jbrowse-plugin-msaview 4.0.0 → 5.0.0

package/dist/AddHighlightModel/index.js

@@ -3,17 +3,8 @@ import { getSession } from '@jbrowse/core/util';
 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/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/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

@@ -24,10 +24,6 @@ function openDialog(self, target) {
             { model: track, handleClose, feature, preferredTranscriptId },
         ]);
     };
-    if ('feature' in target) {
-        open(target.feature);
-        return;
-    }
     target
         .fetchFeature()
         .then(feature => {
@@ -55,14 +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;
 }

package/dist/LaunchMsaView/launchTarget.test.js

@@ -1,132 +1,40 @@
 import { SimpleFeature } from '@jbrowse/core/util';
 import { describe, expect, test } from 'vitest';
-import { isGeneLikeType, launchTarget } from './launchTarget';
-function feature(type, subfeatures = ['CDS']) {
-    return new SimpleFeature({
-        uniqueId: type,
+import { launchTarget } from './launchTarget';
+const host = (type) => ({
+    contextMenuItems: () => [],
+    contextMenuInfo: { item: { featureId: 'f1', type }, displayedRegionIndex: 0 },
+    fetchFullFeature: (featureId) => Promise.resolve(new SimpleFeature({
+        uniqueId: featureId,
         refName: 'chr1',
         start: 0,
         end: 100,
-        type,
-        subfeatures: subfeatures.map((t, i) => ({
-            uniqueId: `${type}-${i}`,
-            refName: 'chr1',
-            start: 0,
-            end: 100,
-            type: t,
-        })),
-    });
-}
-const modernHost = (type) => ({
-    contextMenuItems: () => [],
-    contextMenuInfo: { item: { featureId: 'f1', type }, displayedRegionIndex: 0 },
-    fetchFullFeature: (featureId) => Promise.resolve(feature(`fetched:${featureId}`)),
-});
-const legacyHost = (feat) => ({
-    contextMenuItems: () => [],
-    contextMenuFeature: feat,
-});
-async function fetched(target) {
-    return target && 'fetchFeature' in target
-        ? await target.fetchFeature()
-        : undefined;
-}
-describe('isGeneLikeType', () => {
-    test.each(['gene', 'mRNA', 'transcript', 'lnc_RNA', 'protein_coding_gene'])('accepts %s', type => {
-        expect(isGeneLikeType(type)).toBe(true);
-    });
-    test.each(['CDS', 'exon', 'match', 'SNV', undefined, null, 42])('rejects %s', type => {
-        expect(isGeneLikeType(type)).toBe(false);
-    });
+        type: `fetched:${featureId}`,
+    })),
 });
 describe('launchTarget', () => {
     test('resolves the clicked feature through fetchFullFeature', async () => {
-        const target = launchTarget(modernHost('mRNA'));
-        expect(await fetched(target)).toBeDefined();
-        expect((await fetched(target))?.get('type')).toBe('fetched:f1');
+        const feature = await launchTarget(host('mRNA'))?.fetchFeature();
+        expect(feature?.get('type')).toBe('fetched:f1');
     });
     test('offers nothing for a non-gene click', () => {
-        expect(launchTarget(modernHost('CDS'))).toBeUndefined();
-        expect(launchTarget(modernHost(undefined))).toBeUndefined();
+        expect(launchTarget(host('CDS'))).toBeUndefined();
+        expect(launchTarget(host(undefined))).toBeUndefined();
     });
     test('offers nothing when nothing was clicked', () => {
-        expect(launchTarget({ contextMenuItems: () => [] })).toBeUndefined();
-    });
-    // v4.3.0 and earlier have contextMenuFeature and nothing else; dropping this
-    // fallback once took "Launch MSA view" off every host in the wild.
-    test('falls back to a synchronous contextMenuFeature', () => {
-        const target = launchTarget(legacyHost(feature('mRNA')));
-        expect(target && 'feature' in target && target.feature.get('type')).toBe('mRNA');
-    });
-    test('applies the same gene test on both host shapes', () => {
-        expect(launchTarget(legacyHost(feature('lnc_RNA')))).toBeDefined();
-        expect(launchTarget(legacyHost(feature('exon')))).toBeUndefined();
-    });
-    // gene-like is not enough: an lncRNA translates to nothing, and offering the
-    // item opened a dialog whose Submit never left grey
-    test('declines a gene-like feature with no CDS below it', () => {
-        expect(launchTarget(legacyHost(feature('lnc_RNA', ['exon'])))).toBeUndefined();
-    });
-    // a legacy host can hand over a bare record whose children are a separate
-    // query, and declining it takes the item off an ordinary gene with no word
-    test('offers the item for a gene that arrived with no subfeatures', () => {
-        expect(launchTarget(legacyHost(feature('gene', [])))).toBeDefined();
-    });
-    // a click on an isoform should open the dialog on the gene, so every
-    // transcript is there to pick from
-    test('climbs to the gene from a clicked isoform', () => {
-        const gene = new SimpleFeature({
-            uniqueId: 'gene',
-            refName: 'chr1',
-            start: 0,
-            end: 100,
-            type: 'gene',
-            subfeatures: [
-                {
-                    uniqueId: 'mrna',
-                    refName: 'chr1',
-                    start: 0,
-                    end: 100,
-                    type: 'mRNA',
-                    subfeatures: [
-                        {
-                            uniqueId: 'cds',
-                            refName: 'chr1',
-                            start: 0,
-                            end: 100,
-                            type: 'CDS',
-                        },
-                    ],
-                },
-            ],
-        });
-        const mrna = gene.get('subfeatures')[0];
-        const target = launchTarget(legacyHost(mrna));
-        expect(target && 'feature' in target && target.feature).toBe(gene);
-        // the gene is what the dialog opens on, but the picker still opens on the
-        // isoform the click landed on -- on a v4 host that click is the only place
-        // the choice is ever stated
-        expect(target?.preferredTranscriptId).toBe(mrna.id());
+        expect(launchTarget({ ...host('mRNA'), contextMenuInfo: undefined })).toBeUndefined();
     });
     // the canvas host names the clicked isoform beside the gene it fetches, as
     // its own Collapse introns dialog reads it
-    test('carries the isoform a canvas click landed on', () => {
-        const host = modernHost('gene');
+    test('carries the isoform a click landed on', () => {
+        const h = host('gene');
         const target = launchTarget({
-            ...host,
+            ...h,
             contextMenuInfo: {
-                ...host.contextMenuInfo,
+                ...h.contextMenuInfo,
                 subfeature: { featureId: 'mrna-2' },
             },
         });
         expect(target?.preferredTranscriptId).toBe('mrna-2');
     });
-    // a host that has both shapes must not fall through to the legacy branch and
-    // launch on a stale feature when the click was not on a gene
-    test('a non-gene click on a host carrying both shapes offers nothing', () => {
-        expect(launchTarget({
-            ...modernHost('CDS'),
-            ...legacyHost(feature('mRNA')),
-        })).toBeUndefined();
-    });
 });

package/dist/MsaViewPanel/model.d.ts

@@ -498,16 +498,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
     orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
-    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    querySeqOffset: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    querySeqName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    querySeqOffset: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1509,16 +1509,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
     orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
-    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    querySeqOffset: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    querySeqName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    querySeqOffset: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;

package/dist/MsaViewPanel/model.js

@@ -51,12 +51,7 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        // Plain defaults, not types.stripDefault: that postdates the
-        // mobx-state-tree every released core exposes (present only on main), and
-        // the missing function throws while this model is being built, which
-        // error-pages the whole app rather than just this view. Restore
-        // stripDefault once a release ships it.
-        querySeqName: 'QUERY',
+        querySeqName: types.stripDefault(types.string, 'QUERY'),
         /**
          * #property
          * transcript residues before the query row's first residue, so a
@@ -66,8 +61,7 @@ export default function stateModelFactory() {
          * transcript's first residue put every click off by the trimmed
          * amount. Negative when the row runs past the transcript's start.
          */
-        // see querySeqName above re: types.stripDefault
-        querySeqOffset: 0,
+        querySeqOffset: types.stripDefault(types.number, 0),
         /**
          * #property
          */
@@ -75,8 +69,7 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        // see querySeqName above re: types.stripDefault
-        zoomToBaseLevel: false,
+        zoomToBaseLevel: types.stripDefault(types.boolean, false),
         /**
          * #property
          */

package/dist/MsaViewPanel/resolveConnectedTranscript.js

@@ -50,13 +50,7 @@ async function findTranscript(self, transcriptId) {
     const tracks = transcriptTracks(view.tracks);
     for (const regions of searchWindows(view)) {
         for (const track of tracks) {
-            // a named object keeps sessionId, which v4 hosts read from the args
-            const args = {
-                adapterConfig: getConf(track, 'adapter'),
-                sessionId,
-                regions,
-            };
-            const feats = await session.rpcManager.call(sessionId, 'CoreGetFeatures', args);
+            const feats = await session.rpcManager.call(sessionId, 'CoreGetFeatures', { adapterConfig: getConf(track, 'adapter'), regions });
             for (const feat of feats) {
                 const hit = getTranscriptFeatures(feat).find(t => transcriptMatches(t, transcriptId));
                 if (hit) {