@jbrowse/core 5.0.0-beta.4 → 5.0.0-beta.7

package/esm/util/whenViewSettled.js

@@ -1,6 +1,14 @@
 import { when } from 'mobx';
-const consumed = (view) => view.initialized && view.pendingLaunch === undefined;
-const done = (view) => consumed(view) || !!view.error;
+/**
+ * A view that is up AND has finished applying whatever launched it.
+ *
+ * Both terms, for the reason spelled out on {@link whenViewSettled} below.
+ * Exported because AppReadyMarker decides the same thing from the same model
+ * for the whole app, the two drifted on exactly this second term, and
+ * `readinessTerms.test.tsx` in app-core now holds them together.
+ */
+export const viewSettled = (view) => view.initialized && view.pendingLaunch === undefined;
+const done = (view) => viewSettled(view) || !!view.error;
 /**
  * Wait until a view has either initialized — launch blob consumed and all — or
  * failed, and report which.
@@ -46,7 +54,7 @@ const done = (view) => consumed(view) || !!view.error;
  */
 export async function whenViewSettled(view, escape = () => false) {
     await when(() => escape() || done(view));
-    return consumed(view);
+    return viewSettled(view);
 }
 /**
  * The same wait over several views at once — a synteny view's genome rows. An
@@ -65,5 +73,5 @@ export async function whenViewSettled(view, escape = () => false) {
  */
 export async function whenViewsSettled(views, escape = () => false) {
     await when(() => escape() || views.every(done));
-    return views.every(consumed);
+    return views.every(viewSettled);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.4",
+  "version": "5.0.0-beta.7",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -121,13 +121,17 @@
     "./ui/Snackbar": "./esm/ui/Snackbar.js",
     "./ui/SnackbarModel": "./esm/ui/SnackbarModel.js",
     "./ui/StackTraceButton": "./esm/ui/StackTraceButton.js",
+    "./ui/SvgColorLegend": "./esm/ui/SvgColorLegend.js",
     "./ui/VerticalScrollbar": "./esm/ui/VerticalScrollbar.js",
     "./ui/buildExtraTrackMenuItems": "./esm/ui/buildExtraTrackMenuItems.js",
+    "./ui/colorScale": "./esm/ui/colorScale.js",
     "./ui/colors": "./esm/ui/colors.js",
     "./ui/filterMenuItems": "./esm/ui/filterMenuItems.js",
     "./ui/gpuFallback": "./esm/ui/gpuFallback.js",
     "./ui/highlightChipReveal": "./esm/ui/highlightChipReveal.js",
+    "./ui/hoverBoxStyle": "./esm/ui/hoverBoxStyle.js",
     "./ui/legendSpec": "./esm/ui/legendSpec.js",
+    "./ui/measureLegendText": "./esm/ui/measureLegendText.js",
     "./ui/menuItems": "./esm/ui/menuItems.js",
     "./ui/multiTrackMenuItems": "./esm/ui/multiTrackMenuItems.js",
     "./ui/palette": "./esm/ui/palette.js",
@@ -166,10 +170,12 @@
     "./util/convertCodingSequenceToPeptides": "./esm/util/convertCodingSequenceToPeptides.js",
     "./util/copyText": "./esm/util/copyText.js",
     "./util/createStopTokenRotation": "./esm/util/createStopTokenRotation.js",
+    "./util/createSvgRasterCanvas": "./esm/util/createSvgRasterCanvas.js",
     "./util/deepEqual": "./esm/util/deepEqual.js",
     "./util/deepMerge": "./esm/util/deepMerge.js",
     "./util/diagonalizeRegions": "./esm/util/diagonalizeRegions.js",
     "./util/eventPoint": "./esm/util/eventPoint.js",
+    "./util/featureTransforms": "./esm/util/featureTransforms.js",
     "./util/fetchContext": "./esm/util/fetchContext.js",
     "./util/fetchHub": "./esm/util/fetchHub.js",
     "./util/fetchPhases": "./esm/util/fetchPhases.js",
@@ -203,6 +209,7 @@
     "./util/librpc": "./esm/util/librpc.js",
     "./util/localStorage": "./esm/util/localStorage.js",
     "./util/makeAssembly": "./esm/util/makeAssembly.js",
+    "./util/markEncoding": "./esm/util/markEncoding.js",
     "./util/mst-reflection": "./esm/util/mst-reflection.js",
     "./util/mstUtils": "./esm/util/mstUtils.js",
     "./util/nanoid": "./esm/util/nanoid.js",
@@ -213,14 +220,17 @@
     "./util/parseLineByLine": "./esm/util/parseLineByLine.js",
     "./util/progress": "./esm/util/progress.js",
     "./util/range": "./esm/util/range.js",
+    "./util/renderToStaticMarkup": "./esm/util/renderToStaticMarkup.js",
     "./util/resolveRowHeight": "./esm/util/resolveRowHeight.js",
     "./util/rowStackGeometry": "./esm/util/rowStackGeometry.js",
     "./util/rxjs": "./esm/util/rxjs.js",
     "./util/sameStrings": "./esm/util/sameStrings.js",
     "./util/setStackTraceLimit": "./esm/util/setStackTraceLimit.js",
     "./util/simpleFeature": "./esm/util/simpleFeature.js",
+    "./util/starFusion": "./esm/util/starFusion.js",
     "./util/stats": "./esm/util/stats.js",
     "./util/stopToken": "./esm/util/stopToken.js",
+    "./util/svgColorProps": "./esm/util/svgColorProps.js",
     "./util/tabix": "./esm/util/tabix.js",
     "./util/tickLabels": "./esm/util/tickLabels.js",
     "./util/tracks": "./esm/util/tracks.js",
@@ -275,8 +285,8 @@
     "pako-esm2": "^2.0.2",
     "rxjs": "^7.8.2",
     "source-map-js": "^1.2.1",
-    "@jbrowse/add-track-core": "^5.0.0-beta.4",
-    "@jbrowse/render-core": "^5.0.0-beta.4"
+    "@jbrowse/add-track-core": "^5.0.0-beta.7",
+    "@jbrowse/render-core": "^5.0.0-beta.7"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/configuration/promotableDefaults.d.ts

@@ -1,234 +0,0 @@
-import type { TrackConfigChange } from '../util/trackConfigDelta.ts';
-import type { TogglePin, ValuePin } from './promotablePin.ts';
-import type { PromotedDefaultStore, ResolvableDisplay } from './promotableResolve.ts';
-import type { AnyConfigurationModel, ConfigurationSchemaForModel, ConfigurationSlotName, ConfigurationSlotValueResolved } from './types.ts';
-export type { Pin, TogglePin, ValuePin } from './promotablePin.ts';
-/**
- * #api core/configuration
- * 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, and a widened `self` switches
- * the check off (`HostChecksSlotNames`). A slot name the schema does not
- * declare throws at the first read (`getSlotDefinition`), and a declared but
- * non-promotable one throws in `resolveSlotIn`.
- */
-export declare function isSlotCustomized<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>>>(self: ResolvableDisplay<CONFMODEL>, slot: SLOT): boolean;
-declare const promotablesResolved: unique symbol;
-/**
- * #api core/configuration
- * 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.
- */
-export interface ResolvedConfigSnapshot extends Record<string, unknown> {
-    readonly [promotablesResolved]: true;
-}
-/**
- * #api core/configuration
- * 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.
- */
-export declare function getConfigSnapshotWithPromotables(self: ResolvableDisplay): ResolvedConfigSnapshot;
-/**
- * #api core/configuration
- * 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`.
- */
-export interface TrackConfigWithPromotables {
-    config: Record<string, unknown>;
-    /** `<displayType>.<slot>`, one per value inherited from a promoted default */
-    fromDisplayTypeDefaults: string[];
-}
-/**
- * #api core/configuration
- * See {@link TrackConfigWithPromotables}.
- */
-export declare function getTrackConfigWithPromotables(session: PromotedDefaultStore, trackConfig: AnyConfigurationModel): TrackConfigWithPromotables;
-/**
- * Open displays of this display's type, **one entry per track** — the set the
- * pin's click writes. Module-internal (exercised by promotableDefaults.test.ts);
- * not part of the public barrel.
- *
- * A track open in two views is two display *models* over one display *config* —
- * `TrackConfigurationReference` resolves both through the hydration cache
- * (ADR-031) — so the raw walk yields it twice. That is the ordinary case in a
- * breakpoint-split view, which shows the same track in both halves and is one of
- * the composite shapes `openPromotableDisplays` recurses into. The count reaches
- * the user in the snackbar and the set gets written, and both
- * go wrong on a duplicate: the toast offered to act on "2 tracks" over a single
- * track, and the second write was a no-op against a node the first had already
- * set.
- *
- * Keying on the config node rather than on `trackId` is what keeps this
- * cast-free: the node is a member of `ResolvableDisplay`, and within one display
- * type it is 1:1 with the track.
- */
-export declare function openTracksOfType(self: ResolvableDisplay): ResolvableDisplay[];
-/**
- * Whether `value` is the current session default for `slot`. The live state the
- * pin's filled/outline reflects — a session-wide fact, so it reads the raw
- * promoted default rather than what this display resolves to (a customized track
- * can be showing something else entirely). The named form of the comparison
- * {@link makePin} inlines off a resolution it already holds. Module-internal
- * (exercised by promotableDefaults.test.ts); not part of the public barrel.
- */
-export declare function isPromotableDefault(self: ResolvableDisplay, slot: string, value: unknown): boolean;
-/**
- * Write `value` into each display's own config for `slot`, so the track *holds*
- * it rather than resolving it through the cascade. The pin's click, over every
- * open track of the display type.
- *
- * **A track already showing `value` still has to be written**, which is why this
- * compares the *stored* value and not the resolved one: a follower stores
- * nothing and is showing `value` only by way of some promoted default, so
- * skipping it would leave it to move again the moment that default changed.
- * Comparing the stored value is also what lets a `jexl:` value answer "is this
- * already what we would write?" without being evaluated.
- *
- * Skips dead displays, since the caller supplies the list and MST throws on any
- * read or write to a destroyed node.
- */
-export declare function applySlotToOpenTracks(displays: ResolvableDisplay[], slot: string, value: unknown): void;
-/**
- * #api core/configuration
- * The pin on a radio or slider row: "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 *compact* 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 (sashimi `'down'` vs `'auto'`) stay independent.
- * - **Omit it** for "whatever I'm showing", resolved through the cascade. Use for
- *   a continuous setting where no fixed on-value makes sense (wiggle point size,
- *   arc line width).
- *
- * A checkbox row takes neither: {@link makeTogglePin}.
- *
- * 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.
- */
-export declare function makePin<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>>>(self: ResolvableDisplay<CONFMODEL>, slot: SLOT, ...value: [] | [
-    ConfigurationSlotValueResolved<ConfigurationSchemaForModel<CONFMODEL>, SLOT>
-]): ValuePin;
-/**
- * The two states a checkbox row moves a slot between. Omitted for a
- * `maybeBoolean` slot, where they are `true` and `false`; required for a
- * two-member enum (`linkedReads`: "View as pairs" toggles `'normal'`/`'off'`).
- * A slot with three or more members is a radio group, not a checkbox per
- * member — `readConnections` was two checkboxes over one slot, and the
- * unticked one's pin wrote the whole slot under a label naming only itself.
- */
-export interface ToggleStates<T> {
-    on: T;
-    off: T;
-}
-/**
- * #api core/configuration
- * The pin on a checkbox row: the row's own checkbox, acting on every open track
- * of the display type. `active` mirrors the row, so the pin draws filled
- * exactly when the box is ticked; a click flips the row's state on every open
- * track and offers the new state as the display type's default. It never
- * clears a default the way {@link makePin}'s filled pin does — flipping back
- * and taking the offer promotes the other value, and promoting the base value
- * clears the default (`applyAndOfferDefault`).
- *
- * Replaces a symmetric `makePin(self, slot)` on these rows, which carried the
- * row's current state: beside an unchecked box that applied *off* everywhere
- * and visibly did nothing. It also replaces the per-value `makePin` a checkbox
- * row over a shared enum slot used to carry, which gave two checkbox rows in
- * one submenu two different pins: one filled when its value was promoted and
- * clearing on a second click, the other filled when the box was ticked and
- * flipping. With `states`, a checkbox row is always the toggle kind.
- */
-export declare function makeTogglePin<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>>>(self: ResolvableDisplay<CONFMODEL>, slot: SLOT, ...states: ConfigurationSlotValueResolved<ConfigurationSchemaForModel<CONFMODEL>, SLOT> extends boolean ? [] | [ToggleStates<boolean>] : [
-    ToggleStates<ConfigurationSlotValueResolved<ConfigurationSchemaForModel<CONFMODEL>, SLOT>>
-]): TogglePin;
-/**
- * #api core/configuration
- * 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.
- */
-export declare function getDisplayTypeDefaultChanges(self: ResolvableDisplay): TrackConfigChange[];
-/**
- * #api core/configuration
- * 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 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`).
- */
-export declare function clearPromotedDefaults(self: ResolvableDisplay, slots: Iterable<string>): void;