type: types.literal('LinearSyntenyDisplay') | | LinearSyntenyDisplay |
| **configuration**configuration: ConfigurationReference(configSchema) | | LinearSyntenyDisplay |
| **id**id: ElementId | | [BaseDisplay](../basedisplay#property-id) |
## Volatiles
| Member | Description | Defined by |
| --- | --- | --- |
| **featureData**featureData: undefined as SyntenyFeatureData | undefined | | LinearSyntenyDisplay |
| **instanceData**instanceData: undefined as SyntenyGeometry | undefined | Raw GPU-instance geometry produced by the RPC. The view observes this on every display and uploads it to the shared backend keyed by `displayKey`. Clearing it (undefined) triggers backend eviction. | LinearSyntenyDisplay |
| **hoveredInstanceIdx**hoveredInstanceIdx: -1 | Index into `instanceData` of the GPU instance the pointer is over, or -1. The INSTANCE, not the feature, even though the tooltip and the highlight are both about the feature: a CIGAR-detailed ribbon is a base block plus a tile per indel, and the operator under the cursor is readable from nothing else (`getCigarOpAtInstance`). `getFeature` translates to the feature. Same choice `DotplotDisplay` makes, where the stored index is `hoveredSegmentIdx`. | LinearSyntenyDisplay |
| **clickedInstanceIdx**clickedInstanceIdx: -1 | Clicked twin of `hoveredInstanceIdx` — the instance whose feature stays highlighted after the pointer leaves it. | LinearSyntenyDisplay |
| contextMenuAnchor: undefined as ClickCoord | undefined | | LinearSyntenyDisplay |
| **error**error: undefined as unknown | | [BaseDisplay](../basedisplay#volatile-error) |
| **statusMessage**statusMessage: undefined as string | undefined | | [BaseDisplay](../basedisplay#volatile-statusmessage) |
| **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](../basedisplay#volatile-statusprogress) |
| **fetching**fetching: false | True while an RPC fetch is in-flight. Combined with `ready` it distinguishes a first load (no data yet — full overlay) from a refetch (stale content still on screen — corner indicator). | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#volatile-fetching) |
| **loadedFetchKey**loadedFetchKey: undefined as string | undefined | Fetch-input signature the currently held data was fetched for (each display builds its own `currentFetchKey`). Compared against the live inputs in `dataCurrent` to catch data gone stale after a region/zoom change — including during the pre-refetch debounce gap, where `fetching` is still false and would otherwise report done on content drawn against the old viewport. | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#volatile-loadedfetchkey) |
| **assembliesSwapped**assembliesSwapped: false | Set once at view load by a refName-comparison check, independent of the per-render fetch, so it never re-fires or misfires on zoom. Surfaces through each display's `warnings`. | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#volatile-assembliesswapped) |
| **reloadCounter**reloadCounter: 0 | Bumped by `reload()`. Read unconditionally by `installComparativeFetchAutorun`, so it is always in the autorun's dependency set — which is the whole point: after an error the fetch inputs are unchanged, so nothing else would ever refire the autorun and the error banner's Retry would be a button that does nothing. | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#volatile-reloadcounter) |
| **fetchCanceled**fetchCanceled: false | True from the moment the user clicks Cancel on the loading overlay (`cancelFetchByUser`) until `reload()` clears it. Durable and blocking: `installComparativeFetchAutorun` gates on it, so nothing restarts the load in the meantime — not a zoom, not a region change, and no timer.stopActiveFetch: () => {} | Stops the in-flight RPC. `installComparativeFetchAutorun` hands over its stop-token rotation's `cancel` at install (`setStopActiveFetch`): the rotation lives in that skeleton's closure, one per install and beside the fetch that uses it, and this mixin holds no fetch machinery of its own (ADR-054).LevelDuck | The level (row gap) this display's track sits on. Found by predicate rather than by hop count — see isSyntenyLevel. | LinearSyntenyDisplay |
| **level**number | Index of the level (row gap) this display draws in: between `view.views[level]` and `view.views[level + 1]`. | LinearSyntenyDisplay |
| **displayKey**number | Stable backend key under the view-shared backend. | LinearSyntenyDisplay |
| **height**number | | LinearSyntenyDisplay |
| **adapterConfig**Record<string, unknown> | The track's adapter config verbatim. The **body and return type are now identical to `BaseDisplayModel.adapterConfig`** — this override survives only to hold the note below where someone would go to re-add a key.number | | LinearSyntenyDisplay |
| **offscreenMateTally**{ refName: string; count: number; }[] | The contigs this level fetched alignments to but cannot draw a ribbon for, largest first, because the facing row is not displaying them.{ refName: string; count: number; }[] | The same, for the row below: contigs of the QUERY assembly that the row above is not displaying, which alignments anchored on the target axis run to. Always empty without the bidirectional fetch, since those alignments are never requested. | LinearSyntenyDisplay |
| **culledRibbonMates**CulledRibbonMates | undefined | Every alignment this display drew geometry for, placed on both axes, so either strip can mark the ones the band is currently culling — the facing end is on a contig that row displays and has scrolled off, which no fetch-time tally can answer. ONE PER ROW, because culling is symmetric: an alignment can be undrawable with its query end off screen and its target end in plain sight, and marking it on the query axis puts it at an x the layout rejects. See `culledRibbonMates`.number | Mean on-screen width (px, axis 0) of this display's alignment blocks with every already-wide block counted as `FADE_WIDE_BLOCK_PX`, or 0 until a fetch lands and both views connect. The fade only affects sub-pixel ribbons (perpW < 1), so a capped mean well under 1 means the view is dominated by thin ribbons — exactly what width-proportional fade declutters, and `LinearSyntenyView.fadeThinAlignments` decides 'auto' off the narrowest of these.number | Which CIGAR indel ops are actually painted in the current geometry. The worker only emits an indel instance for an op wide enough to draw (sub-pixel indels are dropped), so a set bit means a visible-width op of that kind is on screen. The legend keys its indel chips off this rather than the coarse "file has any CIGAR" flag, so whole-genome zoom (every indel sub-pixel) shows no dead insertion/deletion swatch. | LinearSyntenyDisplay |
| **warnings**ComparativeWarning[] | Warnings surfaced in the view header. Flags a likely reversed assembly row order, detected once at view load (only when the two assemblies have distinct chromosome names). | LinearSyntenyDisplay |
| **ready**boolean | A fetch has completed (data is present, even if it mapped zero features). Not `numFeats > 0` — an empty-but-finished fetch is ready, otherwise an empty result spins the loading overlay forever. | LinearSyntenyDisplay |
| **fetchInert**boolean | Overrides `SyntenyFetchStateMixin`'s default-false hook with the two states where this display's fetch autorun deliberately never runs: minimized, or a level whose two rows aren't both showing regions. A display in one of them draws nothing (`renderParams` is undefined for exactly the same pair) and has no data coming, so anything waiting on data has to treat it as terminal rather than wait forever. One getter because four places answer it — the autorun's own gate, the loading overlay, the SVG export, and (through the mixin) `displaysSettled`. | LinearSyntenyDisplay |
| **fetchFlags**ComparativeFetchFlags | | LinearSyntenyDisplay |
| **loading**boolean | First load: no data has arrived yet. Drives the full striped LoadingOverlay. | LinearSyntenyDisplay |
| **refetching**boolean | Refetch in-flight: a new fetch is running but stale ribbons are still on screen (e.g. zoom-out across a log2 bucket, region change). Drives a subtle corner indicator instead of the full overlay so the visible ribbons aren't masked on every viewport change. | LinearSyntenyDisplay |
| **regionSignature**string | Contents, order and orientation of both connected views' displayed regions — the inputs the worker's cumBp index is built from, so a change in any of them makes held features stale. Its own getter, not inlined into `currentFetchKey`: this is O(total regions) (a whole-genome view of a scaffold-heavy assembly runs to thousands), while `currentFetchKey`'s other deps flip on every pan past the buffer and every zoom bucket. Split out, MobX memoizes it against `displayedRegions` alone instead of rebuilding the whole string per zoom step. | LinearSyntenyDisplay |
| **currentFetchKey**string | Fetch-input signature (region set/order, snapped fetch window, zoom bucket, CIGAR draw options, LOD tier) for the view's current state — the same tracked deps the fetch autorun refetches on. Reactive: flips the instant any of them changes. Before both connected views are ready it collapses to a degenerate signature (empty region sig, no fetch-window/zoom keys) that no connected fetch can produce — a real fetch requires non-empty displayedRegions — so `dataCurrent` reads false until a real fetch lands. Non-nullable so it mirrors dotplot's. | LinearSyntenyDisplay |
| **dataCurrent**boolean | True when the rendered data was fetched for the view's current inputs. Goes false the instant a region/zoom/draw-option change makes the held ribbons stale — including during the pre-refetch debounce gap where `fetching` is still false so `refetching` alone can't catch it.boolean | Off-screen SVG export gate: "Export SVG" waits on this before drawing (see the [SVG export guide](https://jbrowse.org/jb2-staging/docs/developer_guides/svg_export)). Synteny is not an LGV display — it composes only `BaseDisplay` with its own fetch — so it gets no mixin `svgReady`, but it runs the same shared `computeSvgReady` policy so the two can't drift. Stale-safe on both axes: `dataCurrent` closes the pre-refetch debounce gap (stale window before `fetching` flips) and `!refetching` covers the in-flight RPC, so an export fired right after a zoom/pan waits for fresh ribbons instead of capturing stale ones. No `regionTooLarge` state (synteny never gates on region size).DisplayStatusPhase | The display's own mutually-exclusive state, the way every LGV display publishes one — so `AppReadyMarker` counts this display's fetch, and the app stops reporting itself ready over a ribbon that is still working. Ranked by `comparativeDisplayPhase`, off the shared canvas's `surfaceReadiness` and this display's own fetch state.Uint32Array<ArrayBuffer> | undefined | Main-thread-computed per-instance colors. Recomputes whenever colorBy, featureData, or instanceData descriptors change — this is the gpuProps half of the rpcProps/gpuProps split. colorBy changes flow through here without touching the RPC.readonly string[] | undefined | The chromosome order the chromosome-painting modes color by: the refNames of whichever of this level's two assemblies `effectiveColorBy` resolved to, in the assembly's own order. Undefined for every other mode, and while the assembly is still loading — the color function falls back to its hash there.string | | LinearSyntenyDisplay |
| **trackColor**string | This track's slot in the view's palette, used by `colorBy: 'track'`. Assigned by the view, not locally: pinning a color on one track shifts which automatic slots its siblings can take. | LinearSyntenyDisplay |
| **colorByMode**SyntenyColorBy | The mode this track renders with, before the per-level 'reference' remap: its own override if the user set one, else the view-wide mode. This is the user-facing answer — menus and the legend title read it, so a uniform 'reference' view reports 'reference' rather than the query/target each level resolved it to. | LinearSyntenyDisplay |
| **effectiveColorBy**SyntenyColorBy | `colorByMode` resolved for this specific level, for the renderer. 'reference' is a stacked-view mode that colors every level by the shared anchor assembly's chromosome names; each level maps it to 'query' or 'target' depending on which of its two assemblies is the anchor, so the coloring stays consistent across levels. Every other mode passes through. | LinearSyntenyDisplay |
| **renderInstanceData**string[] | undefined | The hovered ribbon's tooltip, as lines, or undefined when nothing is hovered. Lines rather than an HTML string — see `getTooltipLines`, and `DotplotDisplay.tooltipLines` for the twin. | LinearSyntenyDisplay |
| **connectedViews**{…} | undefined | The two adjacent genome views this level draws between, or undefined until both are initialized with regions. A level draws between an adjacent pair, so both render and fetch depend only on those two views, not the whole stack. Single source of truth for that gate. | LinearSyntenyDisplay |
| **bpPerPxBucketKey**string | undefined | Stable key over the log2 zoom bucket of both connected views. The fetch autorun tracks this (a computed compares its string output) instead of raw bpPerPx, so it only refetches when zoom crosses a doubling rather than on every settled zoom within a bucket. | LinearSyntenyDisplay |
| **lodTier**LodTier | The detail tier this level's fetch asks the adapter for, resolved here on the main thread so it can enter `currentFetchKey`.Region[] | The query axis's (v0) fetch window, and the regions the fetch actually sends: the visible content blocks expanded by the shared pan buffer and snapped outward to a buffer-sized grid, so a pan within the buffer neither refetches nor exposes an unfetched strip. The target axis is not scoped — the fetch is one-dimensional (query regions in, every mate out) — it only contributes its cumBp index, so it appears in `fetchRegionsKey` but not here. | LinearSyntenyDisplay |
| **targetFetchRegions**Region[] | The target axis's (v1) fetch window, or [] unless the view asked for the bidirectional fetch — in which case the worker queries it too, and recovers the alignments anchored there whose query end is on a contig the row above is not displaying. Empty is the signal, so the RPC argument carries nothing when the setting is off. | LinearSyntenyDisplay |
| **fetchRegionsKey**string | undefined | Stable key over the *snapped* fetch window of both connected views. The fetch autorun tracks this (through `currentFetchKey`) so a scroll/zoom that moves either snapped window refetches, while a sub-buffer pan (identical snapped windows) does not — a MobX computed only notifies when its string output changes. Built from the same `fetchRegions` the worker is handed, so the key can't describe a window the fetch didn't use. | LinearSyntenyDisplay |
| **renderParams**{…} | undefined | Per-track render params consumed by the view's aggregator. The view substitutes yTop before handing this to the backend. | LinearSyntenyDisplay |
| **parentTrack**AbstractTrackModel | | [BaseDisplay](../basedisplay#getter-parenttrack) |
| **RenderingComponent**FC<…> | | [BaseDisplay](../basedisplay#getter-renderingcomponent) |
| **DisplayBlurb**boolean | Returns true if the parent track is minimized. Used to skip expensive operations like autoruns when track is not visible. | [BaseDisplay](../basedisplay#getter-isminimized) |
| **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.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".{ type: string; id: string; } | Overridable hook: which widget `openFeatureWidget` opens for one of this display's features. The default is the generic one, which is what a display drawing plain features wants and what the canvas base spelled out by hand.(index: number) => FeatPos | undefined | The parent feature under an INSTANCE index (what the pick engine and the hover/click state carry). Without instanceData the two spaces coincide. Deliberately not `instanceFeatureIdx[index] ?? index`: an out-of-range instance index reads `undefined` there, and falling back to the raw index would silently return a different feature rather than nothing. | LinearSyntenyDisplay |
| **renderingProps**() => MenuItem[] | | [BaseDisplay](../basedisplay#method-trackmenuitems) |
## Actions
| Member | Description | Defined by |
| --- | --- | --- |
| **setRpcData**(idx: number) => void | Point the hover at one GPU instance, or -1 for none. The level's `setHoveredFeature` is what calls this, from a pick hit. | LinearSyntenyDisplay |
| **setClickedInstanceIdx**(idx: number) => void | | LinearSyntenyDisplay |
| (anchor: ClickCoord) => void | | LinearSyntenyDisplay |
| () => void | | LinearSyntenyDisplay |
| **setStatusMessage**(status?: RpcStatus | undefined) => void | | [BaseDisplay](../basedisplay#action-setstatusmessage) |
| **setError**(error?: unknown) => void | | [BaseDisplay](../basedisplay#action-seterror) |
| **clearHoveredFeature**() => void | Overridable hook (default no-op): drop whatever `hoveredFeature` reports. The writing twin of that getter, and what `installClearHoverOnViewportChange` calls.() => void | base display reload does nothing, see specialized displays for details | [BaseDisplay](../basedisplay#action-reload) |
| **setFetching**(arg: boolean) => void | | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#action-setfetching) |
| **setAssembliesSwapped**(arg: boolean) => void | | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#action-setassembliesswapped) |
| **setStopActiveFetch**(stop: () => void) => void | Install-time wiring, called once by `installComparativeFetchAutorun` — see `stopActiveFetch` for why the stop arrives from there rather than being built here. | [SyntenyFetchStateMixin](../syntenyfetchstatemixin#action-setstopactivefetch) |
| **cancelFetchByUser**() => void | The loading overlay's Cancel. Stops the in-flight RPC and lands in the durable `fetchCanceled` state, so the fetch autorun's gate holds until `reload()` reopens it.