: string \| undefined) => void`		TreeSidebarMixin
setSortRowsBy `(arg?: RowSortSpec \| undefined) => void`	Trigger (or clear) a one-shot declarative row sort; consumed and reset by `setupRowSortAutorun`. A display's right-click item calls its own sort directly (instant, the data is already loaded); this is the session-level entry point.	TreeSidebarMixin
setHoveredTreeNode `(node?: HoveredTreeNode \| undefined) => void`		TreeSidebarMixin
setTreeCanvasRef `(ref: HTMLCanvasElement \| null) => void`		TreeSidebarMixin
setMouseoverCanvasRef `(ref: HTMLCanvasElement \| null) => void`		TreeSidebarMixin
openContextMenu `(info: Info) => void`		ContextMenuMixin
closeContextMenu `() => void`		ContextMenuMixin

SharedGCContentModel

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Methods

Actions