@jbrowse/core 4.3.0 → 5.0.0-beta.1

package/README.md

@@ -18,3 +18,786 @@ be linked from [jbrowse.org](http://jbrowse.org).
 ## License
 
 Apache-2.0 © Evolutionary Software Foundation
+
+<!-- API_DOCS_START -->
+
+## API
+
+Auto-generated from `#api` JSDoc tags in this package. Do not edit by hand.
+
+### Band
+
+One band of a display's vertical stack — a coverage histogram, an arc strip, a
+conservation row, a variant lane. The contract is the pair: `active` is whether
+the band exists right now (the display pre-ANDs its settings half, `showX`, with
+its data half, "some lane has ink"), and `height` is the stated height when it
+does. Consumers read pixels through reservedPx or stackBands, never by
+re-combining the pair — the re-combination is where the reserver and the painter
+historically drifted.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/bandLayout.ts)
+
+### boundBandHeight
+
+Bound a band height to its legal range — a config value, a menu choice, or a
+slider position, i.e. anywhere the number is being _stated_ rather than dragged.
+
+The **floor** keeps the band operable at its smallest: for a drag-resized band
+that means keeping the handle grabbable, for a menu-sized one it is the height
+below which its content stops reading. The **ceiling** stops a band from
+swallowing the plot it sits over — every display floors its plot area at 0, so
+an unbounded band takes the rows to zero height rather than to a scrollbar, and
+takes the band's own handle off-screen with them.
+
+The bounds differ per band and the rule does not, which is why this takes them
+rather than each band re-deriving the reasoning — that is how the two
+`clampBandHeight`s in this repo drifted apart, each ending up with one half of
+this rule and a doc comment claiming to be the whole of it.
+
+```js
+// type signature
+(n: number, { min, max }?: BandBounds) => number
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/bandHeight.ts)
+
+### buildColorRampLut
+
+An RGBA lookup table over sampleColorRamp, laid out as the Nx1 texture both GPU
+backends upload and the Canvas2D twins index — entry `i` is the color at
+`t = i / (N - 1)`. N comes off the shader that samples it, so the table and
+`rampColor`'s texel mapping cannot disagree.
+
+```js
+// type signature
+(stops: readonly ColorRampStop[]) => Uint8Array<ArrayBuffer>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/colorRamp.ts)
+
+### canonicalizeViewRefName
+
+Resolve user-authored refName text against the assembly of the view containing
+`node` — the one normalization layer, which resolves aliases and casing
+together. Falls back to the input when the assembly is absent or its aliases
+have not loaded.
+
+Keyed off the VIEW's assembly rather than the track's, because the view is what
+the comparison is against: displayed regions, loaded regions and blocks all
+carry the refNames the view laid out.
+
+Reach for this wherever a refName a _person_ wrote is about to be compared
+against regions, features or blocks, which carry the assembly's canonical name.
+A refName a display copied off a region is canonical already and needs nothing;
+one that arrived in a session spec, a config slot or a URL is whatever the
+author read out of the location box.
+
+Skipping it fails silently and, worse, assembly-dependently: `chr12` matches on
+an assembly canonicalized `chr12` and matches nothing on one canonicalized `12`,
+so the same spec key works on one config and quietly does nothing on the next,
+with no error for anyone to act on.
+
+Resolves through `getCanonicalRefName2`, whose fallback is what keeps a spec
+read before the alias file has loaded from throwing — and the getters that read
+user specs do run from the first render.
+
+Takes a refName, not a spec that might hold one: the resolver reads
+`refName.toLowerCase()`, so anything else throws once the aliases are there, and
+a caller reading an untyped `frozen` slot has to establish that it names a
+refName at all before this is the right question to ask of it.
+
+```js
+// type signature
+(node: IAnyStateTreeNode, refName: string) => string
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### clampBandHeight
+
+Clamp one _resize_ of a drag-resizable band: boundBandHeight, plus the one rule
+a resize needs that a stated height does not.
+
+The floor becomes `min(bounds.min, current)`, never the bare bound: a band whose
+config declares it smaller than the floor must stay where it is. Taking the bare
+floor instead made the _first_ drag on such a band jump it up to the floor
+before honoring the delta. A band at or above the floor is unaffected, one below
+it can still be dragged but never smaller than it already is, and one dragged
+back past the floor regains it.
+
+The ceiling is not relaxed the same way — a band already over its ceiling is the
+state the user is trying to escape, so a resize brings it back inside.
+
+`ResizeHandle` emits one delta per animation frame, so callers driving a drag
+pass `current + distance` as the target and read `current` inside the action — a
+component computing the target from a rendered height drops every tick that
+lands before React re-renders.
+
+```js
+// type signature
+(current: number, target: number, bounds?: BandBounds) => number
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/bandHeight.ts)
+
+### clearPromotedDefaults
+
+Clear the named promoted defaults for this display type, so every track
+following one reverts to its own config value. Backs the badge's "clear session
+default" action, which passes the slots it actually listed
+(`getDisplayTypeDefaultChanges`).
+
+**`slots` is required, and an all-slots default is not the convenience it looks
+like.** It reaches further than any list a dialog can have shown: a promoted
+default the track _customized_ over, or one promoted to a value equal to
+`promotedBase`, is `inherited: false` and so appears in no row, yet still
+governs sibling tracks — so clearing it from a dialog that never showed it moves
+tracks other than the one whose badge was clicked. Clearing every promoted
+default at once is a preferences-scope action, and Preferences → "Reset to
+defaults" is where it lives (`clearPreferenceOverrides`).
+
+```js
+// type signature
+(self: ResolvableDisplay, slots: Iterable<string>) => void
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### getAssemblyHost
+
+The host's assembly manager, for a module that resolves names and nothing else.
+
+Unlike the accessors in `sessionServices.ts` this one buys the caller no smaller
+type graph — an `AssemblyManager` is an MST model a `PluginManager` built, so
+naming it costs what naming a session costs. It is here to say which service is
+wanted, and because that cost is the finding: the assembly manager is the one
+thing on `AbstractSessionModel` a third-party host cannot simply implement.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => AssemblyHost
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getConf
+
+Reads a configuration value from a state model that has a `.configuration`
+member (a track or display state model). For a raw configuration model, use
+`readConfObject` instead.
+
+**This is exactly `readConfObject(model.configuration, path)`** — sugar for the
+`.configuration` hop, and nothing more. The two readers carry the same slot-name
+check, so reaching for the other one does not get a typo past tsc. It does not
+consult the session and has no per-slot behavior; what you read is what the
+track stores.
+
+A `promotable` slot read this way therefore yields the raw stored value,
+`undefined` included — that `undefined` is the cascade's inherit sentinel, and
+`resolveConf` is what turns it into a real value. The read type keeps the
+`undefined` on purpose, so reaching for the wrong reader is a compile error
+rather than a silent one.
+
+```js
+// type signature
+{ (model: {…}): ModelSnapshotType<…>; <…>(model: {…}, slotPath: SLOT, args?: Record<…> | undefined): SLOT extends string ? ConfigurationSlotValue<…> : any; }
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/getConf.ts)
+
+### getConfigSnapshotWithPromotables
+
+The display's full config snapshot with every `promotable` slot overwritten by
+its resolved value in place. For building a worker payload: a promotable slot
+serializes as its raw inherit sentinel (`undefined`, since they're all `maybe*`
+types), which the worker can't interpret — it has no session to resolve against.
+This hands it concrete values instead, with no per-slot bookkeeping, so adding a
+promotable worker-consumed slot needs no rpcProps change and can't silently ship
+a sentinel. Main-thread only (the cascade consults the session). Display-only
+promotable slots the worker never reads (e.g. displayMode) are still excluded by
+the caller — resolving them here is a harmless no-op since they're dropped
+anyway.
+
+The return type is branded (`ResolvedConfigSnapshot`) so a payload builder can
+demand a snapshot that has been through here. The assertion below is the one
+place the brand is applied, and it sits on the line after the resolve.
+
+```js
+// type signature
+(self: ResolvableDisplay) => ResolvedConfigSnapshot
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### getContainingDisplay
+
+Returns the display model that contains the given node. Throws if the node has
+no containing display.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => AbstractDisplayModel
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getContainingTrack
+
+Returns the track model that contains the given node. Throws if the node has no
+containing track.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => AbstractTrackModel
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getContainingView
+
+Returns the view model that contains the given node. Throws if the node has no
+containing view.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => AbstractViewModel
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getDialogHost
+
+Where a display puts a dialog it cannot mount itself.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => DialogHost
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/sessionServices.ts)
+
+### getDisplayTypeDefaultChanges
+
+Effective differences a track following the default inherits from session-wide
+defaults, one per promotable slot whose inherited value differs from its schema
+default. Drives the track-selector "affected by a session default" badge.
+
+```js
+// type signature
+(self: ResolvableDisplay) => TrackConfigChange[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### getEnv
+
+Returns the MST environment for a node, which carries the `pluginManager`.
+
+```js
+// type signature
+(obj: IAnyStateTreeNode) => { pluginManager: PluginManager; }
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getNotificationSink
+
+Where a display puts a message it cannot draw itself.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => NotificationSink
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/sessionServices.ts)
+
+### getPaletteHost
+
+The colors to draw with, and the args that rebuild them in a worker.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => PaletteHost
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/sessionServices.ts)
+
+### getRenderingServices
+
+Everything a display needs of its host in order to draw a region: the
+assemblies, the RPC entry point and the colors.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => RenderingServices
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getRpcHost
+
+The host's RPC entry point, for a module that issues RPCs and nothing else.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => RpcHost
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/sessionServices.ts)
+
+### getSession
+
+Returns the JBrowse session model for any node in the state tree. Throws if the
+node has no session ancestor.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => AbstractSessionModel
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/mstUtils.ts)
+
+### getSessionServices
+
+The services a session offers that cost nothing application-shaped to name.
+Prefer one of the narrower accessors below, which say which of them the calling
+module actually uses.
+
+```js
+// type signature
+(node: IAnyStateTreeNode) => SessionServices
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/sessionServices.ts)
+
+### getTrackConfigWithPromotables
+
+See TrackConfigWithPromotables.
+
+```js
+// type signature
+(session: PromotedDefaultStore, trackConfig: ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>) => TrackConfigWithPromotables
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### hydrateTrackConfig
+
+Hydrate a plain track config into a live config node, dispatching on its `type`
+to find the schema. `session.tracks` holds `types.frozen` plain objects until
+something references a track (ADR-031), so a caller handed one of those has a
+config that reads nothing but what was literally authored: a slot at its schema
+default is absent, `preProcessSnapshot` has not run, and nothing that walks a
+live node — the promotable cascade above all — applies to it.
+
+For the callers that need the resolved answer rather than the authored one and
+cannot know which of the two they were handed. The About dialog's "Copy config"
+is the case this exists for: it is reached from two menus, and one of them
+passes a `session.tracks` entry.
+
+Returns **undefined** rather than throwing when the config names a track type no
+plugin registered, or when it is invalid enough that `create` rejects it — an
+un-hydrated config has never been validated, so a dialog that opens over it must
+not be the thing that discovers this. Callers fall back to treating it as the
+plain object it is.
+
+Shares `TrackConfigurationReference`'s per-PluginManager cache, so hydrating the
+same entry twice returns the same node and a track that gets opened later reuses
+it.
+
+```js
+// type signature
+(pluginManager: PluginManager, config: Record<string, unknown>) => (ModelInstanceTypeProps<Record<string, any>> & { ...; } & IStateTreeNode<...>) | undefined
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/configurationSchema.ts)
+
+### isSlotCustomized
+
+Whether this track has customized the slot (holds a non-default value of its
+own) rather than following the display type's default. The correct "reset to
+default" predicate for a promotable slot: comparing the resolved value to the
+base instead reads as at-default for a track merely _following_ a non-base
+promoted default, so the reset control lights up on a no-op.
+
+`SLOT` is constrained the way `getConf`'s is. A pin or a reset over a slot name
+the schema does not declare is inert and silent — `resolveSlot` answers about
+nothing, so the control draws outline forever — and a widened `self` switches
+the check off (`HostChecksSlotNames`).
+
+```js
+// type signature
+<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>>>(self: ResolvableDisplay<CONFMODEL>, slot: SLOT) => boolean
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### makePin
+
+The pin for one promotable slot: "apply this value to every open track of this
+display type", and — via the snackbar it raises — "keep it as the default for
+the ones opened later".
+
+`value` chooses between the subsystem's two meanings, which are otherwise
+identical:
+
+- **Give it** for a per-value pin — "make _arcs_ the default" — independent of
+  what the track currently shows. Use on an always-visible pin so it can never
+  promote a meaningless value, and so two rows sharing one slot (arcs `'arc'` vs
+  read cloud `'cloud'`; sashimi `'down'` vs `'auto'`) stay independent.
+- **Omit it** for "whatever I'm showing", resolved through the cascade. Use for
+  a symmetric or continuous setting where no fixed on-value makes sense (wiggle
+  point size, arc line width, `mismatchAlpha`).
+
+One function with an optional argument, rather than the two exported builders it
+replaces — a per-value one and a `…CurrentValue…` one, the second of which was
+exactly the first applied to `resolveSlot(self, slot).value`. The pair was one
+function plus a doc section explaining which name to reach for; omitting the
+argument now says what the longer name said.
+
+```js
+// type signature
+<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<…>>(self: ResolvableDisplay<CONFMODEL>, slot: SLOT, ...value: [] | [...]) => Pin
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### openPromotableDisplays
+
+Every display on an open track, across all open views — the reach of anything
+that acts on "the tracks the user is looking at": a promoted default's "apply to
+open tracks", and the share/export bake. One walk so those can't drift apart.
+
+Recurses into composite views. A display nested in one resolves the cascade like
+any other but was invisible to both callers, so the share/export bake didn't
+bake its inherited values and a shared session containing a breakpoint-split or
+synteny view rendered differently for the recipient. `LGVSyntenyDisplay` is only
+ever reached through this branch, so don't flatten the recursion away.
+`hasChildViews` names the one composite shape it does not cover.
+
+A view holding neither (e.g. spreadsheet) drops out via the structural guards. A
+view whose displays declare no promotable slot (e.g. dotplot, which does hold
+tracks) is walked and contributes nothing — harmless, and cheaper than asking
+each display whether it has anything to promote.
+
+```js
+// type signature
+(session: AbstractSessionModel) => ResolvableDisplay[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/openDisplays.ts)
+
+### Pin
+
+The "apply this to every open track of this type" affordance on a menu row — the
+trailing `PushPin`, bundled so the row consumes it as one prop. Built by
+makePin.
+
+`active` = this value is currently the session default (a filled pin), which is
+the state, not the click. `toggle` **applies the value to every open track of
+the display type** and raises a snackbar whose one action promotes it to the
+display type's default; on an already-promoted value it clears that default
+instead, touching no track (see `applyPinClick`).
+
+**`toggle` rather than an `apply`/`clear` pair**, which was tried and dropped:
+the sole renderer is a MUI `ToggleButton` whose `onChange` means exactly "flip",
+so splitting it adds a member _and_ a branch at the one call site that never
+needed one. `active` is already public for a caller that wants to state a
+direction. (The house preference for explicit setters over toggles is about MST
+actions, where a toggle destroys the ability to set a known state; nothing here
+stores a value.)
+
+Lives here, alone and with no imports, rather than beside `makePin` in
+`promotableDefaults.ts`: the menu types describe a pin without building one, and
+`MenuTypes.ts` taking this one interface from that module gave a React-free type
+file a type closure of 374 files. See
+`agent-docs/ideas/barrels-block-extraction.md` and `scripts/moduleClosure.ts`.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotablePin.ts)
+
+### readConfObject
+
+Given a configuration model (an instance of a ConfigurationSchema), read the
+configuration value at the given path. Use this when you hold the configuration
+model directly, e.g. an entry from `session.tracks`.
+
+Wants a **live config node**, not a snapshot of one, and passing a snapshot is a
+type error. Slots are built with `types.stripDefault`, so a slot sitting at its
+default is absent from a snapshot — "unset" and "at its default" are
+indistinguishable there, and a read off one reports a default as missing.
+
+That is enforced in the types only, deliberately: it can't be a runtime check.
+`generateHierarchy` reads slots straight off the **un-hydrated frozen** entries
+of `jbrowse.tracks` on purpose, because hydrating every track to answer the
+track selector is what `types.frozen` exists to avoid — and those reads are
+indistinguishable at runtime from the broken spelling.
+
+```js
+// type signature
+{…}
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/readConfObject.ts)
+
+### readConfSlot
+
+Read a single config slot from a config that may be **either** a live MST node
+or a plain snapshot object, evaluating the value if it is a `jexl:` expression.
+For the dialogs and panels that are handed a track config without knowing which
+of the two they got. An About panel gets a hydrated track config from the
+session and a bare object from an embedded caller.
+
+Reach for `readConfObject` or `readConfigValue` when the shape is known: this
+one decides at runtime, and the plain branch inherits the snapshot caveat (a
+slot at its default is absent from a snapshot, so it reads `undefined`).
+
+```js
+// type signature
+<…>(config: Record<…> | (ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>), slotPath: string | string[], args?: Record<…>, jexl?: JexlInstance | undefined) => T
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/readConfObject.ts)
+
+### relight
+
+Move a color's OKLCH lightness by `lightnessShift` and scale its chroma, holding
+its hue.
+
+For extending a categorical palette past its length. Cycling a nine-color list
+over a 24-chromosome karyotype repeats the color outright; cycling it with a
+lightness shift per lap gives the hue back as a variant still told apart from
+the original — tab20's construction, which pairs a light and a dark of each hue.
+
+SHIFT rather than a fixed lightness, and SCALE rather than a fixed chroma,
+because a categorical palette is uneven on purpose: category10's brown and its
+red are 5 degrees apart in hue and are told apart by chroma alone, so
+re-lighting both to one (lightness, chroma) makes them the same color. Keeping
+each color's own relative chroma keeps brown reading as brown.
+
+In OKLCH rather than through `lighten`/`darken`, which work in sRGB, where the
+same coefficient moves a yellow and a blue by visibly different amounts: a lap
+has to read as one tone across the whole palette or it reads as noise.
+
+```js
+// type signature
+(color: string, lightnessShift: number, chromaScale?: number) => string
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/color/index.ts)
+
+### reservedPx
+
+The pixels a band takes from the plot below it: 0 when off, the (optionally
+bound) stated height when on. This is the single spelling of "off spends 0 px".
+
+```js
+// type signature
+(band: Band) => number
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/bandLayout.ts)
+
+### resolveConf
+
+Reads a `promotable` slot through the display-type-default cascade — the track's
+own value, else the session-wide promoted default for this display type, else
+the slot's `promotedBase`. Always yields a real value, never the `undefined`
+inherit sentinel, so a display's value getter is
+`get displayMode(): DisplayMode { return resolveConf(self, 'displayMode') }`
+with no post-guard and no cast.
+
+Separate from `getConf` rather than folded into it, deliberately: resolution
+consults the session, so it is main-thread only and throws on a detached node.
+Folding it in was built and reverted — ADR-046.
+
+Throws if `slot` isn't promotable — the cascade has nothing to say about a plain
+slot, and `getConf` is what you want there.
+
+Takes no jexl `args`, unlike `getConf`: a promotable slot cannot hold a callback
+(see `SlotResolution`), so there is no per-feature context to supply.
+
+```js
+// type signature
+<…>(model: ResolvableDisplay<...>, slot: SLOT) => ConfigurationSlotValueResolved<...>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/getConf.ts)
+
+### ResolvedConfigSnapshot
+
+A display config snapshot whose promotable slots hold RESOLVED values rather
+than the inherit sentinel — what a worker payload has to be built from.
+
+The brand is required and unforgeable, so a plain `Record<string, unknown>` is
+not assignable to it and neither is `getSnapshot(self.configuration)`. That is
+the whole point. Everything downstream of the resolve is an ERASED container — a
+snapshot is `Record<string, unknown>`, and the payload it becomes is an
+`as`-asserted interface — so a payload builder handed the RAW snapshot instead
+typechecks, ships `undefined` for every promotable slot, and types it as the
+resolved value. That was measured, not supposed: the raw spelling in
+`LinearBasicDisplay`'s `rpcProps()` passed `pnpm typecheck` and every suite in
+`plugins/canvas`, `packages/core/src/configuration` and `products/jbrowse-web`,
+while sending the worker `undefined` for chevrons, subfeature labels and feature
+height.
+
+The rest of this subsystem's guarantees are carried by types that stay connected
+to the schema: a raw read of a promotable `maybe*` slot is `T | undefined` (see
+`ConfigurationSlotValue`), so `getConf` where `resolveConf` was meant is a
+compile error at any typed consumer. The brand is that guarantee re-established
+at the point where the connection is cut.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### sampleColorRamp
+
+The color at `t` in `[0, 1]` across a list of EVENLY SPACED stops, linearly
+interpolated per channel. `t` is clamped, so the ends are the end stops rather
+than an extrapolation past them, and a one-stop ramp is that stop everywhere.
+
+```js
+// type signature
+(stops: readonly ColorRampStop[], t: number) => ColorRampStop
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/colorRamp.ts)
+
+### SessionPaletteProvider
+
+Make JBrowse follow the host's light/dark state — the whole of it, in one mount:
+
+```tsx
+<SessionPaletteProvider session={session} mode={myAppIsDark ? 'dark' : 'light'}>
+  {tracks}
+</SessionPaletteProvider>
+```
+
+A component rather than a documented pair of calls because the pair has a half
+that can be left out with nothing to show for it. `PaletteProvider` is the name
+a host reaches for, and it colors the React side alone; the session write is
+what reaches the RPC worker, which bakes feature labels into the rendered image.
+So a host that mounts only the provider gets light-mode labels on a dark page,
+from a canvas whose every other pixel is right, and nothing errors. See
+useSessionPalette for the mechanism.
+
+The session is the only thing that resolves a palette here, so a host supplying
+colors of its own mounts `PaletteProvider` directly instead.
+
+```js
+// type signature
+({ session, mode, children, }: { session: ThemeModeSession; mode: "dark" | "light"; children: ReactNode; }) => Element
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/ui/PaletteContext.tsx)
+
+### setConf
+
+Write counterpart to `getConf`: sets a slot on a state model that has a
+`.configuration` member (a track or display state model).
+
+**Prefer this over a bare `self.configuration.setSlot('x', v)`.** The constraint
+here mirrors `getConf`'s, so on a model with a concrete schema an unknown slot
+name is a compile error. `setSlot` itself stays untyped on purpose — the config
+editor's slot facade routes dynamic slot names through it
+(`configurationSchema.ts`) — and guards the name at runtime instead (ADR-052),
+so a misspelled write is diagnosed one way or the other.
+
+**The read is the half with no diagnostic at all.** `getConf` for a name the
+schema doesn't declare returns `undefined` and reports nothing, at any layer, so
+the slot keeps reading as its default forever. Which makes the compile-time
+constraint worth keeping _reachable_: it is only as good as the schema of the
+holder handed in, and a holder widened to `AnyConfigurationModel` switches it
+off entirely — the trap a mixin casting to reach its host walks into. Every such
+cast names a concrete schema instead (`ConfigModelForFields`, or the base schema
+when the slot is the base's), and `HostChecksSlotNames` pins each one.
+
+A wrong _value_ type still throws at runtime (MST type-checks the assignment)
+rather than at compile time. `value` is deliberately `unknown` because the
+inherit sentinel (`undefined`/`null`) is a legitimate write on every promotable
+slot, which the declared slot value type doesn't include.
+
+```js
+// type signature
+<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<…> = ConfigurationSlotName<…>>(model: { ...; }, slotName: SLOT, value: unknown) => void
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/getConf.ts)
+
+### stackBands
+
+Fold an ordered set of bands into tops and a bottom. The order is the argument,
+so a display states its band order exactly once; reserve, paint and pick all
+read the same fold, which is what keeps "the reserver and the painter read one
+function" true by construction rather than by prose.
+
+Only the fold is shared. What varies per display stays there: per-lane iteration
+runs this once per lane, sticky-vs-scrolling is a property of how the result is
+projected to the screen, and a band drawn outside its reservation (an overlay)
+carries its own draw rect beside the stack.
+
+```js
+// type signature
+<K extends string>(order: readonly K[], bands: Record<K, Band>) => BandStack<K>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/bandLayout.ts)
+
+### stopsFromRampLut
+
+`n` evenly spaced legend stops read straight out of a buildColorRampLut byte
+table — the same 256×1 RGBA array `uploadColorRampLut` hands the GPU and the
+Canvas2D fillStyle LUTs index — formatted for `SvgGradientLegend`. It holds one
+claim by construction: the swatch at bar fraction `t` is byte-identical to the
+ramp entry at `t` on both backends. Alpha rides `opacity` (the juicebox fade),
+never baked into the color string.
+
+```js
+// type signature
+(lut: Uint8Array<ArrayBufferLike>, n: number) => GradientStop[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/colorRamp.ts)
+
+### TrackConfigWithPromotables
+
+A track config snapshot with every display's `promotable` slots resolved, plus
+the list of values that came from a session-wide default rather than from the
+config itself.
+
+For handing a track's config to somewhere that leaves the cascade for good — the
+About dialog's "Copy config", whose output a user pastes into a `config.json`. A
+raw `getSnapshot` records a slot a track merely _follows_ as absent
+(`stripDefault` collapsed it), so the copied config renders differently from the
+track it was copied from. This is `getComputedStyle` at that boundary, and
+`fromDisplayTypeDefaults` is what lets the UI say so rather than silently
+materializing a session preference into a track config.
+
+Resolves from the display _config_ alone, whether or not the track is open.
+Everything the cascade takes is on the config node: it is the same node an open
+display's `configuration` points at (the hydration cache makes it stable), its
+`type` is the display type the session-wide tier is keyed on (every display
+schema is `explicitlyTyped` under the display type's own name), and the session
+is passed in. So an unopened track — which has no display state at all — still
+has an answer to "what would this render as", by the same code path.
+
+**Writes every promotable slot, including the ones sitting at `promotedBase`,
+and that is the decision — don't "align" it with the share bake.** A pasted
+`config.json` is read by a mechanism with no cascade in it at all, so writing
+only the inherited values would leave every other slot to pick up whatever the
+reader has promoted in their own browser. Pinned by
+`products/jbrowse-web/src/tests/CopyConfigPromotedDefaults.test.ts`.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/configuration/promotableDefaults.ts)
+
+### VIRIDIS_STOPS
+
+The 256 viridis stops, fully opaque. Feed them to buildColorRampLut for the
+texture/fillStyle form, or to sampleColorRamp for legend stops.
+
+```js
+// type signature
+readonly ColorRampStop[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/src/util/colorRamp.ts)
+
+<!-- API_DOCS_END -->