@jbrowse/plugin-linear-genome-view 5.0.0-beta.18 → 5.0.0-beta.19

package/esm/LinearGenomeView/model.js

@@ -2,7 +2,8 @@ import { canonicalLocString } from '@jbrowse/core/TextSearch/places';
 import { getConf, readConfObject } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { exportViewSvg } from '@jbrowse/core/svg/exportViewSvg';
-import { assembleLocString, clamp, getBpDisplayStr, getNotificationSink, getSession, isSessionModelWithWidgets, localStorageGetBoolean, localStorageGetItem, localStorageSetBoolean, localStorageSetItem, springAnimate, sum, } from '@jbrowse/core/util';
+import { highlightListMenuItems } from '@jbrowse/core/ui/menuItems';
+import { assembleLocString, clamp, getBpDisplayStr, getEnv, getNotificationSink, getSession, isSessionModelWithWidgets, localStorageGetBoolean, localStorageGetItem, localStorageSetBoolean, localStorageSetItem, springAnimate, sum, } from '@jbrowse/core/util';
 import { bpToLinearBp, bpToPx, computeMoveToLayout, createOverviewLayout, getLayoutHighlightCoords, getOverviewRegionPxSpan, moveTo, pxToBp, } from '@jbrowse/core/util/Base1DUtils';
 import { scaleBandHeights } from '@jbrowse/core/util/bandHeight';
 import { wholeBaseRegions } from '@jbrowse/core/util/blockTypes';
@@ -297,11 +298,11 @@ export function stateModelFactory(pluginManager) {
         hideNoTracksActive: types.stripDefault(types.boolean, false),
         /**
          * #property
-         * vestigial: the hierarchical selector is the only one that exists, so
-         * this value is ignored. Retained because saved sessions and share
-         * links persist it.
+         * ignored: the hierarchical selector is the only one. Declared because
+         * saved sessions and share links carry it.
+         * @deprecated
          */
-        trackSelectorType: types.stripDefault(types.enumeration(['hierarchical']), 'hierarchical'),
+        trackSelectorType: types.stripDefault(types.string, 'hierarchical'),
         /**
          * #property
          * show the "center line". A personal preference: never in a session
@@ -1332,12 +1333,10 @@ export function stateModelFactory(pluginManager) {
             if (!assemblyName) {
                 throw new Error('the view has no assembly to search yet');
             }
-            const { assemblyManager, textSearchManager } = getSession(self);
             const results = await fetchResults({
+                session: getSession(self),
                 queryString: query,
                 assemblyName,
-                textSearchManager,
-                assembly: await assemblyManager.waitForAssembly(assemblyName),
                 signal: opts?.signal,
             });
             return searchHitsOf(self, results, query, assemblyName, result => navToOption({
@@ -2249,7 +2248,7 @@ export function stateModelFactory(pluginManager) {
          *
          * The coarse blocks are a 500ms throttle, and every consumer trades
          * freshness for not recomputing per animation frame — the location box,
-         * canvas's on-screen feature set, and the two per-bp scans behind
+         * the feature display's on-screen feature set, and the two per-bp scans behind
          * `settledDynamicBlocks`. That trade is only sound while the answer is a
          * few frames old. **A jump makes it unrelated instead**, because there is
          * nothing to coalesce: the viewport left behind is not an approximation of
@@ -2710,16 +2709,26 @@ export function stateModelFactory(pluginManager) {
                 getSession(self).addHighlight(region);
             }
         },
+        /**
+         * #action
+         * navigates to a highlight, zoomed out a little for context. Goes through
+         * a locstring so it reaches a refName the view is not displaying
+         */
+        navToHighlight(highlight) {
+            const { assemblyName, ...region } = highlight;
+            return self.navToLocString(assembleLocString(region), assemblyName, 0.2);
+        },
+    }))
+        .actions(self => ({
         /**
          * #action
          * navigates to the most recently added highlight on this view's
-         * assemblies, zoomed out a little for context
+         * assemblies
          */
         async navigateNewestHighlight() {
             const newest = self.highlights.at(-1);
             if (newest) {
-                const { assemblyName, ...region } = newest;
-                await self.navToLocString(assembleLocString(region), assemblyName, 0.2);
+                await self.navToHighlight(newest);
             }
             else {
                 getSession(self).notify('There are no highlights to navigate to.', 'info');
@@ -2830,11 +2839,10 @@ export function stateModelFactory(pluginManager) {
         },
         /**
          * #method
-         * returns menu items for a highlight context menu. plugins can extend
-         * this via Core-extendPluggableElement to add items
+         * a highlight chip's menu rows after Dismiss; extend this to add one
          */
         highlightMenuItems(_highlight) {
-            return [];
+            return highlightListMenuItems(getSession(self), getEnv(self).pluginManager);
         },
     }))
         .actions(self => {

package/esm/LinearGenomeView/rExport/exportLinearView.js

@@ -2,9 +2,6 @@ import { fullConfSnapshot, readConfObject } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { exportTracksToR } from './rScript.js';
-function trackConf(track) {
-    return track.configuration;
-}
 /** The regions on screen, each displayed region cut to what the view shows of it. */
 function viewRegions(view) {
     const blocks = view.dynamicBlocks.contentBlocks;
@@ -52,10 +49,10 @@ function tracksOf(view) {
             const { heightMode, height } = fullConfSnapshot(display.configuration);
             tracks.push({
                 trackId: track.configuration.trackId,
-                trackName: readConfObject(trackConf(track), 'name') ||
+                trackName: readConfObject(track.configuration, 'name') ||
                     track.configuration.trackId,
                 displayType: display.type,
-                adapter: readConfObject(trackConf(track), 'adapter'),
+                adapter: readConfObject(track.configuration, 'adapter'),
                 display: written,
                 heightMode,
                 height,
@@ -71,6 +68,8 @@ export function exportLinearViewToR(view, out) {
         regions: viewRegions(view),
         assembly: assemblyOf(view),
         bpPerPx: view.bpPerPx,
+        colorByFrame: view.colorByFrame,
+        showAminoAcids: view.showAminoAcids,
         out,
         notes: view.displayedRegions.some(r => r.reversed)
             ? ['view: shown right to left, where the figure runs left to right']

package/esm/LinearGenomeView/rExport/rScript.d.ts

@@ -75,13 +75,17 @@ export declare function locusOf(refName: string, start: number, end: number): st
  * header instead of stopping the figure: a script that quietly differs from
  * its view says so.
  */
-export declare function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, bpPerPx, out, notes: viewNotes, }: {
+export declare function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, bpPerPx, colorByFrame, showAminoAcids, out, notes: viewNotes, }: {
     tracks: readonly RExportTrack[];
     regions: readonly Region[];
     /** The view's assembly config as written, which names its sequence and its contigs' aliases. */
     assembly?: Record<string, unknown>;
     /** The view's zoom, which decides what a feature or quantitative display shows. */
     bpPerPx?: number;
+    /** The view's "CDS reading frame colors", which a feature track takes. */
+    colorByFrame?: boolean;
+    /** The view's "Amino acids when zoomed in", which a feature track takes. */
+    showAminoAcids?: boolean;
     out?: string;
     /** What the caller knows of the view that the figure does not show. */
     notes?: readonly string[];

package/esm/LinearGenomeView/rExport/rScript.js

@@ -93,9 +93,15 @@ const RESERVED = new Set([
     'Inf',
     'NaN',
     'NA',
+    'NA_integer_',
+    'NA_real_',
+    'NA_complex_',
+    'NA_character_',
 ]);
 function isIdentifier(s) {
-    return /^[A-Za-z.][A-Za-z0-9._]*$/.test(s) && !RESERVED.has(s);
+    return (/^([A-Za-z]|\.(?!\d))[A-Za-z0-9._]*$/.test(s) &&
+        !/^(\.\.\.|\.\.\d+)$/.test(s) &&
+        !RESERVED.has(s));
 }
 /**
  * A config value as the R literal ggjbrowse hands the engine: a `list` per
@@ -328,6 +334,16 @@ function trackNames(tracks) {
         return name;
     });
 }
+/**
+ * A track's `jbrowse_stack()` argument, named as the view labels it so its
+ * band is titled. A name `width` would set the stack's own `width`, so that
+ * one goes in a list, whose names title its tracks too.
+ */
+function stackArgument(title, name) {
+    return title === 'width'
+        ? `list(width = ${name})`
+        : `${isIdentifier(title) ? title : rStr(title)} = ${name}`;
+}
 /** What the figure cannot show of a track whose settings ggjbrowse reads. */
 function settingNotes(track) {
     const { color } = track.display.encoding ?? {};
@@ -346,7 +362,7 @@ function settingNotes(track) {
  * header instead of stopping the figure: a script that quietly differs from
  * its view says so.
  */
-export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, bpPerPx, out = 'figure.png', notes: viewNotes = [], }) {
+export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, bpPerPx, colorByFrame = false, showAminoAcids = true, out = 'figure.png', notes: viewNotes = [], }) {
     const notes = [...viewNotes];
     const assembly = assemblySnapshot && assemblyArgument(assemblySnapshot);
     if (assembly && 'skipped' in assembly) {
@@ -360,6 +376,7 @@ export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, b
     const names = trackNames(tracks);
     const reads = [];
     const drawn = [];
+    const bands = [];
     let alignments;
     tracks.forEach((track, i) => {
         const reader = READERS[track.displayType];
@@ -381,10 +398,13 @@ export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, b
             }
             : track.display;
         const width = viewPx !== undefined;
+        const geneTrack = track.displayType === 'LinearBasicDisplay';
         const args = [
             ...(Object.keys(display).length ? [`display = ${rValue(display)}`] : []),
             ...(width ? ['width = width'] : []),
             ...(assemblyValue ? ['assembly = assembly'] : []),
+            ...(geneTrack && colorByFrame ? ['color_by_cds = TRUE'] : []),
+            ...(geneTrack && !showAminoAcids ? ['amino_acids = FALSE'] : []),
             ...(source.index ? [`index = ${rStr(source.index)}`] : []),
         ];
         const name = names[i];
@@ -397,6 +417,7 @@ export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, b
             `  ${['locus', ...args].join(',\n  ')})`,
         ].join('\n'));
         drawn.push(name);
+        bands.push(stackArgument(track.trackName, name));
         if (reader.call === 'jbrowse_alignments') {
             alignments ??= name;
         }
@@ -456,7 +477,7 @@ export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, b
         '',
         reads.join('\n\n'),
         '',
-        `fig <- jbrowse_stack(${drawn.join(', ')})`,
+        `fig <- jbrowse_stack(${bands.join(',\n  ')})`,
         'print(fig)',
         `ggplot2::ggsave(${rStr(out)}, fig, width = jbrowse_width(fig), height = jbrowse_height(fig))`,
         '',

package/esm/LinearGenomeView/showRegionsWithUndo.d.ts

@@ -6,7 +6,7 @@ import type { Region } from '@jbrowse/core/util/types';
  *
  * This is the "navigate the view you are looking at" half of a launcher, as
  * against `session.addView`, which opens a second one. Two features do it —
- * plugin-canvas's collapsed introns and plugin-alignments' "view mate region" —
+ * plugin-features's collapsed introns and plugin-alignments' "view mate region" —
  * and both had their own copy of the same fifteen lines, including the same two
  * decisions worth stating once:
  *

package/esm/LinearGenomeView/showRegionsWithUndo.js

@@ -6,7 +6,7 @@ import { transaction } from 'mobx';
  *
  * This is the "navigate the view you are looking at" half of a launcher, as
  * against `session.addView`, which opens a second one. Two features do it —
- * plugin-canvas's collapsed introns and plugin-alignments' "view mate region" —
+ * plugin-features's collapsed introns and plugin-alignments' "view mate region" —
  * and both had their own copy of the same fifteen lines, including the same two
  * decisions worth stating once:
  *

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -39,7 +39,9 @@ export async function renderToSvg(model, opts) {
         textHeight,
         trackLabels,
     });
-    notifySkippedSvgTracks(session, skippedTracks);
+    if (opts.announceSkipped !== false) {
+        notifySkippedSvgTracks(session, skippedTracks);
+    }
     // read after the displays' waits, and handed to SVGHeader rather than read
     // again, so the reserved `tracksTop` and the drawn header are one layout
     const { width, effectiveShowCytobands } = model;

package/esm/LinearGenomeView/util.d.ts

@@ -25,7 +25,7 @@ interface CenterKeepingView {
  * A caller building a view SNAPSHOT does: it has no model to call
  * `fitAllRegions()` on, and naming `bpPerPx`/`offsetPx` instead is dropped
  * whenever the snapshot also carries a `windowWidthBp` — which one copied off an
- * existing view always does. plugin-canvas's collapsed-intron launch is that
+ * existing view always does. plugin-features's collapsed-intron launch is that
  * caller. A live view calls `fitAllRegions()`.
  *
  * `width` enters only through the zoom-in floor, which bites for a region set

package/esm/LinearGenomeView/util.js

@@ -18,7 +18,7 @@ import { tickLabelsWorthDrawing } from '@jbrowse/core/util/tickLabels';
  * A caller building a view SNAPSHOT does: it has no model to call
  * `fitAllRegions()` on, and naming `bpPerPx`/`offsetPx` instead is dropped
  * whenever the snapshot also carries a `windowWidthBp` — which one copied off an
- * existing view always does. plugin-canvas's collapsed-intron launch is that
+ * existing view always does. plugin-features's collapsed-intron launch is that
  * caller. A live view calls `fitAllRegions()`.
  *
  * `width` enters only through the zoom-in floor, which bites for a region set

package/esm/displayKitTests/perRegionTestEnv.d.ts

@@ -31,7 +31,7 @@ export interface PerRegionTestControl {
      */
     estimateBytes: number;
     estimateCalls: number;
-    /** the display's own density verdict, canvas's second too-large axis */
+    /** the display's own density verdict, the feature display's second too-large axis */
     densityTooLarge: boolean;
     /**
      * What the next fetch stores, so a test can tell the payload a refetch
@@ -45,7 +45,7 @@ export interface PerRegionTestControl {
  * displays compose this foundation, and every one of them adds a plugin's worth
  * of behavior on top — so a test that boots one is testing that plugin as much
  * as the foundation, which is how the foundation's own autoruns came to be
- * pinned only by canvas's suite.
+ * pinned only by the feature display's suite.
  */
 /** Which of the gate's opt-in hooks this display overrides. */
 export interface GateOptIns {
@@ -266,7 +266,9 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
     readonly plotKeys: string[];
     readonly plot: import("@jbrowse/core/configuration").Plot;
     readonly configNotices: string[];
+} & {
     readonly notices: string[];
+} & {
     readonly cornerNotices: string[];
     readonly plotExamples: readonly import("@jbrowse/core/configuration").PlotExample[];
     readonly configDocsUrl: string;
@@ -498,12 +500,12 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
      */
     estimateBytes?: number;
 }): {
-    createDisplay: ({ displayedRegions, displaySnapshot, skipWidth, regionsInSnapshot, }?: {
+    createDisplay: (args_0?: {
         displayedRegions?: import("@jbrowse/core/util").Region[];
         displaySnapshot?: Record<string, unknown>;
         skipWidth?: boolean;
         regionsInSnapshot?: boolean;
-    }) => {
+    } | undefined) => {
         session: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
             name: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
             view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyModelType>;
@@ -804,7 +806,9 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly plotKeys: string[];
             readonly plot: import("@jbrowse/core/configuration").Plot;
             readonly configNotices: string[];
+        } & {
             readonly notices: string[];
+        } & {
             readonly cornerNotices: string[];
             readonly plotExamples: readonly import("@jbrowse/core/configuration").PlotExample[];
             readonly configDocsUrl: string;
@@ -1231,7 +1235,9 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly plotKeys: string[];
             readonly plot: import("@jbrowse/core/configuration").Plot;
             readonly configNotices: string[];
+        } & {
             readonly notices: string[];
+        } & {
             readonly cornerNotices: string[];
             readonly plotExamples: readonly import("@jbrowse/core/configuration").PlotExample[];
             readonly configDocsUrl: string;

package/esm/index.js

@@ -4,7 +4,6 @@ import { isAbstractMenuManager } from '@jbrowse/core/util';
 import { VIEW_TRACK_LABEL_MODES } from '@jbrowse/display-kit/types';
 import { types } from '@jbrowse/mobx-state-tree';
 import LineStyleIcon from '@mui/icons-material/LineStyle';
-import FeatureTrackF from './FeatureTrack/index.js';
 import LaunchLinearGenomeViewF from './LaunchLinearGenomeView/index.js';
 import SequenceFeatureHoverHighlightExtensionF from './LinearGenomeView/components/SequenceFeatureHoverHighlightExtension.js';
 import LinearGenomeViewF from './LinearGenomeView/index.js';
@@ -33,7 +32,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
         },
     });
     install(pluginManager) {
-        FeatureTrackF(pluginManager);
         LinearGenomeViewF(pluginManager);
         LaunchLinearGenomeViewF(pluginManager);
         SequenceFeatureHoverHighlightExtensionF(pluginManager);

package/esm/searchUtils.d.ts

@@ -3,7 +3,7 @@ import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import type TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 import type { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { AssemblyHost, NotificationSink, TrackCatalog } from '@jbrowse/core/util';
+import type { AbstractSessionModel, AssemblyHost, NotificationSink, TrackCatalog } from '@jbrowse/core/util';
 declare module '@jbrowse/core/PluginManager' {
     interface ExtensionPointRegistry {
         'LinearGenomeView-searchResultSelected': {
@@ -67,7 +67,19 @@ interface SearchArgs {
     assembly?: Assembly;
     signal?: AbortSignal;
 }
-export declare function fetchResults(args: SearchArgs): Promise<BaseResult[]>;
+interface SessionSearchArgs {
+    session: Pick<AbstractSessionModel, 'assemblyManager' | 'textSearchManager'>;
+    queryString: string;
+    assemblyName: string;
+    searchType?: SearchType;
+    signal?: AbortSignal;
+}
+/**
+ * The search box's hits for a query: refNames and text-index results, merged.
+ * Pass the session and the function finds the index manager and the assembly
+ * itself; passing `textSearchManager` and `assembly` is the older form.
+ */
+export declare function fetchResults(args: SessionSearchArgs | SearchArgs): Promise<BaseResult[]>;
 export declare function nameNotFound(input: string, assemblyName: string, { indexCount, failures }: {
     indexCount: number;
     failures: unknown[];

package/esm/searchUtils.js

@@ -1,11 +1,11 @@
 import { RefSequenceResult } from '@jbrowse/core/TextSearch/BaseResults';
-import { groupByPlace } from '@jbrowse/core/TextSearch/places';
-import { dedupe, getEnv, getNotificationSink, getSession, matchRefNames, MAX_GLOB_REGIONS, UnknownRefNameError, } from '@jbrowse/core/util';
+import { groupByPlace, landsInAssembly } from '@jbrowse/core/TextSearch/places';
+import { dedupe, getEnv, getNotificationSink, getSession, matchRefNames, MAX_GLOB_REGIONS, rankRefNames, UnknownRefNameError, } from '@jbrowse/core/util';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { parseLocStrings } from './LinearGenomeView/util.js';
 // Budget for refName suggestions from a query. Deliberately far below the
-// autocomplete's ~100-row display cap: refNames are returned ahead of the text
-// search hits, so a scaffold-heavy assembly would otherwise fill every row with
+// autocomplete's ~100-row display cap: exact and prefix refName hits are
+// returned ahead of the text search hits, so a scaffold-heavy assembly would otherwise fill every row with
 // scaffolds and push the gene hits out of the list entirely. Raising this to
 // match the display cap looks like a consistency fix and is not one.
 const MAX_REFNAME_HITS = 10;
@@ -274,16 +274,20 @@ export async function handleSelectedRegion({ input, model, assemblyName, grow, s
         }
         else {
             // no search hits: still try to resolve the input as a locstring (bare
-            // refname, "ref start end" triplet, etc). if that also can't find a
-            // refname AND the input is a single bare token (a plausible gene name),
-            // reframe the unknown-ref error as a name miss; keep the specific ref
-            // error for coordinate/multi-part queries
+            // refname, "ref start end" triplet, etc). If that also can't find a
+            // refname and the input names no sequence and no coordinate — a gene
+            // name, or a phrase like "breast cancer" — reframe the unknown-ref error
+            // as a name miss; keep the specific ref error for coordinate-shaped input
             try {
                 await navToLocstrings();
                 return true;
             }
             catch (e) {
-                const isPlainName = !input.includes(':') && !input.includes(' ');
+                const isPlainName = !input.includes(':') &&
+                    input
+                        .trim()
+                        .split(/\s+/)
+                        .every(token => !isRef(token) && !/^\d[\d,]*$/.test(token));
                 if (e instanceof UnknownRefNameError && isPlainName) {
                     throw nameNotFound(input, assemblyName, found);
                 }
@@ -308,17 +312,39 @@ async function searchNames({ queryString, searchType, assemblyName, textSearchMa
     // not itself kick off the lazy load. A load failure just leaves allRefNames
     // undefined, so this still returns whatever the text search turned up
     await assembly?.load().catch(() => { });
-    const refNameResults = assembly
+    const { strong, weak } = assembly
         ? searchRefNames(assembly, queryString, searchType)
-        : [];
+        : { strong: [], weak: [] };
     return {
-        results: dedupe([...refNameResults, ...(report?.results ?? [])], elt => elt.getId()),
+        results: dedupe([
+            ...strong,
+            ...(report?.results ?? []).filter(r => landsInAssembly(r, assembly)),
+            ...weak,
+        ], elt => elt.getId()),
         indexCount: report?.indexCount ?? 0,
         failures: report?.failures ?? [],
     };
 }
+/**
+ * The search box's hits for a query: refNames and text-index results, merged.
+ * Pass the session and the function finds the index manager and the assembly
+ * itself; passing `textSearchManager` and `assembly` is the older form.
+ */
 export async function fetchResults(args) {
-    return (await searchNames(args)).results;
+    if ('session' in args) {
+        const { session, ...rest } = args;
+        const assembly = await session.assemblyManager
+            .waitForAssembly(args.assemblyName)
+            .catch(() => undefined);
+        return (await searchNames({
+            ...rest,
+            textSearchManager: session.textSearchManager,
+            assembly,
+        })).results;
+    }
+    else {
+        return (await searchNames(args)).results;
+    }
 }
 // A miss says when an index could not answer: with none answering it is a
 // failure, and with some answering it is still a miss, naming what failed
@@ -333,30 +359,24 @@ export function nameNotFound(input, assemblyName, { indexCount, failures }) {
             })
             : new SearchResultsNotFoundError(`${miss} (a search index failed: ${failure})`, { cause: failure });
 }
-// Scan assembly refnames for query matches, resolving aliases (e.g. 'contigB')
-// to the canonical refname ('ctgB') so the dropdown shows the name that matches
-// the FASTA / displayed regions. allRefNames can hold ~10^6 entries, so stop
-// once enough unique canonical hits accumulate rather than lowercasing and
-// scanning the entire list on every keystroke.
+// The refNames a query names, through the same ranking the dropdown's fallback
+// list uses. A refName the query is only a substring of is the weakest kind of
+// hit, so it goes behind the text-search results rather than ahead of them
 function searchRefNames(assembly, queryString, searchType) {
-    const q = queryString.toLowerCase();
-    // canonical name -> whether any alias of it matched the query exactly, so
-    // "contigb" is an exact hit on ctgB even though the canonical name is not
-    // the query. Same collapsing as before, now carrying the flag through it
-    const canonicalHits = new Map();
-    for (const ref of assembly.allRefNames ?? []) {
-        const lower = ref.toLowerCase();
-        const exact = lower === q;
-        const isMatch = searchType === 'exact' ? exact : lower.startsWith(q);
-        if (isMatch) {
-            const canonical = assembly.getCanonicalRefName2(ref);
-            canonicalHits.set(canonical, exact || !!canonicalHits.get(canonical));
-            if (canonicalHits.size >= MAX_REFNAME_HITS) {
-                break;
-            }
-        }
-    }
-    return [...canonicalHits].map(([r, exact]) => new RefSequenceResult({ label: r, refName: r, exact }));
+    const hits = rankRefNames(assembly, queryString, MAX_REFNAME_HITS)
+        .filter(({ tier }) => searchType !== 'exact' || tier === 'exact')
+        .map(({ refName, tier }) => ({
+        tier,
+        result: new RefSequenceResult({
+            label: refName,
+            refName,
+            exact: tier === 'exact',
+        }),
+    }));
+    return {
+        strong: hits.filter(h => h.tier !== 'substring').map(h => h.result),
+        weak: hits.filter(h => h.tier === 'substring').map(h => h.result),
+    };
 }
 // splits on the last instance of a character
 export function splitLast(str, split) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "5.0.0-beta.18",
+  "version": "5.0.0-beta.19",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -24,13 +24,13 @@
     "@jbrowse/mobx-state-tree": "^6.10.0",
     "@mui/icons-material": "^9.5.0",
     "@mui/material": "^9.5.0",
-    "mobx": "^7.1.1",
-    "mobx-react": "^10.0.2",
-    "@jbrowse/display-ui": "^5.0.0-beta.18",
-    "@jbrowse/display-kit": "^5.0.0-beta.18",
-    "@jbrowse/launch-args": "^5.0.0-beta.18",
-    "@jbrowse/render-core": "^5.0.0-beta.18",
-    "@jbrowse/core": "^5.0.0-beta.18"
+    "mobx": "^7.1.3",
+    "mobx-react": "^10.0.3",
+    "@jbrowse/core": "^5.0.0-beta.19",
+    "@jbrowse/display-kit": "^5.0.0-beta.19",
+    "@jbrowse/launch-args": "^5.0.0-beta.19",
+    "@jbrowse/display-ui": "^5.0.0-beta.19",
+    "@jbrowse/render-core": "^5.0.0-beta.19"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -41,7 +41,7 @@
   },
   "sideEffects": false,
   "devDependencies": {
-    "@jbrowse/display-test-utils": "^5.0.0-beta.18"
+    "@jbrowse/display-test-utils": "^5.0.0-beta.19"
   },
   "scripts": {
     "prebuild": "pnpm clean",