type: types.literal('LGVSyntenyDisplay') | | LGVSyntenyDisplay |
| **configuration**configuration: ConfigurationReference(schema) | | LGVSyntenyDisplay |
| **lodMode**id: ElementId | | [BaseDisplay](../basedisplay#property-id) |
## Volatiles
| Member | Description | Defined by |
| --- | --- | --- |
| **debugArcGeometry**debugArcGeometry: false | Draws the arc band's own geometry over the canvas — see `ArcDebugOverlay`. Volatile rather than a config slot: it is a diagnostic for "why is this arc this shape", not a display setting, so it should not survive into a saved session or a shared link. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-debugarcgeometry) |
| **featureIdUnderMouse**featureIdUnderMouse: undefined as undefined | string | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-featureidundermouse) |
| **mouseoverExtraInformation**contextMenuFeature: undefined as Feature | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-contextmenufeature) |
| contextMenuFeatureId: undefined as string | undefined | The read/feature id under a right-click, known synchronously (the hit test carries it) unlike `contextMenuFeature`, which only lands after an RPC. A menu item that can act from the id alone — or fetch the feature in its own onClick — reads this, so it doesn't blink into existence a fetch later. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-contextmenufeatureid) |
| contextMenuAnchor: undefined as ContextMenuAnchor | undefined | Viewport point the right-click menu opens at, and the single "is the menu open" flag. Undefined = closed. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-contextmenuanchor) |
| contextMenuHit: undefined as ContextMenuHit | undefined | Everything the right-click's hit test resolved — the block, the clicked column, and whichever mark answered — as one value, so a consumer can't read a block without its hit and closing the menu can't forget a field. See `ContextMenuHit`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-contextmenuhit) |
| **rpcDataMap**rpcDataMap: regionDataMap<GroupedAlignmentsResult>('rpcDataMap') | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-rpcdatamap) |
| **scrollTop**scrollTop: 0 | pileup vertical scroll offset in px. Also read by the BreakpointSplitView overlay to position its SVG curves. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-scrolltop) |
| **collapsedGroups**collapsedGroups: observable.set<string>() | Group keys whose pileup is collapsed to just its coverage band (in-track grouping). Keyed by group key so it survives re-fetches; volatile so it resets on reload. A key means nothing outside the grouping that issued it — `''` is the ungrouped lane AND several dimensions' catch-all bucket — so the whole set is dropped when `groupKeySpace` moves (`AlignmentsGroupKeySpaceReset`). | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-collapsedgroups) |
| **groupMaxHeightOverrides**groupMaxHeightOverrides: observable.map<string, number>() | Per-group pileup height override in px (in-track grouping). Keyed by group key, volatile like `collapsedGroups` and dropped alongside it on a key-space change; absent keys fall back to the display-wide `maxHeight`. Lets a dense section be shrunk independently. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-groupmaxheightoverrides) |
| **fittedHeightPx**fittedHeightPx: 0 | Cache of the current fitted read height in px, kept in sync by the afterAttach autorun while `fitHeightToDisplay` is on. A volatile (not a getter) because the fit height derives from late layout getters that the early `featureHeight` getter can't reference — the autorun bridges that ordering. 0 until first computed / when nothing fits. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-fittedheightpx) |
| **highlightedChainReadIds**highlightedChainReadIds: [] as string[] | Read ids of the chain under the cursor — NOT chain ids; see `readIdsByChainName`, which is where they come from. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-highlightedchainreadids) |
| **selectedChainReadIds**selectedChainReadIds: [] as string[] | Read ids of the clicked chain. Same id space as the hover set above. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-selectedchainreadids) |
| **overCigarItem**overCigarItem: false | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-overcigaritem) |
| **hoverCoverageBand**hoveredArcHighlight: undefined as ArcHighlight | undefined | The read-connection arc under the cursor, as the ink to draw over it — `ArcHoverOverlay`'s whole input. A SNAPSHOT, resolved at the mousemove that found the arc, exactly like the tooltip it appears with: both describe where the cursor was, and both refresh on the next move. `undefined` when not on an arc. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#volatile-hoveredarchighlight) |
| **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) |
| **loadedRegions**loadedRegions: regionDataMap<LoadedRegion>('loadedRegions') | regions whose data has been fetched and committed, keyed by displayedRegionIndex; populated only after the fetch work callback returns | [MultiRegionDisplayMixin](../multiregiondisplaymixin#volatile-loadedregions) |
| **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](../regiontoolargemixin#volatile-forceloadtrack) |
| **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](../regiontoolargemixin#volatile-byteestimate) |
| **gateMeasuredViewportKey**gateMeasuredViewportKey: undefined as string | undefined | The viewport key the gate last asked the adapter about, on either axis. Separate from `byteEstimate` because a density refusal measures no bytes. | [RegionTooLargeMixin](../regiontoolargemixin#volatile-gatemeasuredviewportkey) |
| **canvasDrawn**canvasDrawn: false | flips true on first paint; read by test selectors to detect render | [RenderLifecycleMixin](../renderlifecyclemixin#volatile-canvasdrawn) |
| **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` and narrowed with `as B` inside the autoruns. Don't "fix" the cast. | [RenderLifecycleMixin](../renderlifecyclemixin#volatile-currentrenderingbackend) |
| **renderTick**renderTick: 0 | counter the render autorun observes; bumped to force a re-render | [RenderLifecycleMixin](../renderlifecyclemixin#volatile-rendertick) |
| **autorunsInstalled**autorunsInstalled: false | guards attachRenderingBackend so the autorun pair spawns once per instance | [RenderLifecycleMixin](../renderlifecyclemixin#volatile-autorunsinstalled) |
| **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](../renderlifecyclemixin#volatile-rendererror) |
| **activeStopToken**activeStopToken: undefined as StopToken | undefined | stop token of the in-flight fetch, or undefined when idle | [FetchMixin](../fetchmixin#volatile-activestoptoken) |
| **fetchGeneration**fetchGeneration: 0 | bumps at every fetch end; autoruns read it to re-evaluate, and it doubles as the staleness epoch inside runFetch | [FetchMixin](../fetchmixin#volatile-fetchgeneration) |
| **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 both LGV fetch foundations compose, the same argument that put `fetchInert` below; the comparative family carries its own on `SyntenyFetchStateMixin` (ADR-054). | [FetchMixin](../fetchmixin#volatile-reloadcounter) |
| **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 `createStopTokenRotation` by a display that also runs a bare-autorun fetch — see `StatusReporter`. | [FetchMixin](../fetchmixin#volatile-statuswindow) |
| **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](../fetchmixin#volatile-fetchcanceled) |
| **fetchRotation**{ type: string; id: string; } | synteny features open the SyntenyFeatureWidget; the inherited `selectFeature` action reads this getter, so no override is needed. | LGVSyntenyDisplay |
| **featureNoun**string | A row here is a PAF block, not a read — the group-label chips say "Show all features". The ONE place that word is chosen: the two menu builders below that take a `noun` read it from here rather than spelling it again, so the chips and the menus cannot end up naming the same row two different things. | LGVSyntenyDisplay |
| **derivativePathEvidence**DerivativePathEvidence | A chain here is one contig's blocks, and an assembly carries one or two contigs across a locus, so one is a route. Nothing names a block the view has not fetched (a PAF line has no SA tag), so a route is only what is on screen. | LGVSyntenyDisplay |
| **hideSelfAlignments**boolean | Whether the view's own assembly lane is hidden — see the slot. | LGVSyntenyDisplay |
| ReadonlySet<string> | The lane an all-vs-all track draws for the view's own assembly: its mate-assembly group key IS that assembly name. Hidden as a group key rather than filtered out of the fetch, so unchecking the option shows it again without a refetch.boolean | Whether this track's adapter has tiered storage to switch between — gates the "Level of detail" menu. | LGVSyntenyDisplay |
| **lodTier**LodTier | The tier this display's fetch asks for. Resolved here, on the main thread, so it lands in `rpcProps` — which is the refetch cache key, so a tier flip trips a refetch and a mid-zoom threshold crossing cannot go unnoticed. Forwarding a raw `bpPerPx` instead would invalidate every fetch on every zoom step; this changes only when the tier flips. | LGVSyntenyDisplay |
| **linkedReads**"normal" | "off" | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-linkedreads) |
| **pairsDisplayTypeDefault**Pin | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-pairsdisplaytypedefault) |
| **showBezierConnections**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showbezierconnections) |
| **showCoverage**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showcoverage) |
| **showPileup**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showpileup) |
| **coverageHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-coverageheight) |
| **coverageSnpMinFrequency**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-coveragesnpminfrequency) |
| **showMismatches**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showmismatches) |
| **showInterbaseIndicators**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showinterbaseindicators) |
| **flipStrandLongReadChains**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-flipstrandlongreadchains) |
| **colorSupplementaryChains**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-colorsupplementarychains) |
| **drawInter**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-drawinter) |
| **drawProperPairArcs**boolean | Whether ordinary concordant pairs get an arc. Same definition of concordant as `filterBy.properPairs`, which hides the reads themselves — see `isConcordantPairRead`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-drawproperpairarcs) |
| **minInterchromSupport**number | Reads a translocation must gather, within one fragment length on both sides, before its connector ticks are drawn. See `clusteredInterchromSupport` — the count is over a window because a mate-pair breakpoint is not localized to a base. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-mininterchromsupport) |
| **drawLongRange**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-drawlongrange) |
| **arcColorByType**"insertSize" | "insertSizeAndOrientation" | "orientation" | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arccolorbytype) |
| **readConnections**"arc" | "cloud" | "off" | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readconnections) |
| **arcsDisplayTypeDefault**Pin | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arcsdisplaytypedefault) |
| **readCloudDisplayTypeDefault**Pin | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readclouddisplaytypedefault) |
| **readConnectionsDown**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readconnectionsdown) |
| **readConnectionsDownDisplayTypeDefault**Pin | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readconnectionsdowndisplaytypedefault) |
| **showSashimiArcs**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showsashimiarcs) |
| **showSashimiArcsDisplayTypeDefault**Pin | "make the current sashimi on/off state the default for all tracks" control (pin) for the submenu's own checkbox. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showsashimiarcsdisplaytypedefault) |
| **sashimiArcsMode**"auto" | "down" | "up" | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-sashimiarcsmode) |
| **minSashimiScore**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-minsashimiscore) |
| **sashimiArcsHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-sashimiarcsheight) |
| **readConnectionsHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readconnectionsheight) |
| **showSoftClipping**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showsoftclipping) |
| **softClippingDisplayTypeDefault**Pin | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-softclippingdisplaytypedefault) |
| **view**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-ischainmode) |
| **showLinkedReadLines**boolean | Whether to draw the straight-line pass connecting normal read-pairs in pileup layout. Only meaningful when bezier connections are on AND we are in pileup mode — chain layout has its own connecting-line pass that already covers normal pairs WITHIN a region. Neither pass reaches across one (both are per region, one buffer each); that is `bezierArcScope`'s `crossRegion`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showlinkedreadlines) |
| **selectedFeatureId**string | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-selectedfeatureid) |
| **TooltipComponent**LazyExoticComponent<…> | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-tooltipcomponent) |
| **detectedModifications**ReadonlyMap<string, string> | Modification type code -> painted color, for every type the reads of the LOADED regions declare. This is what the data CONTAINS; what is actually drawn is filtered separately by isModificationTypeVisible and by `presentModifications`, so don't rename this back to "visible".boolean | Whether the MM/ML header parse has an answer for what is on screen — a fetch has landed, so an empty `detectedModifications` means "these reads carry none" rather than "nothing has arrived yet". The modifications menu shows "Loading modifications..." until this turns true, and offers the submenu after.string[] | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-detectedmodificationtypes) |
| **colorBy**ColorBy | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-colorby) |
| **filterBy**FilterBy | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-filterby) |
| **isFitting**boolean | True when fit-to-display mode is on AND a pitch has been computed (`fittedHeightPx > 0`, i.e. there are rows and room to fit them). The single gate both size getters read, so it's obvious they either both split the fitted pitch or both fall back to config — never a mix. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-isfitting) |
| **featureHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-featureheight) |
| **featureSpacing**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-featurespacing) |
| **rowHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-rowheight) |
| **configuredFeatureHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-configuredfeatureheight) |
| **maxHeight**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-maxheight) |
| **showSashimiLabels**boolean | Whether to draw the supporting-read count on each sashimi arc. Resolved through the promotable-slot tiers (resolveConf): an explicit track value pins labels on or off; otherwise it follows the session-wide default, falling back to off. A `maybeBoolean` slot, so (like mismatchAlpha) a session default of "on" can be customized back off on a single track. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showsashimilabels) |
| **showSashimiLabelsDisplayTypeDefault**Pin | "make the current sashimi-label state the default for all tracks" control (pin): symmetric, so it promotes whichever value the track currently shows. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showsashimilabelsdisplaytypedefault) |
| **hideNonCanonicalJunctions**boolean | Whether junctions with a non-canonical splice motif are dropped from the sashimi arcs. Promotable like `showSashimiLabels`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-hidenoncanonicaljunctions) |
| **hideNonCanonicalJunctionsDisplayTypeDefault**Pin | "make the current non-canonical filter state the default for all tracks" control (pin). | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-hidenoncanonicaljunctionsdisplaytypedefault) |
| **readIdsByChainName**Map<string, string[]> | Chain name → the ids of the READS in it. The two id spaces are easy to confuse and nothing else in this model crosses them: `chainNames` (the key here) is a chain's own identity, `readIds` (the values) are the reads', and every consumer of this map resolves the values through `readIdToIndex` / `readIdIndexMap`. Hence the names carried downstream — `highlightedChainReadIds`, `selectedChainReadIds`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readidsbychainname) |
| **showLowFreqMismatches**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showlowfreqmismatches) |
| **filterMismatchesByFrequency**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-filtermismatchesbyfrequency) |
| **mismatchAlpha**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-mismatchalpha) |
| **mismatchAlphaDisplayTypeDefault**Pin | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-mismatchalphadisplaytypedefault) |
| **sortedBy**SortedBy | undefined | The single read of the `sortedBy` slot, so the RPC args and the menu checkmarks cannot disagree about which sort is active.boolean | Lay out the widest features in the lowest pileup rows (main-thread tier-2 relayout via laidOutPileupMap). LGVSyntenyDisplay defaults it on. Ignored while an explicit `sortedBy` position sort is active. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-largefeaturesfirst) |
| **splicedReadsFirst**boolean | Lay out reads whose CIGAR carries a skip in the lowest pileup rows (tier-2 relayout). Ignored while an explicit `sortedBy` position sort is active. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-splicedreadsfirst) |
| **groupBy**GroupBy | undefined | In-track stacked grouping dimension (undefined = ungrouped). Falls back to the `groupBy` config slot, so a track can be pre-grouped declaratively. Sent to the worker via rpcProps; the worker partitions one fetch into N sections. The slot is `frozen` (unvalidated JSON), so `normalizeGroupBy` is the chokepoint that keeps an unrecognized type or a tag grouping with no tag name from reaching the worker. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-groupby) |
| **effectiveGroupBy**GroupBy | undefined | The grouping the fetch will actually partition by, which is what the worker resolves too (`executeRenderAlignmentData`): chain mode degrades a per-read dimension to ungrouped without the slot moving, so the slot alone never says which sections come back. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-effectivegroupby) |
| **groupKeySpace**string | Identity of the key space the fetched group keys live in, and so of every collection this model keys by group key — see `groupKeySpaceOf` for why a key alone cannot name its grouping. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-groupkeyspace) |
| **prefersOffset**boolean | Offset the track label above the visualization when grouping, so the stacked group sections aren't hidden behind an overlapping label.boolean | Whether each group draws as a single row, its overlap depth carried by the tint layer rather than by stacking — "is the collapse IN EFFECT". Reads `canCollapseGroupRows` rather than the slot alone, because the slot can be a track-config default (LGVSyntenyDisplay sets one) that either of that getter's conditions leaves inert: ungrouped it would flatten the whole pileup onto one row, and chain mode lays true stacks whatever the slot says (`collapsesRows`). Chain mode is reachable with the slot already ticked and drops the menu row that would untick it, so the two have to agree — the label chip words its height button off this getter. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-collapsegrouprows) |
| **canCollapseGroupRows**boolean | Whether collapsing can take effect at all, and so whether the "Show..." menu offers the toggle: the grouping has to be honored, and chain mode never collapses (`collapsesRows`) because a chain row is a chain and one row would drop the connecting lines the mode exists for. The menu omits the row rather than showing it disabled, since a click would write a slot no getter reads. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-cancollapsegrouprows) |
| **sortReadsBlockedReason**string | undefined | Why an explicit read ordering cannot take effect, or `undefined` when it can — one value carrying both the gate and the copy that names the switch, so a surface cannot grey a control out without saying which setting brings it back, and the two reasons cannot get out of step with the condition that produced them.boolean | Whether an explicit read ordering can take effect, and so whether the ordering controls are live. The sibling of `canCollapseGroupRows`, and read by both surfaces that can set an ordering — the track menu's "Sort by..." and the context menu's position-anchored sorts — so the two can't answer it differently. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-cansortreads) |
| **canSizeGroupHeights**boolean | Whether a single group's pileup height can be set on its own, and so whether the two surfaces that write `groupMaxHeightOverrides` are offered: the label chip's expand/fit button and the per-group drag handles. Both write the same volatile, so they answer this together — the chip used to be offered where the handle was hidden.ReadonlyMap<string, number> | The per-lane pileup-height overrides IN EFFECT, which is not the set banked. Fit derives one read pitch from every lane's FULL row count (`fittedReadPitch`), so a lane the layout still caps at its own override shows fewer rows than the pitch was solved for and leaves exactly that much of the display blank — the one thing the mode promises not to do.WiggleScaleType | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-coveragescaletype) |
| **coverageDomain**[number, number] | undefined | The autoscaled depth domain, spanning every SHOWN group (each block contributes one entry per group's coverage): a shared scale is what makes stacked sections visually comparable, and ungrouped is the one-group case. Hidden lanes are excluded — sizing the visible lanes' axis against a lane the user hid is exactly the comparability this scale exists to give. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-coveragedomain) |
| **coverageDepthDomain**[number, number] | undefined | The domain the coverage band draws against — `coverageDomain` with a log scale's floor pulled up to one read (see `coverageDepthDomain`).YScaleTicks | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-coverageticks) |
| **colorLegendCategories**Set<ReadColorCategory> | Read-color buckets actually present across the rendered reads, the single input that lets the legend list only relevant swatches (see legendUtils). Reads the same baked categories the renderer paints, so the two can't disagree. Empty while the legend is hidden so the O(reads) scan is skipped; MobX memoizes it against `laidOutByGroup`, which already folds in the scheme and the classification opts. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-colorlegendcategories) |
| **presentTagValues**ReadonlySet<string> | undefined | The per-read values the CPU-baked schemes actually painted in the rendered reads — tag values, or mate refNames under chromosome painting. The whole swatch list for those schemes, since their color is a pure function of the value (`bakedValueColor`) and so needs no discovered-value table to look up. It replaced one: `colorTagMap` only ever grew, so after panning it held every value the track had ever seen and keyed swatches for a chromosome the user had navigated away from.ReadonlySet<string> | undefined | The modification types actually drawn in the rendered reads. The twin of `presentTagValues`, against the same failure: `detectedModifications` takes each region's types as that region's fetch lands and is never cleared, so keying it whole named every type the track had ever seen — pan off the one locus carrying 6mA and the box still listed 6mA.ColorPalette | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-colorpalette) |
| **arcLegendCategories**Set<ReadColorCategory> | The arc color slots actually plotted, mapped to legend buckets — curved paired-end arcs and the read cloud's flat lines and endpoint squares alike, since both paint from `arcColorByType`. Its own vocabulary when the fills use a different scheme (a track colored by strand still draws insert-size-colored arcs), so it keys its own legend section then and folds into the read key otherwise — see `arcColorsMatchReads`. Empty unless an overlay is on with the legend shown. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arclegendcategories) |
| **arcColorsMatchReads**boolean | Whether the arc key folds into the read key — the overlay speaking the reads' own vocabulary, in the categories both are actually painting. `arcKeyFoldsIntoReadKey` holds the rule and the reasons the scheme names alone do not settle it. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arccolorsmatchreads) |
| **overlapLegendKind**"chain" | "collapsed" | undefined | Which overlap mark the reader is looking at, for the legend row that names it — undefined when there is none to name. The two layouts that put more than one feature on a row are drawn differently and the row differs with them: chain mode fills the span with a neutral that is no read category, collapsed rows tint what is underneath (overlap.slang)."Arc colors" | "Read cloud colors" | Heading for the overlay's own color key, named after the overlay the reader is looking at: flat read-cloud lines are not arcs. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arclegendtitle) |
| **arcBandInput**Map<string, ReadonlySet<string>> | Per group, which junctions draw in the strip below coverage (by `junctionKey`). The single sashimi side decision: `sashimiDownArcLanes` reads it to reserve the strip and `sashimiArcSections` reads it to place each arc, so the space reserved and the arcs drawn into it can't disagree. Memoized because the 'auto' assignment is O(junctions²) per lane.Set<string> | Group keys whose junctions land in the strip below coverage, i.e. the lanes that strip is reserved for. `belowCoverageBandsInput` only needs whether any lane wants the strip, `sections` needs which. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-sashimidownarclanes) |
| **belowCoverageBandsSettings**BelowCoverageBandsSettings | The settings half of the below-coverage band geometry — whether each strip MAY be reserved and how tall it is, with neither data half answered. Its two consumers answer those differently: the pooled `belowCoverageBandsInput` asks once for the whole stack, the fit budget once per lane. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-belowcoveragebandssettings) |
| **belowCoverageBandsInput**{…} | Inputs to `belowCoverageBandsGeometry` — the settings above, plus whether ANY lane has arcs or a sashimi junction bound for its strip. Both data halves are pooled over the lanes, which `computeStackedSections` asks per lane: the geometry here is the one ungrouped answer, and there the lanes agree with it because there is only the one. The grouped stack's own total is `totalBandOverhead`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-belowcoveragebandsinput) |
| **totalBandOverhead**number | What the below-coverage strips cost the fit-to-viewport row budget over the whole stack: every lane's own reserved bands, summed the way `computeStackedSections` reserves them.LaidOutByGroup | Per-group laid-out data: group key → (region index → laid-out data). Each group lays out independently (own `maxRows` cap) so a dense group can't starve the rest. When grouped, the default cap fits all sections into the viewport (`fitGroupMaxRows`) so the stack doesn't tower and need scrolling; a per-group height drag / expand still overrides it.boolean | Whether the unpaired chain-strand framing is live, as a BOOLEAN and in its own computed. The boolean is the point: nine of the schemes give one of two answers, so MobX's value comparison stops a scheme switch from invalidating `laidOutByGroupFramed` unless the answer actually moved. Reading `framesUnpairedChainStrand` inline there instead would make the frame solve depend on `colorBy` itself and re-run on every switch — which is what it used to do. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-frameschainstrand) |
| **laidOutByGroupFramed**LaidOutByGroup | The laid-out data with every chain's strand frame settled — see `applyChainStrandFrames`, which says why the two passes are here and not in the colour bake below. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-laidoutbygroupframed) |
| **laidOutByGroup**ColoredByGroup | Per-group laid-out data with the per-read color arrays baked on. Every consumer reads this one; `laidOutByGroupUncolored` exists only to be its layout half.((refName: string) => number | undefined) | undefined | Where a mate's reference sits in this assembly's own chromosome order, for chromosome painting — the alignments twin of `LinearSyntenyDisplay.paintedChromosomeOrder`, and the thing that lets the palette be handed out rather than hashed into (`refNameColor`).GroupId[] | Group keys + labels in stacking order; a single entry (key '') when ungrouped. Derived straight from the fetched `rpcDataMap` (not from the layout pass), so group identity/order stays stable across relayouts. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-grouporder) |
| **showsGroupLabels**boolean | Whether the stacked section labels + dividers are drawn. Deliberately NOT `isGrouped`: grouping that happens to yield one section (a region with reads on one strand, a tag with a single value) still reserves the label offset (`prefersOffset`) and still wants its section named and collapsible — otherwise it reads as an ungrouped track with mysterious blank space above it. `isGrouped` stays about the scroll model (>1 section scrolls coverage with its section), which one section doesn't change. Reads the fetched sections rather than `groupBy` — see `hasNamedGroups` for why the setting is the wrong signal. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showsgrouplabels) |
| **rawDataByGroup**Map<string, Map<number, WorkerPileupData>> | Raw (un-laid-out) data regrouped as group key → (region idx → data), insertion-ordered so the first key is the primary group. The arc compute and the per-section sashimi overlay both read one group's raw map from here; ungrouped is the single key `''`.((refName: string) => string) | undefined | Normalizer for a refName that arrives in the BAM's own spelling (an SA tag's or RNEXT's `chr1`) rather than the assembly-canonical one a fetched read carries (`1`). Undefined when no assembly is resolved (`loadedAssembly`), where the consumers fall back to identity.ArcsByGroupResult | THE arc resolution, whole: both halves of what this fetch's reads say, from one pass. Read it through `arcsByGroup` (what a per-region pass draws) or `crossRegionArcsByGroup` (what only the overlay can), which are its two faces and are documented there.Map<string, Map<number, ArcsUploadData>> | The per-region GPU/Canvas2D upload feed. Every consumer that packs, draws or hit-tests a region's arcs reads this; the arcs it does NOT contain are the cross-region ones, which no per-region pass can draw (`CrossRegionArc`) and which `crossRegionArcsByGroup` carries instead. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arcsbygroup) |
| **crossRegionArcsByGroup**Map<string, CrossRegionArc[]> | Arcs whose two feet are in different displayed regions, per group. Drawn by an SVG overlay across the whole view, because the per-region passes map bp to x through the block's own range and would each extrapolate the far foot to a place the other block is not — see `CrossRegionArc` for the measurement. Empty in a single-region view. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-crossregionarcsbygroup) |
| **hasReadsForDerivativePaths**boolean | Whether there are reads to reconstruct FROM, as opposed to reads that describe no rearrangement. An empty `derivativePathCandidates` means either, and they call for opposite responses: widen the window, or narrow it. A window too large for the track's byte budget renders as `force load` with nothing behind it, and reporting that as "no path is supported here" sends a reader looking for an event that was never fetched. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-hasreadsforderivativepaths) |
| **medianReadSpanBp**number | Median aligned length of the reads in view, in bp — how much reference one alignment covers, which is what decides whether a read can carry a junction at all. The picker's empty state reads it to tell a library that cannot describe a rearrangement from a window that happens to hold none.DerivativeCandidate[] | Derivative-allele paths the reads in view describe, most-supported first. Each read's SA chain is already an ordered, oriented list of reference intervals — a derivative path — so the proposal is a grouping of those chains rather than any new analysis. Empty when no reads are loaded, which `hasReadsForDerivativePaths` distinguishes.number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-modificationthreshold) |
| **colorSchemeIndex**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-colorschemeindex) |
| **showModifications**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showmodifications) |
| **showPerBaseQuality**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showperbasequality) |
| **showPerBaseLetter**boolean | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showperbaseletter) |
| **readIdIndexMap**ReadIdIndexMap | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readidindexmap) |
| **layoutReady**boolean | Whether `searchFeatureByID` has a pileup to search. Same name and meaning as the canvas display's; see MultiRegionDisplayMixin. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-layoutready) |
| **readConnectionsLineWidth**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readconnectionslinewidth) |
| **belowCoverageBands**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-coveragedisplayheight) |
| **lanes**AlignmentLane[] | The stacked lanes, in stacking order: one `AlignmentLane` per drawn group, ungrouped being the one-lane case.AlignmentLane[] | The lanes actually laid out, or the one SYNTHETIC lane. `sections` has to produce a section before any fetch lands — and a grouped fetch over an empty region partitions to zero lanes — so the section pipeline is never handed an empty list. Every collection on it is empty by construction, `maxY` included. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-drawnlanes) |
| **pileupTruncated**boolean | True when any pileup hit the display-wide `maxHeight` and overflow reads were collapsed. Reads every lane, not just an ungrouped one: the ceiling is display-wide, so a stacked lane clipped by it is exactly as unreachable as an ungrouped pileup would be, and the per-label affordance deliberately steps aside for it.SectionsLayout | Single source of all vertical band geometry, one entry per lane. `computeStackedSections` reproduces the prior ungrouped reserved layout exactly for its single-section (N==1) case, so ungrouped is not a special branch here — it is the one-lane call, over `drawnLanes` so a display with no data still has a section. The sticky-coverage-vs-scroll distinction lives downstream in `buildSectionRenders`, keyed off section count. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-sections) |
| **renderSections**LaneSection[] | Every lane paired with its band geometry, in stacking order: the list the overlays, the hit-test pipeline and both renderers all walk.BezierArcScope | What the SVG connection overlay is responsible for drawing — see `BezierArcScope`. Chain mode claims `crossRegion` even with the curved connectors unticked, because it is the only pass that can join a chain's two ends when they land in different displayed regions; the per-region connecting line covers everything else.Set<number> | Connection types (LINKED_READ_COLOR_*) actually drawn as bezier/line arcs in view, the input that lets the legend list only the connection colors present. `bezierPairSections` is already narrowed to what the overlay draws (`enumerateBezierPairs` applies the scope's own predicate), so this scans the same list the curves come from rather than re-deriving the skip rule beside it. Empty while the legend is hidden so the scan is skipped. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-bezierconnectioncolortypes) |
| **sashimiArcSections**SashimiArcSection[] | Per-section sashimi arcs, in stacking order. The overlay and the SVG export both map over this, so it is the single source for sashimi geometry and neither path can drift; ungrouped is the single-section case (sticky band below sticky coverage). Empty when sashimi is off.boolean | True when reads are stacked into >1 group section. Drives the scroll model: ungrouped keeps coverage sticky (only the pileup scrolls); grouped scrolls the whole coverage+pileup stack as one. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-isgrouped) |
| **scrollModel**ScrollModel | The scroll-projection inputs (`sectionScreen.ts`) every overlay needs to map a content-space Y into screen space. Built once here so the label / resize-handle / coverage-axis overlays don't each re-assemble `{ isGrouped, scrollTop, canvasHeight }` inline. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-scrollmodel) |
| **pileupViewportHeight**number | Height of the scrollable viewport. Ungrouped excludes the sticky coverage band; grouped scrolls the entire display. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-pileupviewportheight) |
| **pileupContentHeight**number | Total scrollable content height. Grouped is the full stacked-sections height; ungrouped is the pileup band alone (coverage is sticky), which is the stacked height minus that sticky coverage band. Both read the laid-out `sections` so the scroll extent tracks the geometry actually drawn — when `showPileup` is off or the group is collapsed the section reserves no pileup rows, so this collapses to 0 and no phantom scroll region opens up below the coverage band. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-pileupcontentheight) |
| **growTargetHeight**number | HeightModeMixin's grow hook: the full laid-out content height (coverage + pileup + arcs), before the `growMaxHeight` cap. Independent of `self.height` — `laidOutByGroup` fits to `growMaxHeight` in grow mode (not the reactive `height`), and `featureHeight` is the configured value there rather than the fitted pitch — which is what lets the mixin's `height` return it without cycling. `grownHeight`, the `height` override and the grow-aware `resizeHeight` all come from the mixin. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-growtargetheight) |
| **scalebarOverlapLeft**number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-scalebaroverlapleft) |
| **showOutline**any | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-showoutline) |
| **visibleLabels**VisibleLabel[] | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-visiblelabels) |
| **highlightChainReadIds**string[] | Read ids of the hovered chain's members, empty unless in chain mode. Single source for the "is this a chain highlight" decision that both `highlightBoxes` (which ids to box) and `HighlightOverlay` (how strongly to shade them) read, so the two can't drift. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-highlightchainreadids) |
| **highlightBoxes**HighlightBox[] | Screen boxes for the hovered read / chain, painted by the `HighlightOverlay` div. Deliberately NOT part of `renderState`: the hovered id changes on nearly every mousemove, and routing it through the canvas would repaint the whole pileup each move. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-highlightboxes) |
| **readCategoryLabel**(c: ReadColorCategory) => string | undefined | Names one read color bucket for the hover, with the active scheme's rewording already applied — the same `readCategoryLabelOverrides` the legend box uses, so the tooltip and the swatch it sends the reader to cannot say different things about one color. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-readcategorylabel) |
| **fittedFeatureHeight**number | The read height that makes every uncollapsed group's reads fill the display without scrolling — the fractional pitch, the 1px floor and the Normal-pitch cap all being `fittedReadPitch`'s.number | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-scrollableheight) |
| **sortTag**string | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-sorttag) |
| **renderState**{…} | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-renderstate) |
| **arcsYDomainBp**number | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-arcsydomainbp) |
| **insertSizeTickSections**{ groupKey: string; ticks: YScaleTicks; }[] | The read cloud's insert-size ruler, per section — see `computeInsertSizeTickSections`. Empty outside read-cloud mode, which is the only mode that puts \|TLEN\| on the band's Y axis. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-insertsizeticksections) |
| **crossRegionArcSections**number | Genomic bp one per-base cell stands for in the worker's extract: `subPixelBinBp` off the debounced zoom, and `1` in every color mode that does not paint a wall of them.number | The same bin off the LIVE zoom, and read by `dataSuperseded` alone.SimpleFeature | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-hoveredfeature) |
| **regionFetchKey**string | `MultiRegionDisplayMixin`'s per-region content axis: what a fetch issued right now would produce. Only the per-base bin moves it, so in every other color mode this is one constant string and a zoom never refetches on its account; in the two per-base modes a bin flip refetches the regions on screen and leaves the rest of the held data alone, which is the whole reason the bin is not in `rpcProps`.boolean | `MultiRegionDisplayMixin`'s supersession hook: the settled per-base bin has not moved yet, but the live zoom has already left it, so the clear is inevitable and not yet committed.{ max: number; } | The legal range for any of the three drag-resizable bands stacked over the pileup (coverage, read connections, sashimi).boolean | Opt into RegionTooLargeMixin's byte gate: `fetchNeeded` passes `resolvedByteLimit()` to `RenderAlignmentData`, whose first await is the index estimate — so an over-budget region is refused before a single read is downloaded. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#getter-gateenabled) |
| **parentTrack**AbstractTrackModel | | [BaseDisplay](../basedisplay#getter-parenttrack) |
| **RenderingComponent**FC<…> | | [BaseDisplay](../basedisplay#getter-renderingcomponent) |
| **DisplayBlurb**Record<string, unknown> | | [BaseDisplay](../basedisplay#getter-adapterconfig) |
| **isMinimized**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) |
| **height**number | | [TrackHeightMixin](../trackheightmixin#getter-height) |
| **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)."fit" | "fixed" | "grow" | The resolved track-height strategy (`fixed`/`grow`/`fit`). Promotable sentinel slot: resolveConf walks the customized-track -> session-default -> `fixed` cascade and never returns the `inherit` sentinel. | [HeightModeMixin](../heightmodemixin#getter-heightmode) |
| **fitTargetHeight**number | The drag-resizable track height as stored in the config slot — the fit target the fit/grow layout scales or packs content into. Read there instead of the reactive `height` getter to break the grow-mode cycle (`height`->grownHeight->layout->height). Equals `height` in fixed/fit. | [HeightModeMixin](../heightmodemixin#getter-fittargetheight) |
| **growMaxHeight**number | Ceiling `grow` mode sizes the track to, in px (content past it scrolls). Lives here rather than as a constant so a track whose whole point is a deep pileup can raise it; both displays that own a `grownHeight` read this, so the two can't diverge. | [HeightModeMixin](../heightmodemixin#getter-growmaxheight) |
| **autoHeight**boolean | `grow` mode as a boolean, derived from the unified `heightMode` slot. | [HeightModeMixin](../heightmodemixin#getter-autoheight) |
| **fitHeightToDisplay**boolean | `fit` mode as a boolean, derived from the unified `heightMode` slot. | [HeightModeMixin](../heightmodemixin#getter-fitheighttodisplay) |
| **grownHeight**number | Target track height for `grow`: what the content wants, capped so a deep stack doesn't grow the track to thousands of px (the remainder scrolls). What `installGrowExitBake` bakes into the slot on exit. | [HeightModeMixin](../heightmodemixin#getter-grownheight) |
| **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](../multiregiondisplaymixin#getter-host) |
| **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.boolean | Overrides `RenderLifecycleMixin`'s default-true hook with the LGV precondition both foundations share — see `foundationCanRender`. | [MultiRegionDisplayMixin](../multiregiondisplaymixin#getter-canrender) |
| **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.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](../multiregiondisplaymixin#getter-viewportempty) |
| **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](../multiregiondisplaymixin#getter-renderblocks) |
| **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 this (not "the first datum arrived") is what keeps a multi-region/whole-genome export complete.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](../multiregiondisplaymixin#getter-svgready) |
| **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](../multiregiondisplaymixin#getter-paintinert) |
| **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 `computeLoadingTerm` reaches all three without being wired three times.boolean | Whether the density axis applies. `CanvasFeatureGateMixin` contributes `true` beside its measurement; byte-only displays leave it. | [RegionTooLargeMixin](../regiontoolargemixin#getter-densitygateenabled) |
| **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](../regiontoolargemixin#getter-bytegateadapterconfig) |
| **configuredFetchSizeLimit**number | The display's `fetchSizeLimit` slot, from `regionTooLargeConfigSchemaFields`. | [RegionTooLargeMixin](../regiontoolargemixin#getter-configuredfetchsizelimit) |
| **densityTooLarge**boolean | The density axis's verdict; canvas overrides it. | [RegionTooLargeMixin](../regiontoolargemixin#getter-densitytoolarge) |
| **byteGateAdapterPath**string[] | 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](../regiontoolargemixin#getter-bytegateadapterpath) |
| **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](../regiontoolargemixin#getter-adapterfetchsizelimit) |
| **configForceLoad**boolean | The declarative `forceLoad` slot. | [RegionTooLargeMixin](../regiontoolargemixin#getter-configforceload) |
| **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. 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. | [RegionTooLargeMixin](../regiontoolargemixin#getter-gateviewport) |
| **byteGateAdapterKey**string | Which tier the estimate is about, as a comparable string. | [RegionTooLargeMixin](../regiontoolargemixin#getter-bytegateadapterkey) |
| **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](../regiontoolargemixin#getter-aboveforceloadfloor) |
| **gateExempt**boolean | Nothing may gate on either axis: the `forceLoad` slot or the button. | [RegionTooLargeMixin](../regiontoolargemixin#getter-gateexempt) |
| **estimatedFetchBytes**number | undefined | The stored estimate's bytes; undefined when nothing has been measured. | [RegionTooLargeMixin](../regiontoolargemixin#getter-estimatedfetchbytes) |
| **gateMeasurementStale**boolean | Whether the last measurement is about a viewport the user has since left. True before any measurement. | [RegionTooLargeMixin](../regiontoolargemixin#getter-gatemeasurementstale) |
| **gateByteLimit**number | The byte budget: the adapter's limit, else the display's, doubled below `AUTO_FORCE_LOAD_BP`. Read only through `resolvedByteLimit()`. | [RegionTooLargeMixin](../regiontoolargemixin#getter-gatebytelimit) |
| **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](../regiontoolargemixin#getter-gateactive) |
| **densityGateActive**boolean | `gateActive` plus the density axis's own terms: the axis is on, and the span is above the floor. | [RegionTooLargeMixin](../regiontoolargemixin#getter-densitygateactive) |
| **tooLargeStatus**RegionTooLargeStatus | The verdict and its banner text, from the stored estimate against `resolvedByteLimit()` and the density axis when it may act. | [RegionTooLargeMixin](../regiontoolargemixin#getter-toolargestatus) |
| **regionTooLarge**boolean | | [RegionTooLargeMixin](../regiontoolargemixin#getter-regiontoolarge) |
| **regionTooLargeReason**string | Banner text for the axis that tripped; empty when not too large. | [RegionTooLargeMixin](../regiontoolargemixin#getter-regiontoolargereason) |
| **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](../regiontoolargemixin#getter-zoomcanreleasegate) |
| **gateSkipsMeasuredViewport**boolean | The skip both fetch skeletons apply: the banner is up and its measurement already describes the viewport on screen. | [RegionTooLargeMixin](../regiontoolargemixin#getter-gateskipsmeasuredviewport) |
| **rendersCanvas**boolean | Overridable hook (default true): whether this display paints a canvas in its **current** configuration, as opposed to a deliberate static placeholder (LD with the triangle off, sequence past base resolution — both render a message where the ` | [RenderLifecycleMixin](../renderlifecyclemixin#getter-renderscanvas) |
| **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 saying otherwise is a lie that never resolves.boolean | true while a fetch is active | [FetchMixin](../fetchmixin#getter-isloading) |
| **isLoadingOrCanceled**boolean | `isLoading` widened to cover a user-canceled load. **This, not `isLoading`, is what a `displayPhase` loading term wants.** `cancelFetchByUser` clears the stop token synchronously, so `isLoading` goes false the instant the user clicks Cancel — and the loading overlay that unmounts on it is carrying the Retry button, which is the only way back: the state is deliberately durable, so no autorun restarts the fetch on its own. A bare `isLoading` therefore reads as `ready` over a display that is stopped, empty and offering nothing.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.boolean | Overridable hook (default false), read only by the dev-only retry 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.string | The RPC cache key both fetch foundations invalidate on: this display's `rpcProps()` payload serialized to a string. `serializeRpcProps` owns the why, including the silently-dead-axis corollary.string | | [ScoreScaleMixin](../scorescalemixin#getter-scaletype) |
| **autoscaleType**string | | [ScoreScaleMixin](../scorescalemixin#getter-autoscaletype) |
| **numStdDev**number | | [ScoreScaleMixin](../scorescalemixin#getter-numstddev) |
| **minScore**number | Raw slot value, sentinel intact — see the class comment. | [ScoreScaleMixin](../scorescalemixin#getter-minscore) |
| **maxScore**number | Raw slot value, sentinel intact — see the class comment. | [ScoreScaleMixin](../scorescalemixin#getter-maxscore) |
| **defaultScoreDomain**[number | undefined, number | undefined] | Overridable hook: what each end of the domain falls back to where the config leaves its bound unset. `[undefined, undefined]` — the default — means autoscale both ends, which is right for a track whose scores have no absolute meaning (a bigwig's units are its own).number | undefined | Resolved lower bound; `undefined` means autoscale this end. | [ScoreScaleMixin](../scorescalemixin#getter-minscorebound) |
| **maxScoreBound**number | undefined | Resolved upper bound; `undefined` means autoscale this end. | [ScoreScaleMixin](../scorescalemixin#getter-maxscorebound) |
| **showLegend**boolean | Whether the legend is drawn. Resolved through the promotable-slot tiers (`resolveConf`): an explicit track value customizes it either way, otherwise it follows the session-wide default for this display type, falling back to the slot's `promotedBase`. | [LegendMixin](../legendmixin#getter-showlegend) |
| **showLegendDisplayTypeDefault**Pin | The "make the current legend visibility the default for all tracks" control. Symmetric, so it promotes whichever value the track currently shows. `showLegendCheckboxItem` takes this as its `pin`. | [LegendMixin](../legendmixin#getter-showlegenddisplaytypedefault) |
## Methods
| Member | Description | Defined by |
| --- | --- | --- |
| **rpcProps**() => {…} | Adds the resolved detail tier to the base alignments RPC payload. | LGVSyntenyDisplay |
| () => MenuItem[] | | LGVSyntenyDisplay |
| (mode: "auto" | "down" | "up") => Pin | "make this arc placement the default for all tracks" control (pin), one per option of the radio group. A method rather than a getter per value: the options share one slot and differ only in the on-value, so naming each combination was what made the base value 'up' look unpinnable. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-sashimiarcsmodedisplaytypedefault) |
| **isGroupCollapsed**(key: string) => boolean | Whether a stacked group's pileup is collapsed to just its coverage. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-isgroupcollapsed) |
| **hasGroupHeightOverride**(key: string) => boolean | Whether a stacked group carries a custom pileup-height override — set by expanding it (show all reads) or dragging its resize handle (taller or shorter). Drives the group label's restore-to-fit affordance.() => LegendItem[] | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-legenditems) |
| **arcLegendItems**() => LegendItem[] | Key for the paired-end arc / read-cloud colors. Empty when no overlay is drawn, or when it shares the reads' scheme and merged into their key — either way its legend section drops out of the box. A *partial* overlap is not resolved here: this stays the complete arc key, and `getAlignmentsLegendSections` folds it into one deduped list. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-arclegenditems) |
| **findFeatureInRpcData**(featureId: string) => ReadHit | undefined | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-findfeatureinrpcdata) |
| **laneFor**(key: string) => AlignmentLane | undefined | One lane by group key, for the per-key questions a component asks with a `groupKey` in hand. `undefined` for a key that isn't drawn. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-lanefor) |
| **groupClippedBy**(key: string) => RowCapSource | undefined | Which cap hid reads from a lane's pileup, or `undefined` when nothing was hidden — including for a key that isn't drawn. A read of what the layout pass recorded (`RowCapSource` names them), not a re-derivation: the pass is handed its cap with the policy attached, so the answer comes back out of the layout instead of being reconstructed from a row count afterwards.(key: string) => boolean | True when a lane's pileup was clipped by a cap the per-lane expand can actually raise — the rule behind the "show all" affordance, which must not appear where it would do nothing. The chip itself asks `laneExpandable` off the section it already holds; this is the same question for the callers that have only a key, like `isGroupCeilingClipped` beside it.(key: string) => boolean | True when THIS lane's pileup was clipped by the display-wide `maxHeight` and its overflow reads were collapsed. Drives the rule drawn across the bottom of the clipped rows — see `PileupTruncationRule`, which is per section because the notice marks the place where the reads stop rather than a state of the whole track.() => LegendItem[] | Legend swatches for the linked-read connection curves, empty unless the overlay has something to draw (`bezierArcScope`) and at least one connection is in view — including the cross-region connectors chain mode draws without the curved-connector box ticked, since those are colored by the same rules and a color on screen needs its key. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-bezierlegenditems) |
| **groupPileupOffset**(groupKey: string) => number | Content-space Y of a group's pileup relative to the reserved below-coverage height, i.e. how far a read's row shifts because its group is stacked below the others. 0 for the ungrouped/first section, except when that lane drops its arc band (`hasArcs` false), where it goes slightly negative — callers add `coverageDisplayHeight` back, so the sum is the section's real `pileupTop` either way. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-grouppileupoffset) |
| **searchFeatureByID**(rpcData: WorkerPileupData, index: number) => string[] | Read ids sharing a chain with the read at `index` in `rpcData` — the read's own included, since it is a member of its chain. Empty when the read isn't part of a chain. Shared by hover-highlight and click-select so the two paths can't drift. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-readidssharingchain) |
| **getFeatureInfoById**(groupKey: string, dropped: number, kept: number) => void | Warn that a lane's cross-region arcs were capped — once per NUMBER rather than once per evaluation. `crossRegionArcSections` re-projects every foot through `view.bpToPx`, so it reads `view.offsetPx` and MobX re-evaluates it on every pan frame; that is correct and necessary, but a bare `console.warn` in there fires per frame for as long as a capped lane is on screen, which is a console nobody can read anything else in. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#method-reportarccap) |
| **renderingProps**(_displayedRegionIndex: number) => boolean | Overridable hook (default true): whether the display can actually draw what this region is marked loaded over. Two different displays want it for two different reasons, and both are real:(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 `regionFetchKey` (what a fetch now would produce) and `regionHasData` (did the last one store anything), and this compares the key against the one the region was fetched under. A subclass that changes what it fetches spells the change in the key, and one that forgets gets a redundant fetch rather than a cached answer for a zoom the data was never fetched at. | [MultiRegionDisplayMixin](../multiregiondisplaymixin#method-iscachevalid) |
| **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](../regiontoolargemixin#method-resolvedbytelimit) |
| **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](../regiontoolargemixin#method-gatefetchstate) |
## Actions
| Member | Description | Defined by |
| --- | --- | --- |
| **setHideSelfAlignments**(flag: boolean) => void | Show/hide the view's own assembly lane of an all-vs-all track. | LGVSyntenyDisplay |
| **setLodMode**(arg: LodMode) => void | | LGVSyntenyDisplay |
| **setShowCoverage**(show: boolean) => void | The other half of the sashimi/coverage tie. Without it, hiding coverage left "Show sashimi arcs" ticked over a display drawing none — and the worker skips the junction scan entirely when the band is off (`runCoveragePipeline`), so the arcs the checkbox advertised had no data behind them either. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowcoverage) |
| **clearMouseoverState**() => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-clearmouseoverstate) |
| **setError**(error?: unknown) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-seterror) |
| **setRpcData**() => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-cleardisplayspecificdata) |
| **clearSelection**() => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-clearselection) |
| **setSelectedChainReadIds**(ids: string[]) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setselectedchainreadids) |
| **setColorScheme**(colorBy: ColorBy) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setcolorscheme) |
| **setFilterBy**(filterBy: FilterBy) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setfilterby) |
| **setShowSoftClipping**(value: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowsoftclipping) |
| **setMismatchAlpha**(value: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setmismatchalpha) |
| **setSortedBy**(type: string, tag?: string | undefined) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setsortedby) |
| **setSortSlot**() => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-clearsortedby) |
| **setLargeFeaturesFirst**(flag: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setlargefeaturesfirst) |
| **setSplicedReadsFirst**(flag: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setsplicedreadsfirst) |
| **setGroupBy**(groupBy?: GroupBy | undefined) => void | Set (or remove, when undefined) the in-track stacked grouping dimension. A tier-1 refetch setting (in `rpcProps`) — the worker re-partitions the fetch into N sections. Resets the Y scroll since the stacked content height changes. Ungrouping stores an explicit `null` override (not a cleared override) so it beats a configured `groupBy` default rather than falling back to it.() => void | Forget every collapse and height override. Each is keyed by group key, and a group key only names a lane within the grouping that issued it, so a key-space change invalidates all of them at once. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-dropgrouplanestate) |
| **setCollapseGroupRows**(flag: boolean) => void | Draw each group as one row (overlap depth shows as tint shading) rather than as its own stack. Clears the per-group height overrides: an override means "this lane opted out of the collapse", which is meaningless once every lane is a stack again. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setcollapsegrouprows) |
| **toggleGroupCollapsed**(key: string) => void | Collapse/expand a stacked group's pileup (coverage stays visible). | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-togglegroupcollapsed) |
| **toggleGroupExpanded**(key: string) => void | Expand a fit-to-viewport group back to the full `maxHeight` cap (show all its reads), or, if it already carries a height override (from expand or a drag), drop the override to return it to the fit budget. Expanding makes the stack overflow the viewport, which engages the pileup scroll. Pairs with `hasGroupHeightOverride`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-togglegroupexpanded) |
| **resizeGroupHeight**(key: string, dy: number) => void | Drag a stacked group's pileup band taller/shorter by `dy` px, capping how many rows that group lays out. The continuous-accumulation policy (seed once, floor at a row, pin/skip a fully-shown group) lives in the pure `nextGroupHeightOverride`; this action just gathers the group's live state and commits the result (undefined = leave on the fit budget). Pairs with `hasGroupHeightOverride` / `toggleGroupExpanded`. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-resizegroupheight) |
| **setFeatureHeight**(height?: number | undefined) => void | Set the per-read pixel size. The track-sizing mode is a mostly independent axis (changed via setHeightMode): grow keeps growing at the new size. Fit is the exception — it derives the size, so a chosen size would be dormant; picking one drops back to fixed so the pick takes effect. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setfeatureheight) |
| **setMaxHeight**(height?: number | undefined) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setmaxheight) |
| **setHeightMode**(mode: "fit" | "fixed" | "grow") => void | The two pieces of transient state a uniform fit/grow contradicts that HeightModeMixin can't know about. The slot write and the scroll reset are its `setHeightMode`, captured as super above. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setheightmode) |
| **setFittedHeightPx**(px: number) => void | Cache the fitted read height so the `featureHeight`/`featureSpacing` getters can split it into a body + derived gap. Written only by the driving autorun. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setfittedheightpx) |
| **setShowSashimiArcs**(show: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowsashimiarcs) |
| **setReadConnections**(mode?: "arc" | "cloud" | "off" | undefined) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setreadconnections) |
| **setReadConnectionsDown**(down: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setreadconnectionsdown) |
| **setDebugArcGeometry**(on: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setdebugarcgeometry) |
| **setShowPileup**(show: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowpileup) |
| **setCoverageHeight**(height: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setcoverageheight) |
| **setCoverageSnpMinFrequency**(fraction: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setcoveragesnpminfrequency) |
| **setReadConnectionsHeight**(height: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setreadconnectionsheight) |
| **setSashimiArcsHeight**(height: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setsashimiarcsheight) |
| **setMinSashimiScore**(score: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setminsashimiscore) |
| **setSashimiArcsMode**(mode: "auto" | "down" | "up") => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setsashimiarcsmode) |
| **setShowSashimiLabels**(show: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowsashimilabels) |
| **setHideNonCanonicalJunctions**(hide: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-sethidenoncanonicaljunctions) |
| **setReadConnectionsLineWidth**(width: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setreadconnectionslinewidth) |
| **setDrawInter**(draw: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setdrawinter) |
| **setDrawProperPairArcs**(draw: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setdrawproperpairarcs) |
| **setMinInterchromSupport**(support: number) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setmininterchromsupport) |
| **setDrawLongRange**(draw: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setdrawlongrange) |
| **setArcColorByType**(show: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowmismatches) |
| **setShowInterbaseIndicators**(show: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowinterbaseindicators) |
| **setFlipStrandLongReadChains**(flag: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setflipstrandlongreadchains) |
| **setColorSupplementaryChains**(flag: boolean) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setcolorsupplementarychains) |
| **setLinkedReads**(mode: "normal" | "off") => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setlinkedreads) |
| **setShowBezierConnections**(flag: boolean) => void | Toggle the paired-read connection overlay. A main-thread tier-2/4 setting (read in `laidOutPileupMap` + `renderState`), not in `rpcProps` — toggling it never refetches. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setshowbezierconnections) |
| **setFeatureIdUnderMouse**(feature?: string | undefined) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setfeatureidundermouse) |
| **setMouseoverExtraInformation**(extra?: TooltipPayload | undefined) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setmouseoverextrainformation) |
| **setHoverState**(state: {…}) => void | The whole hover state in one action. Every branch of the pileup's mousemove handler goes through here — including the plain-read branch, which used to fire three or four separate setters per move and was the only one that left `hoverCoverageBand` stale. `highlightedChainReadIds` is empty outside chain mode. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-sethoverstate) |
| (feature?: Feature | undefined) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-setcontextmenufeature) |
| () => void | Close the right-click menu and release the hover it pinned. `openContextMenu` boxes the read the menu acts on and `handleMouseLeave` holds that box while the menu is up, so this is the only place the pin comes off — without it the box outlives the menu until the cursor next crosses the pileup, which it need not do at all when the item clicked opened a drawer widget. Mirrors canvas LinearBasicDisplay.closeContextMenu. | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-closecontextmenu) |
| **selectFeature**(feature: Feature) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-selectfeature) |
| **startRenderingBackend**(backend: AlignmentsRenderingBackend) => void | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-startrenderingbackend) |
| **withFeatureById**(featureId: string) => Promise<void> | | [LinearAlignmentsDisplay](../linearalignmentsdisplay#action-selectfeaturebyid) |
| () => void | Fills `BaseDisplay`'s hover-clear hook, which the fetch foundation's reaction calls on every viewport change.(status?: RpcStatus | undefined) => void | | [BaseDisplay](../basedisplay#action-setstatusmessage) |
| **reload**() => void | base display reload does nothing, see specialized displays for details | [BaseDisplay](../basedisplay#action-reload) |
| **setScrollTop**(scrollTop: number) => void | Clamped into `[0, scrollableHeight]`, so no caller has to remember the bound. Unbounded for a display that leaves `scrollableHeight` at its `Infinity` default. | [TrackHeightMixin](../trackheightmixin#action-setscrolltop) |
| **setHeight**(displayHeight: number) => number | | [TrackHeightMixin](../trackheightmixin#action-setheight) |
| **resizeHeight**(distance: number) => number | | [TrackHeightMixin](../trackheightmixin#action-resizeheight) |
| **expandToContentHeight**() => number | Grow the track by exactly the content it is currently hiding, so a display scrolled over a taller stack ends up showing all of it. The track's resize handle runs this on a double click.(displayedRegionIndex: number) => void | Forget one region — for a display pruning what has scrolled off screen. | [MultiRegionDisplayMixin](../multiregiondisplaymixin#action-droploadedregion) |
| **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](../multiregiondisplaymixin#action-clearallrpcdata) |
| **fetchRegions**() => void | installs the fetch-lifecycle autoruns (DisplayedRegionsChange, FetchVisibleRegions, SettingsInvalidate, ClearBlockingStateOnViewportChange) | [MultiRegionDisplayMixin](../multiregiondisplaymixin#action-afterattach) |
| **setByteEstimate**() => void | Drops the estimate and the viewport stamp. `forceLoadTrack` survives: it is a track-wide approval. | [RegionTooLargeMixin](../regiontoolargemixin#action-clearbyteestimate) |
| **setForceLoadTrack**(flag: boolean) => void | | [RegionTooLargeMixin](../regiontoolargemixin#action-setforceloadtrack) |
| **commitFetchBytes**() => void | The banner's button: exempt the track on both axes and refetch. | [RegionTooLargeMixin](../regiontoolargemixin#action-forceload) |
| **markCanvasDrawn**() => void | | [RenderLifecycleMixin](../renderlifecyclemixin#action-markcanvasdrawn) |
| **resetCanvasDrawn**() => void | | [RenderLifecycleMixin](../renderlifecyclemixin#action-resetcanvasdrawn) |
| **stopRenderingBackend**() => void | | [RenderLifecycleMixin](../renderlifecyclemixin#action-stoprenderingbackend) |
| **renderNow**() => void | | [RenderLifecycleMixin](../renderlifecyclemixin#action-rendernow) |
| **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](../renderlifecyclemixin#action-setrendererror) |
| **attachRenderingBackend**() => 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](../fetchmixin#action-stopactivefetch) |
| **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.() => 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](../fetchmixin#action-cancelfetch) |
| **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](../fetchmixin#action-cancelfetchbyuser) |
| **beforeDestroy**() => void | Release an in-flight fetch's stop token 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](../fetchmixin#action-beforedestroy) |
| **endFetch**(current: boolean, stopToken: StopToken) => 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: whoever superseded it — a newer `begin`, or `cancel` — already released this token. | [FetchMixin](../fetchmixin#action-endfetch) |
| **runFetch**(work: (ctx: FetchContext) => Promise<void>) => Promise<void> | Run a cancel-safe fetch (cancels any prior). The work callback gets a FetchContext with a stopToken to forward to the RPC and an isStale() check to short-circuit commits once the user has moved on.(scaleType: string) => void | | [ScoreScaleMixin](../scorescalemixin#action-setscaletype) |
| **setAutoscale**(val?: string | undefined) => void | | [ScoreScaleMixin](../scorescalemixin#action-setautoscale) |
| **setMinScore**(val?: number | undefined) => void | | [ScoreScaleMixin](../scorescalemixin#action-setminscore) |
| **setMaxScore**(val?: number | undefined) => void | | [ScoreScaleMixin](../scorescalemixin#action-setmaxscore) |
| **setShowLegend**(arg: boolean) => void | | [LegendMixin](../legendmixin#action-setshowlegend) |