@jbrowse/plugin-linear-genome-view 5.0.0-beta.1 → 5.0.0-beta.3

package/esm/displayKitTests/perRegionTestEnv.js

@@ -28,47 +28,49 @@ function makeStateModel(control, gate, configSchema) {
         .volatile(() => ({
         /** every `fetchNeeded` call, as the region list it was handed */
         fetchLog: [],
-        loadedData: new Map(),
         /**
-         * What `regionFetchKey` answers. A volatile, not a `control` knob, and
+         * What `zoomFetchKey` answers. A volatile, not a `control` knob, and
          * that is the point: a real display's key reads view state, so the
          * autorun re-runs when it moves. A plain closure value would be memoized
          * by the computed and never invalidate.
          */
         fetchKey: '',
     }))
+        .views(self => {
+        // chained, not replaced: `staleAnswers` forces a false answer for a
+        // bounded number of calls, and everything else is the foundation's own
+        // store-derived default
+        const superRegionHasData = self.regionHasData;
+        return {
+            regionHasData(displayedRegionIndex) {
+                control.cacheValidCalls += 1;
+                if (control.staleAnswers > 0) {
+                    control.staleAnswers -= 1;
+                    return false;
+                }
+                return superRegionHasData.call(self, displayedRegionIndex);
+            },
+        };
+    })
         .views(self => ({
+        /** the fetched payloads, off the foundation's store */
+        get loadedData() {
+            return self.regionPayloads;
+        },
         get gateEnabled() {
             return gate.gateEnabled ?? false;
         },
-        get densityGateEnabled() {
-            return gate.densityGateEnabled ?? false;
-        },
         get densityTooLarge() {
             return control.densityTooLarge;
         },
-        get regionFetchKey() {
+        get zoomFetchKey() {
             return self.fetchKey;
         },
-        regionHasData(_displayedRegionIndex) {
-            control.cacheValidCalls += 1;
-            if (control.staleAnswers > 0) {
-                control.staleAnswers -= 1;
-                return false;
-            }
-            return true;
-        },
     }))
         .actions(self => ({
         setFetchKey(key) {
             self.fetchKey = key;
         },
-        setLoaded(displayedRegionIndex, value) {
-            self.loadedData.set(displayedRegionIndex, value);
-        },
-        clearDisplaySpecificData() {
-            self.loadedData.clear();
-        },
     }))
         .actions(self => ({
         fetchNeeded(needed) {
@@ -93,17 +95,15 @@ function makeStateModel(control, gate, configSchema) {
                     // budget means no measurement at all, which is why `estimateCalls`
                     // stays at zero for an ungated display.
                     if (byteLimit === undefined) {
-                        return { value: 'data' };
+                        return { value: control.payloadTag };
                     }
                     control.estimateCalls += 1;
                     const bytes = control.estimateBytes;
                     return bytes > byteLimit
                         ? { regionTooLarge: true, bytes }
-                        : { value: 'data', bytes };
-                },
-                onResult: (idx, result) => {
-                    self.setLoaded(idx, result.value);
+                        : { value: control.payloadTag, bytes };
                 },
+                onResult: (_idx, result) => result.value,
             });
         },
     }));
@@ -121,6 +121,7 @@ export function createPerRegionTestEnvironment({ measuresBytes = false, gate, es
         estimateBytes,
         estimateCalls: 0,
         densityTooLarge: false,
+        payloadTag: 'data',
     };
     const optIns = gate ?? { gateEnabled: measuresBytes };
     const env = createDisplayTestEnvironment({

package/esm/index.d.ts

@@ -16,12 +16,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly description: 'Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.';
                 readonly advanced: true;
             };
-            readonly maxFeatureScreenDensity: {
-                readonly type: "number";
-                readonly description: "maximum features per pixel before showing a \"too many features\" message";
-                readonly defaultValue: 1;
-                readonly advanced: true;
-            };
             readonly height: {
                 readonly type: "number";
                 readonly defaultValue: 100;
@@ -92,7 +86,6 @@ export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/Hea
 export { searchBoxMenuItems, useSearchBoxPrefs, } from './LinearGenomeView/components/useSearchBoxPrefs.ts';
 export type { SearchBoxPrefs } from './LinearGenomeView/components/useSearchBoxPrefs.ts';
 export { normalizeTrackInit } from '@jbrowse/core/util/tracks';
-export { linearGenomeViewPropKeys, partitionLaunchKeys, } from './LinearGenomeView/initKeys.ts';
 export { applyInitHighlights } from './LinearGenomeView/afterAttach.ts';
 export { MultiLevelRubberband } from './MultiLevelRubberband/index.ts';
 export { fetchResults, SearchResultsNotFoundError } from './searchUtils.ts';
@@ -102,6 +95,7 @@ export type { ScalebarRefNameLabel } from './LinearGenomeView/util.ts';
 export type { RegionsOrientation } from './LinearGenomeView/util.ts';
 export { makeTicks } from './LinearGenomeView/util.ts';
 export type { Tick } from './LinearGenomeView/util.ts';
+export { containingLgv } from './LinearGenomeView/containingLgv.ts';
 export { showRegionsWithUndo } from './LinearGenomeView/showRegionsWithUndo.ts';
 export type { SharedFit } from './LinearGenomeView/sharedScaleContainer.ts';
 export { fitAllRegionsWindow } from './LinearGenomeView/util.ts';
@@ -117,8 +111,7 @@ export { default as ExportSvgDialog } from './LinearGenomeView/components/Export
 export { GetSequenceDialog } from './LinearGenomeView/lazyDialogs.ts';
 export { default as ConnectedHoverHighlight } from './LinearGenomeView/components/ConnectedHoverHighlight.tsx';
 export { default as HoverPositionHighlight } from './LinearGenomeView/components/HoverPositionHighlight.tsx';
-export { TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
-export { FloatingSvgOverlay } from './LinearGenomeView/FloatingSvgOverlay.tsx';
+export { FloatingSvgOverlay, TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
 export type { HoverHighlightPosition } from './LinearGenomeView/components/HoverPositionHighlight.tsx';
 export { SvgChrome, SvgClipRect } from '@jbrowse/core/svg/SvgExport';
 export { svgSafeId } from '@jbrowse/core/svg/svgId';

package/esm/index.js

@@ -85,7 +85,6 @@ export { default as HeaderSearchBoxes } from './LinearGenomeView/components/Head
 export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/HeaderSearchBoxRow.js';
 export { searchBoxMenuItems, useSearchBoxPrefs, } from './LinearGenomeView/components/useSearchBoxPrefs.js';
 export { normalizeTrackInit } from '@jbrowse/core/util/tracks';
-export { linearGenomeViewPropKeys, partitionLaunchKeys, } from './LinearGenomeView/initKeys.js';
 export { applyInitHighlights } from './LinearGenomeView/afterAttach.js';
 export { MultiLevelRubberband } from './MultiLevelRubberband/index.js';
 export { fetchResults, SearchResultsNotFoundError } from './searchUtils.js';
@@ -99,6 +98,7 @@ export { makeTicks } from './LinearGenomeView/util.js';
 // The two halves of "show these regions instead": navigate the view you are
 // looking at, or seed a snapshot for a new one. A caller deriving either itself
 // lands on a viewport property the model no longer reads — see each for how.
+export { containingLgv } from './LinearGenomeView/containingLgv.js';
 export { showRegionsWithUndo } from './LinearGenomeView/showRegionsWithUndo.js';
 export { fitAllRegionsWindow } from './LinearGenomeView/util.js';
 export { renderToSvg } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView.js';
@@ -125,8 +125,7 @@ export { default as HoverPositionHighlight } from './LinearGenomeView/components
 // mounts it, and so does an embedder mounting `RenderingComponent` directly —
 // who otherwise supplies no node at all and gets display chrome buried under
 // their own region masks.
-export { TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
-export { FloatingSvgOverlay } from './LinearGenomeView/FloatingSvgOverlay.js';
+export { FloatingSvgOverlay, TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
 export { SvgChrome, SvgClipRect } from '@jbrowse/core/svg/SvgExport';
 // for a display that hand-rolls a <clipPath> instead of using SvgClipRect (an
 // inset or non-rect clip); ids built from a trackId/refName need it

package/esm/searchUtils.d.ts

@@ -32,28 +32,31 @@ export declare function unanimousResult({ results, model, session, assembly, }:
     session: TrackCatalog;
     assembly?: Assembly;
 }): BaseResult | undefined;
-export declare function showSearchResults({ results, query, model, assemblyName, grow, }: {
+export declare function showSearchResults({ results, query, model, assemblyName, grow, showHitTrack, }: {
     results: BaseResult[];
     query: string;
     model: LinearGenomeViewModel;
     assemblyName: string;
     grow?: number;
+    showHitTrack?: boolean;
 }): Promise<boolean>;
-export declare function navToOption({ option, model, assemblyName, grow, }: {
+export declare function navToOption({ option, model, assemblyName, grow, showHitTrack, }: {
     model: LinearGenomeViewModel;
     option: BaseResult;
     assemblyName: string;
     grow?: number;
+    showHitTrack?: boolean;
 }): Promise<void>;
 export declare class SearchResultsNotFoundError extends Error {
     name: string;
 }
 export declare function notifySearchFailure(session: NotificationSink, e: unknown): void;
-export declare function handleSelectedRegion({ input, model, assemblyName, grow, }: {
+export declare function handleSelectedRegion({ input, model, assemblyName, grow, showHitTrack, }: {
     input: string;
     model: LinearGenomeViewModel;
     assemblyName: string;
     grow?: number;
+    showHitTrack?: boolean;
 }): Promise<boolean>;
 export declare function checkRef(str: string, isRef: (name: string) => boolean): boolean;
 export declare function fetchResults({ queryString, searchType, assemblyName, textSearchManager, assembly, stopToken, }: {

package/esm/searchUtils.js

@@ -86,6 +86,24 @@ function trackRank(result, model, session) {
         return session.getTrackById(trackId) ? 1 : 3;
     }
 }
+// The pick is a stable minimum, so a linear scan rather than a sort: only the
+// best rung is taken, and keeping the first strictly-lowest one is what leaves
+// an agreeing group with nothing to choose between in the order the ranking
+// handed it. Ranked once per hit for the reason `destinations` above it is:
+// `trackRank` reaches `session.getTrackById`, and a comparator asks O(n log n)
+// times for an answer that does not vary.
+function bestRanked(results, model, session) {
+    let best = results[0];
+    let bestRank = trackRank(best, model, session);
+    for (let i = 1; i < results.length; i++) {
+        const rank = trackRank(results[i], model, session);
+        if (rank < bestRank) {
+            best = results[i];
+            bestRank = rank;
+        }
+    }
+    return best;
+}
 // The picker exists to disambiguate, and hits that name one feature at one
 // place are not ambiguous — they are several indexes having found it. An
 // instance carrying a handful of gene tracks turns every gene search into a
@@ -97,16 +115,12 @@ export function unanimousResult({ results, model, session, assembly, }) {
     const destinations = results.map(r => destination(r, assembly));
     const agree = destinations[0] !== undefined &&
         destinations.every(d => d === destinations[0]);
-    // stable, so an agreeing group with nothing to choose between keeps the
-    // order the ranking handed it
-    return agree
-        ? [...results].sort((a, b) => trackRank(a, model, session) - trackRank(b, model, session))[0]
-        : undefined;
+    return agree ? bestRanked(results, model, session) : undefined;
 }
 // Every multi-hit result set reaches the picker through here, so the two
 // search surfaces cannot disagree about when one is worth raising. Returns
 // whether the view moved.
-export async function showSearchResults({ results, query, model, assemblyName, grow, }) {
+export async function showSearchResults({ results, query, model, assemblyName, grow, showHitTrack, }) {
     const session = getSession(model);
     const unanimous = unanimousResult({
         results,
@@ -115,7 +129,13 @@ export async function showSearchResults({ results, query, model, assemblyName, g
         assembly: session.assemblyManager.get(assemblyName),
     });
     if (unanimous) {
-        await navToOption({ option: unanimous, model, assemblyName, grow });
+        await navToOption({
+            option: unanimous,
+            model,
+            assemblyName,
+            grow,
+            showHitTrack,
+        });
         return true;
     }
     else {
@@ -127,7 +147,11 @@ export async function showSearchResults({ results, query, model, assemblyName, g
 // own edges, which is what this default is; a caller that asked for a specific
 // padding gets that instead.
 const SEARCH_HIT_GROW = 0.2;
-export async function navToOption({ option, model, assemblyName, grow, }) {
+// A hit lands with the track its index came from shown, which is what a name
+// typed into the search box wants. A session spec that named its own tracks
+// passes false: it asked for those tracks, and a hosted config's full RefSeq
+// appearing beside the curated one it listed read as a bug.
+export async function navToOption({ option, model, assemblyName, grow, showHitTrack = true, }) {
     // getLocation() can be an empty string when a result reports hasLocation()
     // but carries no coordinates; treat that as "no location" and fall back to
     // the label rather than forwarding '' into an empty, view-blanking parse
@@ -136,8 +160,8 @@ export async function navToOption({ option, model, assemblyName, grow, }) {
     const session = getSession(model);
     const { assemblyManager } = session;
     await model.navToLocations(parseLocStrings(location, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName, grow ?? SEARCH_HIT_GROW);
-    if (trackId && isAlive(model)) {
-        model.showTrack(trackId);
+    if (showHitTrack && trackId && isAlive(model)) {
+        await model.launchTrack(trackId);
     }
     // same detach hazard as showTrack above: navToLocations awaits, and handlers
     // read off the view (the canvas one calls getSession(model) and model.tracks),
@@ -174,7 +198,7 @@ export function notifySearchFailure(session, e) {
 // about where to go and so raise the picker, and a view detached while the
 // search RPC ran — and each of them resolves, so a caller awaiting this cannot
 // otherwise tell "showing it" from "asked you which one".
-export async function handleSelectedRegion({ input, model, assemblyName, grow, }) {
+export async function handleSelectedRegion({ input, model, assemblyName, grow, showHitTrack, }) {
     const { assemblyManager, textSearchManager } = getSession(model);
     // resolves only once regions/aliases are loaded, which isValidRefName needs
     // (it throws otherwise). A load failure is not this function's to report:
@@ -260,6 +284,7 @@ export async function handleSelectedRegion({ input, model, assemblyName, grow, }
                 model,
                 assemblyName,
                 grow,
+                showHitTrack,
             });
         }
         else if (results.length === 1) {
@@ -272,6 +297,7 @@ export async function handleSelectedRegion({ input, model, assemblyName, grow, }
                 model,
                 assemblyName,
                 grow,
+                showHitTrack,
             });
             return true;
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "5.0.0-beta.1",
+  "version": "5.0.0-beta.3",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -22,14 +22,14 @@
   ],
   "dependencies": {
     "@jbrowse/mobx-state-tree": "^6.5.1",
-    "@mui/icons-material": "^9.3.1",
-    "@mui/material": "^9.3.1",
+    "@mui/icons-material": "^9.4.0",
+    "@mui/material": "^9.4.0",
     "mobx": "^7.0.3",
     "mobx-react": "^10.0.2",
-    "@jbrowse/core": "^5.0.0-beta.1",
-    "@jbrowse/render-core": "^5.0.0-beta.1",
-    "@jbrowse/display-ui": "^5.0.0-beta.1",
-    "@jbrowse/display-kit": "^5.0.0-beta.1"
+    "@jbrowse/core": "^5.0.0-beta.3",
+    "@jbrowse/display-kit": "^5.0.0-beta.3",
+    "@jbrowse/display-ui": "^5.0.0-beta.3",
+    "@jbrowse/render-core": "^5.0.0-beta.3"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -40,7 +40,7 @@
   },
   "sideEffects": false,
   "devDependencies": {
-    "@jbrowse/display-test-utils": "^5.0.0-beta.1"
+    "@jbrowse/display-test-utils": "^5.0.0-beta.3"
   },
   "scripts": {
     "prebuild": "pnpm clean",

package/esm/LinearGenomeView/FloatingSvgOverlay.d.ts

@@ -1,5 +0,0 @@
-export declare const FloatingSvgOverlay: ({ width, height, children, }: {
-    width: number;
-    height: number;
-    children: React.ReactNode;
-}) => import("react").JSX.Element;

package/esm/LinearGenomeView/FloatingSvgOverlay.js

@@ -1,25 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { TrackOverlayPortal } from '@jbrowse/display-ui';
-import { observer } from 'mobx-react';
-// Lifts an SVG legend / chrome above the inter-region padding masks: a
-// full-track, pointer-events:none <svg> portaled into the TrackContainer overlay
-// node (see TrackOverlayPortal). The SVG counterpart to the HTML overlays
-// (FloatingLegend, HicOverlayPanel) — used where the same legend
-// markup is also drawn by an SVG-export path, so it must stay <svg>.
-//
-// Children draw in <svg> user space; the wrapping <svg> stays pointer-events:none
-// so it doesn't eat canvas events, so any interactive sub-content (a dismiss
-// "×", clickable swatches) must set pointer-events:auto on its own element.
-// fallbackInline={false}: outside a TrackContainer it renders nothing, matching
-// callers whose export path draws its own inline legend.
-export const FloatingSvgOverlay = observer(function FloatingSvgOverlay({ width, height, children, }) {
-    return (_jsx(TrackOverlayPortal, { fallbackInline: false, children: _jsx("svg", { style: {
-                position: 'absolute',
-                top: 0,
-                left: 0,
-                width,
-                height,
-                pointerEvents: 'none',
-                overflow: 'hidden',
-            }, children: children }) }));
-});

package/esm/LinearGenomeView/initKeys.d.ts

@@ -1,13 +0,0 @@
-export declare function partitionLaunchKeys(spec: object, viewPropKeys: ReadonlySet<string>): {
-    init: Record<string, unknown>;
-    viewProps: Record<string, unknown>;
-    unknown: Record<string, unknown>;
-};
-export declare function linearGenomeViewPropKeys(pluginManager: {
-    getViewType: (name: string) => {
-        stateModel: {
-            properties: object;
-        };
-    };
-}): ReadonlySet<string>;
-export declare function warnUnknownLaunchKeys(surface: string, unknown: object): void;

package/esm/LinearGenomeView/initKeys.js

@@ -1,104 +0,0 @@
-// The init keys are derived from their interface so they can't drift: the
-// Record requires exactly one entry per key, so adding a field without listing
-// it here is a compile error rather than a key that silently warns as "unknown".
-//
-// There is no matching list for the plain view props, and there must not be:
-// they are whatever the state model declares, read off it by the caller and
-// passed in as `viewPropKeys`. A hand-written eight is what left `hideHeader`,
-// `showGridlines`, `showCytobands` and five others declared, menu-settable and
-// silently unreachable from any spec — the same failure LinearSyntenyView's
-// `drawLocationMarkers` had.
-//
-// #launchKeys LinearGenomeView — the URL parameters page renders this list
-// rather than restating it; each of these keys has its own `&param=` section
-// there, which is why no description is attached here.
-const knownInitKeyMap = {
-    loc: true,
-    grow: true,
-    assembly: true,
-    displayedRegionNames: true,
-    tracks: true,
-    tracklist: true,
-    nav: true,
-    highlight: true,
-};
-const knownInitKeys = new Set(Object.keys(knownInitKeyMap));
-// Never settable from a spec, whatever the model declares: `type` picks the
-// view and `id` is passed top-level so MST's optional identifier honors it.
-const RESERVED = new Set(['id', 'type', 'init']);
-// The viewport keys from before it was stored as a window. They are no longer
-// declared properties, so the model's own property list does not contain them
-// and they would partition as typos — reported as unknown and dropped. They are
-// not typos: `preProcessSnapshot` still converts them, so they belong in the
-// snapshot bucket, and a URL or saved spec that names them goes on working.
-//
-// Deletable with `legacyBpPerPx` in the model, and for the same reason.
-const LEGACY_VIEWPORT_PROPS = new Set(['bpPerPx', 'offsetPx']);
-// Partition launch keys three ways, once, for every caller that needs to know
-// which is which:
-//
-// - `init`: resolution keys (loc, tracks, highlight, …) with no direct MST
-//   representation, which afterAttach applies on attach and then discards
-// - `viewProps`: plain persisted props MST restores natively, so they belong on
-//   the view snapshot rather than in the blob
-// - `unknown`: neither, i.e. a typo. MST silently drops unknown snapshot keys and
-//   `init` is a frozen blob, so nothing else would notice
-//
-// The two callers differ only in what they do with each bucket: the launcher
-// spreads a flat spec across the new view's snapshot and warns about the typos,
-// while afterAttach — which only ever sees an already-built blob — warns about
-// both a typo and a view prop that ended up inside it.
-export function partitionLaunchKeys(spec, 
-// The view's declared property names. Callers with a live node read it off
-// `getPropertyMembers(self).properties`; callers building a snapshot read it
-// off the registered view type's `stateModel.properties` — see
-// `linearGenomeViewPropKeys`.
-viewPropKeys) {
-    const init = {};
-    const viewProps = {};
-    const unknown = {};
-    for (const [key, value] of Object.entries(spec)) {
-        const bucket = knownInitKeys.has(key)
-            ? init
-            : (viewPropKeys.has(key) || LEGACY_VIEWPORT_PROPS.has(key)) &&
-                !RESERVED.has(key)
-                ? viewProps
-                : unknown;
-        bucket[key] = value;
-    }
-    return { init, viewProps, unknown };
-}
-// The registered LinearGenomeView's declared property names, for a caller that
-// has a PluginManager but no view yet (a launcher, or a synteny row being built).
-// A caller holding a live node reads the same thing off
-// `getPropertyMembers(self).properties` instead.
-//
-// `getViewType` THROWS on an unregistered name, and that is left alone: this is
-// only ever called from code that is about to add a LinearGenomeView, so an
-// absent view type is a broken plugin manager rather than a case to degrade
-// through — and degrading would mean silently dropping every property the
-// caller asked for, which is the failure this whole mechanism exists to end.
-//
-// Cached: the set is fixed for the life of the manager, and a launch that opens
-// a stack of rows would otherwise rebuild it per row.
-const propKeyCache = new WeakMap();
-export function linearGenomeViewPropKeys(pluginManager) {
-    const cached = propKeyCache.get(pluginManager);
-    if (cached) {
-        return cached;
-    }
-    const { stateModel } = pluginManager.getViewType('LinearGenomeView');
-    const keys = new Set(Object.keys(stateModel.properties));
-    propKeyCache.set(pluginManager, keys);
-    return keys;
-}
-// Report the `unknown` bucket. Both callers say the same thing about the same
-// mistake and differ only in which surface they name, so the wording lives next
-// to the partition that produces the bucket rather than in two hand-written
-// copies that drift.
-export function warnUnknownLaunchKeys(surface, unknown) {
-    const keys = Object.keys(unknown);
-    if (keys.length) {
-        console.warn(`${surface} ignored unknown key(s): ${keys.join(', ')}`);
-    }
-}