jbrowse-plugin-msaview 3.10.0 → 5.0.0

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { isMsaView } from '../MsaViewPanel/model';
+import { isMsaView } from '../MsaViewPanel/isMsaView';
 import { hasHoverPosition, useStyles } from './util';
 const GenomeMouseoverHighlight = observer(function ({ model, }) {
     const { hovered, views } = getSession(model);

package/dist/AddHighlightModel/index.js

@@ -1,19 +1,10 @@
 import React from 'react';
 import { getSession } from '@jbrowse/core/util';
-import { isMsaView } from '../MsaViewPanel/model';
+import { isMsaView } from '../MsaViewPanel/isMsaView';
 import HighlightComponents from './HighlightComponents';
 export default function AddHighlightComponentsModelF(pluginManager) {
-    pluginManager.addToExtensionPoint(
-    // @ts-expect-error v4 hosts have no contributeToExtensionPoint
-    'LinearGenomeView-TracksContainerComponent', (rest, { model }) => {
+    pluginManager.contributeToExtensionPoint('LinearGenomeView-TracksContainerComponent', ({ model }) => {
         const { views } = getSession(model);
-        const hasMsaView = views.some(v => isMsaView(v) && v.connectedViewId === model.id);
-        if (!hasMsaView) {
-            return rest;
-        }
-        return [
-            ...rest,
-            React.createElement(HighlightComponents, { key: "highlight_protein_viewer_msaview", model: model }),
-        ];
+        return views.some(v => isMsaView(v) && v.connectedViewId === model.id) ? (React.createElement(HighlightComponents, { key: "highlight_protein_viewer_msaview", model: model })) : undefined;
     });
 }

package/dist/LaunchMsaView/codingFeature.d.ts

@@ -1,14 +1,2 @@
 import type { Feature } from '@jbrowse/core/util';
-export declare function isGeneLikeType(type: unknown): boolean;
 export declare function isCodingFeature(feature: Feature): boolean;
-/**
- * Whether the feature is known not to code for anything.
- *
- * Not simply `!isCodingFeature`: a feature that arrived with no subfeatures at
- * all says nothing either way, and a host is free to hand one over that way.
- * Reading that as "no protein here" takes the menu item off a perfectly
- * ordinary gene, silently, which is worse than opening a dialog that then has
- * nothing to translate.
- */
-export declare function isKnownNonCoding(feature: Feature): boolean;
-export declare function geneLikeRoot(feature: Feature): Feature;

package/dist/LaunchMsaView/codingFeature.js

@@ -1,12 +1,3 @@
-// Copied from @jbrowse/core's featureTypes rather than imported: the barrel
-// only exports it from v5, and a bundle resolving it on a v4 host reads
-// undefined.
-const GENE_LIKE_TYPE = /gene(_segment)?$|rna$|transcript/;
-// `unknown` rather than `string | undefined`, because the type comes off a
-// host's hit-test item and nothing here built it.
-export function isGeneLikeType(type) {
-    return typeof type === 'string' && GENE_LIKE_TYPE.test(type.toLowerCase());
-}
 function isCDS(feature) {
     return feature.get('type')?.toLowerCase() === 'cds';
 }
@@ -15,24 +6,3 @@ function isCDS(feature) {
 export function isCodingFeature(feature) {
     return isCDS(feature) || !!feature.get('subfeatures')?.some(isCodingFeature);
 }
-/**
- * Whether the feature is known not to code for anything.
- *
- * Not simply `!isCodingFeature`: a feature that arrived with no subfeatures at
- * all says nothing either way, and a host is free to hand one over that way.
- * Reading that as "no protein here" takes the menu item off a perfectly
- * ordinary gene, silently, which is worse than opening a dialog that then has
- * nothing to translate.
- */
-export function isKnownNonCoding(feature) {
-    return !!feature.get('subfeatures')?.length && !isCodingFeature(feature);
-}
-// The outermost gene-like ancestor, so a click on an isoform opens the dialog
-// on the gene with every transcript to choose from, as the canvas host does.
-export function geneLikeRoot(feature) {
-    let root = feature;
-    for (let parent = root.parent?.(); parent && isGeneLikeType(parent.get('type')); parent = parent.parent?.()) {
-        root = parent;
-    }
-    return root;
-}

package/dist/LaunchMsaView/codingFeature.test.js

@@ -1,6 +1,6 @@
 import { SimpleFeature } from '@jbrowse/core/util';
 import { describe, expect, it } from 'vitest';
-import { geneLikeRoot, isCodingFeature, isGeneLikeType, isKnownNonCoding, } from './codingFeature';
+import { isCodingFeature } from './codingFeature';
 function feature(type, subfeatures = []) {
     return new SimpleFeature({
         uniqueId: `${type}-${Math.random()}`,
@@ -11,29 +11,6 @@ function feature(type, subfeatures = []) {
         subfeatures: subfeatures.map(s => s.toJSON()),
     });
 }
-describe('isGeneLikeType', () => {
-    it('accepts the SO spellings of gene, transcript and RNA', () => {
-        for (const t of [
-            'gene',
-            'mRNA',
-            'transcript',
-            'ncRNA_gene',
-            'protein_coding_gene',
-            'V_gene_segment',
-            'primary_transcript',
-            'pseudogenic_transcript',
-            'lnc_RNA',
-        ]) {
-            expect(isGeneLikeType(t)).toBe(true);
-        }
-    });
-    it('rejects regions, matches and CDS', () => {
-        for (const t of ['intergenic_region', 'cDNA_match', 'CDS', 'exon']) {
-            expect(isGeneLikeType(t)).toBe(false);
-        }
-        expect(isGeneLikeType(undefined)).toBe(false);
-    });
-});
 describe('isCodingFeature', () => {
     it('finds a CDS anywhere below the feature', () => {
         const gene = feature('gene', [
@@ -49,27 +26,3 @@ describe('isCodingFeature', () => {
         expect(isCodingFeature(feature('CDS'))).toBe(true);
     });
 });
-describe('isKnownNonCoding', () => {
-    it('is true for a transcript whose subfeatures are all exons', () => {
-        expect(isKnownNonCoding(feature('lnc_RNA', [feature('exon'), feature('exon')]))).toBe(true);
-    });
-    // a host is free to hand over a bare record, and reading that as "no protein
-    // here" takes the menu item off an ordinary gene without a word
-    it('is false for a feature that arrived with no subfeatures at all', () => {
-        expect(isKnownNonCoding(feature('gene'))).toBe(false);
-    });
-    it('is false when a CDS is somewhere below', () => {
-        expect(isKnownNonCoding(feature('gene', [feature('mRNA', [feature('CDS')])]))).toBe(false);
-    });
-});
-describe('geneLikeRoot', () => {
-    it('climbs from an isoform to its gene', () => {
-        const gene = feature('gene', [feature('mRNA', [feature('CDS')])]);
-        const mrna = gene.get('subfeatures')[0];
-        expect(geneLikeRoot(mrna)).toBe(gene);
-    });
-    it('stays put with no gene-like parent', () => {
-        const mrna = feature('mRNA', [feature('CDS')]);
-        expect(geneLikeRoot(mrna)).toBe(mrna);
-    });
-});

package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js

@@ -103,16 +103,14 @@ const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, ch
                             selectedTranscript: selectedTranscript.toJSON(),
                             proteinSequence,
                         };
-                    submit(() => {
-                        launchConnectedView({
-                            view,
-                            feature: selectedTranscript,
-                            placement,
-                            displayName: getBlastViewTitle(feature, selectedTranscript),
-                            ...builtAlignmentLook,
-                            blastParams,
-                        });
-                    });
+                    submit(() => launchConnectedView({
+                        view,
+                        feature: selectedTranscript,
+                        placement,
+                        displayName: getBlastViewTitle(feature, selectedTranscript),
+                        ...builtAlignmentLook,
+                        blastParams,
+                    }));
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.js

@@ -85,17 +85,15 @@ const BlastManualPanel = observer(function ({ handleClose, feature, model, child
                     React.createElement(QueryRowSelector, { ...queryRow })))),
         React.createElement(SubmitCancelActions, { model: model, submitDisabled: !selectedTranscript || !msaText.trim(), onSubmit: placement => {
                 if (selectedTranscript) {
-                    submit(() => {
-                        launchConnectedView({
-                            view,
-                            feature: selectedTranscript,
-                            placement,
-                            displayName: getGeneDisplayName(selectedTranscript),
-                            querySeqName: queryRow.querySeqName,
-                            querySeqOffset: queryRow.querySeqOffset,
-                            data: { msa: msaText, tree: treeText },
-                        });
-                    });
+                    submit(() => launchConnectedView({
+                        view,
+                        feature: selectedTranscript,
+                        placement,
+                        displayName: getGeneDisplayName(selectedTranscript),
+                        querySeqName: queryRow.querySeqName,
+                        querySeqOffset: queryRow.querySeqOffset,
+                        data: { msa: msaText, tree: treeText },
+                    }));
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.js

@@ -70,8 +70,10 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
             displayName: `BLAST - ${getResultDisplayName(cached)}`,
             ...builtAlignmentLook,
             data: { msa, tree, treeMetadata },
+        }).then(handleClose, (e) => {
+            console.error(e);
+            setOperationError(e);
         });
-        handleClose();
     };
     const displayError = error ?? operationError;
     return displayError ? (React.createElement(ErrorMessage, { error: displayError })) : isLoading ? (React.createElement(Typography, null, "Loading cached results...")) : results.length === 0 ? (React.createElement(Typography, { color: "textSecondary" }, "No cached BLAST results found for this gene. Run a BLAST query to cache results.")) : (React.createElement("div", null,

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js

@@ -80,22 +80,20 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                 (inputMethod === 'file' && !msaFileLocation) ||
                 (inputMethod === 'text' && !msaText.trim()), onSubmit: placement => {
                 if (selectedTranscript) {
-                    submit(() => {
-                        launchConnectedView({
-                            view,
-                            feature: selectedTranscript,
-                            placement,
-                            displayName: getGeneDisplayName(selectedTranscript),
-                            querySeqName: queryRow.querySeqName,
-                            querySeqOffset: queryRow.querySeqOffset,
-                            ...(inputMethod === 'file'
-                                ? {
-                                    msaFilehandle: msaFileLocation,
-                                    treeFilehandle: treeFileLocation,
-                                }
-                                : { data: { msa: msaText, tree: treeText } }),
-                        });
-                    });
+                    submit(() => launchConnectedView({
+                        view,
+                        feature: selectedTranscript,
+                        placement,
+                        displayName: getGeneDisplayName(selectedTranscript),
+                        querySeqName: queryRow.querySeqName,
+                        querySeqOffset: queryRow.querySeqOffset,
+                        ...(inputMethod === 'file'
+                            ? {
+                                msaFilehandle: msaFileLocation,
+                                treeFilehandle: treeFileLocation,
+                            }
+                            : { data: { msa: msaText, tree: treeText } }),
+                    }));
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js

@@ -60,24 +60,22 @@ const OrthologPanel = observer(function ({ handleClose, feature, model, preferre
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection })),
         React.createElement(SubmitCancelActions, { model: model, hint: React.createElement(SequenceStatusMessage, { status: sequenceStatus }), submitDisabled: !proteinSequence || !rowCountValid, onSubmit: placement => {
                 if (selectedTranscript) {
-                    submit(() => {
-                        launchConnectedView({
-                            view,
-                            feature: selectedTranscript,
-                            placement,
-                            displayName: `Orthologs - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
-                            ...builtAlignmentLook,
-                            orthologParams: {
-                                taxId,
-                                source,
-                                maxSpecies: rowCount,
-                                geneCandidates,
-                                msaAlgorithm,
-                                selectedTranscript: selectedTranscript.toJSON(),
-                                proteinSequence,
-                            },
-                        });
-                    });
+                    submit(() => launchConnectedView({
+                        view,
+                        feature: selectedTranscript,
+                        placement,
+                        displayName: `Orthologs - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                        ...builtAlignmentLook,
+                        orthologParams: {
+                            taxId,
+                            source,
+                            maxSpecies: rowCount,
+                            geneCandidates,
+                            msaAlgorithm,
+                            selectedTranscript: selectedTranscript.toJSON(),
+                            proteinSequence,
+                        },
+                    }));
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -82,25 +82,23 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
             // dataset that does not cover this gene
             submitDisabled: !selectedTranscript || !msaData?.length || !querySeqName, onSubmit: placement => {
                 if (selectedTranscript && msaText) {
-                    submit(() => {
-                        launchConnectedView({
-                            view,
-                            feature: selectedTranscript,
-                            placement,
-                            displayName: getGeneDisplayName(selectedTranscript),
-                            treeAreaWidth: 200,
-                            treeWidth: 100,
-                            drawNodeBubbles: false,
-                            labelsAlignRight: true,
-                            showBranchLen: false,
-                            colWidth: 10,
-                            rowHeight: 12,
-                            colorSchemeName: 'percent_identity_dynamic',
-                            querySeqName,
-                            querySeqOffset: queryRow.querySeqOffset,
-                            data: { msa: msaText },
-                        });
-                    });
+                    submit(() => launchConnectedView({
+                        view,
+                        feature: selectedTranscript,
+                        placement,
+                        displayName: getGeneDisplayName(selectedTranscript),
+                        treeAreaWidth: 200,
+                        treeWidth: 100,
+                        drawNodeBubbles: false,
+                        labelsAlignRight: true,
+                        showBranchLen: false,
+                        colWidth: 10,
+                        rowHeight: 12,
+                        colorSchemeName: 'percent_identity_dynamic',
+                        querySeqName,
+                        querySeqOffset: queryRow.querySeqOffset,
+                        data: { msa: msaText },
+                    }));
                 }
             }, onCancel: handleClose })));
 });

package/dist/LaunchMsaView/components/fetchSeq.d.ts

@@ -7,5 +7,5 @@ export declare function fetchSeq({ start, end, refName, session, assemblyName, }
     session: AbstractSessionModel;
 }): Promise<{
     seq: string;
-    assemblyGeneticCodeId: number | undefined;
+    assemblyGeneticCodeId: number;
 }>;

package/dist/LaunchMsaView/components/fetchSeq.js

@@ -5,11 +5,8 @@ export async function fetchSeq({ start, end, refName, session, assemblyName, })
     if (!assembly) {
         throw new Error('assembly not found');
     }
-    const sessionId = 'getSequence';
-    // a named object keeps sessionId, which v4 hosts read from the args
-    const args = {
+    const feats = await rpcManager.call('getSequence', 'CoreGetFeatures', {
         adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-        sessionId,
         regions: [
             {
                 start,
@@ -18,15 +15,11 @@ export async function fetchSeq({ start, end, refName, session, assemblyName, })
                 assemblyName,
             },
         ],
-    };
-    const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', args);
+    });
     return {
         seq: feats[0]?.get('seq') ?? '',
         // travels with the sequence because the caller needs both to translate, and
         // resolving the assembly twice to get them is the shape that lost it
-        assemblyGeneticCodeId: geneticCodeId(assembly, refName),
+        assemblyGeneticCodeId: assembly.getGeneticCodeId(refName),
     };
 }
-function geneticCodeId(assembly, refName) {
-    return assembly.getGeneticCodeId?.(refName);
-}

package/dist/LaunchMsaView/components/launchConnectedView.d.ts

@@ -15,9 +15,9 @@ export declare function launchConnectedView({ view, feature, placement, ...snaps
     view: LinearGenomeViewModel;
     feature?: Feature;
     placement: MsaViewPlacement;
-} & Record<string, unknown>): void;
+} & Record<string, unknown>): Promise<import("@jbrowse/core/util").AbstractViewModel>;
 /** runs a panel's launch, closing the dialog on success and keeping the error */
 export declare function useLaunchSubmit(handleClose: () => void): {
     launchError: unknown;
-    submit: (launch: () => void) => void;
+    submit: (launch: () => Promise<unknown>) => void;
 };

package/dist/LaunchMsaView/components/launchConnectedView.js

@@ -12,7 +12,7 @@ export const builtAlignmentLook = {
  * through `feature` to the transcript whose codons its query row is read by.
  */
 export function launchConnectedView({ view, feature, placement, ...snapshot }) {
-    launchMsaView(getSession(view), {
+    return launchMsaView(getSession(view), {
         placement,
         connectedViewId: view.id,
         connectedFeature: feature?.toJSON(),
@@ -25,15 +25,11 @@ export function useLaunchSubmit(handleClose) {
     return {
         launchError,
         submit: (launch) => {
-            try {
-                setLaunchError(undefined);
-                launch();
-                handleClose();
-            }
-            catch (e) {
+            setLaunchError(undefined);
+            launch().then(handleClose, (e) => {
                 console.error(e);
                 setLaunchError(e);
-            }
+            });
         },
     };
 }

package/dist/LaunchMsaView/components/useFeatureSequence.d.ts

@@ -9,7 +9,7 @@ export declare function useFeatureSequence({ view, feature, }: {
     proteinSequence: string;
     sequence: {
         seq: string;
-        assemblyGeneticCodeId: number | undefined;
+        assemblyGeneticCodeId: number;
     } | undefined;
     error: unknown;
     isLoading: boolean;

package/dist/LaunchMsaView/index.js

@@ -1,8 +1,9 @@
+import { lazy } from 'react';
 import { getContainingTrack, getSession } from '@jbrowse/core/util';
 import AddIcon from '@mui/icons-material/Add';
 import { isCodingFeature } from './codingFeature';
-import LaunchMsaViewDialog from './components/LaunchMsaViewDialog';
 import { launchTarget } from './launchTarget';
+const LaunchMsaViewDialog = lazy(() => import('./components/LaunchMsaViewDialog'));
 function isDisplay(elt) {
     return elt.name === 'LinearBasicDisplay';
 }
@@ -23,10 +24,6 @@ function openDialog(self, target) {
             { model: track, handleClose, feature, preferredTranscriptId },
         ]);
     };
-    if ('feature' in target) {
-        open(target.feature);
-        return;
-    }
     target
         .fetchFeature()
         .then(feature => {
@@ -54,14 +51,8 @@ export function extendStateModel(stateModel) {
             contextMenuItems() {
                 const target = launchTarget(self);
                 return [
-                    // .call(self), not a bare call: a host's own contextMenuItems may
-                    // reach its sibling views through `this`, which is undefined when the
-                    // captured super is invoked detached. It throws, the ErrorBoundary the
-                    // menu builds inside swallows it, and the user right-clicks a feature
-                    // and gets no menu at all -- the host's own rows gone too, which is
-                    // worse than this plugin contributing nothing. jbrowse-components hit
-                    // exactly this with `this.isGeneLike` and fixed its side in
-                    // 104bbfc581, but a plugin cannot choose which host build it runs on.
+                    // a detached call leaves `this` undefined for a host method that
+                    // reads it, and the throw takes the host's own rows with it
                     ...superContextMenuItems.call(self),
                     ...(target
                         ? [

package/dist/LaunchMsaView/launchTarget.d.ts

@@ -1,4 +1,3 @@
-import { isGeneLikeType } from './codingFeature';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { Feature } from '@jbrowse/core/util';
 export interface ContextMenuInfo {
@@ -14,43 +13,21 @@ export interface ContextMenuInfo {
 export interface DisplayModel {
     contextMenuItems: () => MenuItem[];
     contextMenuInfo?: ContextMenuInfo;
-    fetchFullFeature?: (featureId: string, displayedRegionIndex: number) => Promise<Feature | undefined>;
-    contextMenuFeature?: Feature;
+    fetchFullFeature: (featureId: string, displayedRegionIndex: number) => Promise<Feature | undefined>;
 }
 /**
- * What the menu item launches on. A legacy host hands over the whole feature,
- * so whether it codes for anything is known while the menu is built; a canvas
- * host's hit test carries a type and an id, so that question can only be
- * answered after the fetch, and the caller answers it there.
+ * What the menu item launches on. The hit test carries a type and an id, so
+ * whether the feature codes for anything can only be answered after the fetch,
+ * and the caller answers it there.
  */
-interface ClickedTranscript {
+export interface MenuTarget {
+    fetchFeature: () => Promise<Feature | undefined>;
     /**
      * The isoform the click actually landed on, when the dialog opens on its
      * gene. Climbing to the gene is what puts every isoform in the picker, and it
      * threw away which one the user pointed at: the picker then opened on the
-     * longest transcript, and on a v4 host that is the only place the choice was
-     * ever stated.
+     * longest transcript.
      */
     preferredTranscriptId?: string;
 }
-export type MenuTarget = (ClickedTranscript & {
-    feature: Feature;
-}) | (ClickedTranscript & {
-    fetchFeature: () => Promise<Feature | undefined>;
-});
-export { isGeneLikeType };
-/**
- * How to get the right-clicked feature, or nothing when there is nothing to
- * launch on. Both host shapes reduce to one target, so the menu item is built
- * and the dialog is opened by one code path — and the same gene test decides
- * both. The strict three-name set the legacy branch used to carry disagreed
- * with the loose one above, so a `lnc_RNA` offered the menu item on a 4.3 host
- * and not on a 3.7 one.
- *
- * Gene-like is not enough on its own: an lncRNA has no protein to align, and
- * accepting it opened a dialog whose Submit never left grey, with nothing
- * saying why. Where the whole feature is in hand the CDS decides here -- but
- * only where there are subfeatures to read it off, since a feature that came
- * with none has not answered the question.
- */
 export declare function launchTarget(self: DisplayModel): MenuTarget | undefined;

package/dist/LaunchMsaView/launchTarget.js

@@ -1,53 +1,14 @@
-import { geneLikeRoot, isGeneLikeType, isKnownNonCoding } from './codingFeature';
-// Read off the clicked item rather than off the display.
-//
-// LinearBasicDisplay used to publish an `isGeneLike` getter and this gated on
-// it. jbrowse-components 684142b3 (2026-08-16) inlined that getter into its own
-// `contextMenuItems`, and every host built after it returns `undefined` here --
-// so the gate was never satisfied, `onClick` stayed undefined, and the item
-// silently left the right-click menu on every gene track. Nothing failed loudly:
-// the display still had contextMenuInfo and fetchFullFeature, and the menu still
-// opened with its own items in it.
-//
-// A predicate over the type we were already given cannot go the same way, and it
-// costs one comparison. Deliberately the same loose case-insensitive test the
-// host applies (`isGeneLikeType` in collapseIntronsMenu.ts): real GFFs carry
-// 'mRNA', 'lnc_RNA', 'protein_coding_gene', 'transcript'.
-export { isGeneLikeType };
-/**
- * How to get the right-clicked feature, or nothing when there is nothing to
- * launch on. Both host shapes reduce to one target, so the menu item is built
- * and the dialog is opened by one code path — and the same gene test decides
- * both. The strict three-name set the legacy branch used to carry disagreed
- * with the loose one above, so a `lnc_RNA` offered the menu item on a 4.3 host
- * and not on a 3.7 one.
- *
- * Gene-like is not enough on its own: an lncRNA has no protein to align, and
- * accepting it opened a dialog whose Submit never left grey, with nothing
- * saying why. Where the whole feature is in hand the CDS decides here -- but
- * only where there are subfeatures to read it off, since a feature that came
- * with none has not answered the question.
- */
+import { isGeneLikeType } from '@jbrowse/core/util';
+// Read off the clicked item rather than off the display: LinearBasicDisplay's
+// `isGeneLike` getter was inlined into its own `contextMenuItems`
+// (jbrowse-components 684142b3), and gating on it silently took the item off
+// every gene track.
 export function launchTarget(self) {
     const info = self.contextMenuInfo;
-    const fetchFullFeature = self.fetchFullFeature;
-    // exclusive, not a fallthrough: a display publishing contextMenuInfo has
-    // already said what was clicked, and reading contextMenuFeature after it
-    // rejects the click can only answer with some other feature
-    if (info && fetchFullFeature) {
-        return isGeneLikeType(info.item.type)
-            ? {
-                fetchFeature: () => fetchFullFeature(info.item.featureId, info.displayedRegionIndex),
-                preferredTranscriptId: info.subfeature?.featureId,
-            }
-            : undefined;
-    }
-    const legacy = self.contextMenuFeature;
-    if (!legacy) {
-        return undefined;
-    }
-    const root = geneLikeRoot(legacy);
-    return isGeneLikeType(root.get('type')) && !isKnownNonCoding(root)
-        ? { feature: root, preferredTranscriptId: legacy.id() }
+    return info && isGeneLikeType(info.item.type)
+        ? {
+            fetchFeature: () => self.fetchFullFeature(info.item.featureId, info.displayedRegionIndex),
+            preferredTranscriptId: info.subfeature?.featureId,
+        }
         : undefined;
 }