jbrowse-plugin-msaview 3.2.0 → 3.4.0

package/dist/MsaViewPanel/doLaunchOrthologs.test.js

@@ -1,8 +1,9 @@
 import { beforeEach, describe, expect, test, vi } from 'vitest';
-import { doLaunchOrthologs } from './doLaunchOrthologs';
 import { launchMSA } from '../utils/msa';
 import { defaultMaxSpecies, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+import { fetchPantherOrthologs } from '../utils/pantherOrthologs';
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
+import { doLaunchOrthologs } from './doLaunchOrthologs';
 // Every network call is mocked and nothing else is. What is under test is the
 // argument shaping either side of those calls -- which species get asked for,
 // what becomes the QUERY row, and whether the row earns the Accession that
@@ -14,11 +15,15 @@ vi.mock('../utils/ncbiOrthologs', async (importOriginal) => ({
     fetchProteinForGene: vi.fn(),
     fetchOrthologRows: vi.fn(),
 }));
+vi.mock('../utils/pantherOrthologs', () => ({
+    fetchPantherOrthologs: vi.fn(),
+}));
 vi.mock('../utils/msa', () => ({ launchMSA: vi.fn() }));
 vi.mock('../utils/taxonomyNames', () => ({ fetchTaxonomyInfo: vi.fn() }));
 const mockResolveGeneId = vi.mocked(resolveGeneId);
 const mockFetchProtein = vi.mocked(fetchProteinForGene);
 const mockFetchRows = vi.mocked(fetchOrthologRows);
+const mockFetchPanther = vi.mocked(fetchPantherOrthologs);
 const mockLaunchMSA = vi.mocked(launchMSA);
 const mockFetchTaxonomy = vi.mocked(fetchTaxonomyInfo);
 const HUMAN = 9606;
@@ -199,3 +204,103 @@ describe('the Accession that drives the domain overlay', () => {
         expect(queryMetadata(result).Accession).toBeUndefined();
     });
 });
+// The second source. What is under test is the dispatch and what the PANTHER
+// result becomes on the query row -- the rows themselves are shaped upstream,
+// and the tail of the launch (labels, aligner, metadata) is the same code the
+// NCBI tests above already cover.
+describe('the PANTHER source', () => {
+    const YEAST = 559292;
+    const found = {
+        matched: 'CDC28',
+        query: {
+            code: 'YEAST',
+            accession: 'P00546',
+            geneRef: 'SGD=S000000364',
+            sequence: 'MSGELANYKRLEKVGEGTYGVVYKA',
+        },
+        rows: [
+            {
+                taxId: HUMAN,
+                label: 'human',
+                scientificName: 'Homo sapiens',
+                commonName: 'human',
+                geneId: 'HGNC=1771',
+                protein: 'P24941',
+                sequence: 'MENFQKVEKIGEGTYGVVYKARNK',
+            },
+        ],
+    };
+    beforeEach(() => {
+        mockFetchPanther.mockResolvedValue(found);
+        mockFetchTaxonomy.mockResolvedValue(new Map([[YEAST, { sciname: 'Saccharomyces cerevisiae' }]]));
+    });
+    test('source omitted is NCBI, so an old launch never reaches PANTHER', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(mockFetchPanther).not.toHaveBeenCalled();
+        expect(mockResolveGeneId).toHaveBeenCalled();
+    });
+    test('source panther asks PANTHER with the same species semantics, and skips NCBI', async () => {
+        await doLaunchOrthologs({
+            self: makeModel({
+                taxId: YEAST,
+                source: 'panther',
+                geneCandidates: ['CDC28'],
+                msaAlgorithm: 'clustalo',
+                taxa: [HUMAN, YEAST],
+                maxSpecies: 7,
+            }),
+        });
+        expect(mockResolveGeneId).not.toHaveBeenCalled();
+        expect(mockFetchRows).not.toHaveBeenCalled();
+        const { candidates, taxId, taxa, exclude, limit } = mockFetchPanther.mock.calls[0][0];
+        expect(candidates).toEqual(['CDC28']);
+        expect(taxId).toBe(YEAST);
+        expect([...taxa]).toEqual([HUMAN, YEAST]);
+        expect(exclude).toBe(YEAST);
+        expect(limit).toBe(7);
+    });
+    test("the query row is PANTHER's own entry for the gene when no sequence was supplied, and carries its UniProt accession for the domain overlay", async () => {
+        const result = await doLaunchOrthologs({
+            self: makeModel({
+                taxId: YEAST,
+                source: 'panther',
+                geneCandidates: ['CDC28'],
+                msaAlgorithm: 'clustalo',
+            }),
+        });
+        expect(queryRowName()).toBe('Saccharomyces_cerevisiae_query');
+        expect(queryRowSent()).toBe(found.query.sequence);
+        expect(queryMetadata(result)).toEqual({
+            'Gene ID': 'SGD=S000000364',
+            Accession: 'P00546',
+        });
+        expect(JSON.parse(result.treeMetadata).human).toMatchObject({
+            Accession: 'P24941',
+            'Gene ID': 'HGNC=1771',
+        });
+    });
+    test('a supplied sequence still wins, and a different isoform earns no Accession', async () => {
+        const result = await doLaunchOrthologs({
+            self: makeModel({
+                taxId: YEAST,
+                source: 'panther',
+                geneCandidates: ['CDC28'],
+                msaAlgorithm: 'clustalo',
+                proteinSequence: 'MDIFFERENTISOFORM',
+            }),
+        });
+        expect(queryRowSent()).toBe('MDIFFERENTISOFORM');
+        expect(queryMetadata(result).Accession).toBeUndefined();
+    });
+    test('names PANTHER when it has no protein for the query row', async () => {
+        mockFetchPanther.mockResolvedValue({ ...found, query: undefined });
+        await expect(doLaunchOrthologs({
+            self: makeModel({
+                taxId: YEAST,
+                source: 'panther',
+                geneCandidates: ['CDC28'],
+                msaAlgorithm: 'clustalo',
+            }),
+        })).rejects.toThrow(/PANTHER returned no representative protein/);
+    });
+});

package/dist/MsaViewPanel/genomeToMSA.js

@@ -1,9 +1,11 @@
 import { getSession } from '@jbrowse/core/util';
-import { hasHoverPosition } from './util';
+import { hasHoverPosition, hasQueryRow } from './util';
 export function genomeToMSA({ model }) {
     const { hovered } = getSession(model);
     const { querySeqName, transcriptToMsaMap, connectedView, mafRegion } = model;
-    if (!connectedView?.initialized || !hasHoverPosition(hovered)) {
+    if (!connectedView?.initialized ||
+        !hasHoverPosition(hovered) ||
+        !hasQueryRow(model)) {
         return undefined;
     }
     const { coord, refName } = hovered.hoverPosition;

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -19,6 +19,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
+            rows: [['hg38.chr1', 'ACGTACGTAC']],
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -38,6 +39,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
+            rows: [['hg38.chr1', 'ACGTACGTAC']],
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -62,6 +64,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(5);
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -90,6 +93,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -116,6 +120,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -142,6 +147,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -167,6 +173,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -195,6 +202,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(10);
             const model = {
                 querySeqName: 'QUERY',
+                rows: [['QUERY', 'MKVLTAEEK']],
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     // g2p is keyed by 0-based genome position, the hover coord is 1-based
@@ -220,6 +228,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn();
             const model = {
                 querySeqName: 'QUERY',
+                rows: [['QUERY', 'MKVLTAEEK']],
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1004: 10 },
@@ -240,6 +249,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'QUERY',
+                rows: [['QUERY', 'MKVLTAEEK']],
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1000: 0 }, // No entry for 1004
@@ -261,6 +271,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'QUERY',
+            rows: [['QUERY', 'MKVLTAEEK']],
             transcriptToMsaMap: undefined,
             mafRegion: undefined,
             connectedView: { initialized: true },
@@ -269,4 +280,27 @@ describe('genomeToMSA', () => {
         const result = genomeToMSA({ model });
         expect(result).toBeUndefined();
     });
+    // seqPosToVisibleCol answers 0 for a row name it does not know, so without a
+    // guard an alignment whose query row is missing -- the default 'QUERY' on an
+    // uploaded file, or the empty name the manual panel leaves when it matches
+    // nothing -- lights column 0 on every genome hover
+    test('returns undefined when querySeqName names no row here', () => {
+        mockGetSession.mockReturnValue({
+            hovered: {
+                hoverFeature: {},
+                hoverPosition: { coord: 1005, refName: 'chr1' },
+            },
+        });
+        const seqPosToVisibleCol = vi.fn(() => 0);
+        const model = {
+            querySeqName: 'QUERY',
+            rows: [['some_other_row', 'MKVLTAEEK']],
+            transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
+            mafRegion: undefined,
+            connectedView: { initialized: true },
+            seqPosToVisibleCol,
+        };
+        expect(genomeToMSA({ model })).toBeUndefined();
+        expect(seqPosToVisibleCol).not.toHaveBeenCalled();
+    });
 });

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,6 @@
 export type { MSAFormat } from 'msa-parsers';
+import type { BlastDatabase, MsaAlgorithm, PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { MafRegion, MsaViewInitState } from './types';
-import type { BlastDatabase, MsaAlgorithm } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -11,15 +11,43 @@ export interface IRegion {
     start: number;
     end: number;
 }
-export interface BlastParams {
-    blastDatabase: BlastDatabase;
-    msaAlgorithm: MsaAlgorithm;
+/**
+ * A search to run, discriminated by the program that runs it: the two arms
+ * differ in which databases they name and in whether an aligner runs at all, so
+ * splitting them is what lets doLaunchBlast read the database without asserting
+ * whose it is.
+ *
+ * The field is still `blastDatabase` rather than `database`: it is persisted in
+ * session snapshots and in the IndexedDB result cache, so renaming it would
+ * orphan every row already written.
+ */
+export type BlastParams = {
     selectedTranscript?: Feature;
     proteinSequence: string;
-}
+} & ({
+    /** absent on params written before phmmer existed, which were all blastp */
+    searchProgram?: 'blastp';
+    blastDatabase: BlastDatabase;
+    msaAlgorithm: MsaAlgorithm;
+} | {
+    searchProgram: 'phmmer';
+    /** phmmer names its databases its own way: `swissprot`, not `uniprotkb_swissprot` */
+    blastDatabase: PhmmerDatabase;
+    /** phmmer aligns as it searches, so there is no aligner to choose */
+    msaAlgorithm?: undefined;
+});
+/**
+ * Where the ortholog set comes from. NCBI's sets cover vertebrates and
+ * insects; PANTHER's span its 144 reference proteomes, human to yeast to
+ * Arabidopsis, so a gene from outside NCBI's scope aligns only through it.
+ */
+export declare const orthologSources: readonly ["ncbi", "panther"];
+export type OrthologSource = (typeof orthologSources)[number];
 export interface OrthologParams {
     /** NCBI taxon id of the assembly the query gene came from */
     taxId: number;
+    /** `ncbi` when omitted, so every launch written before this key keeps its meaning */
+    source?: OrthologSource;
     /**
      * taxon ids to include as rows. The query taxon has its own row already, so
      * it is excluded from this set whether or not it is named.
@@ -57,7 +85,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "height" | "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -71,7 +99,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
+}, "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -477,10 +505,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         setTreeMetadata(treeMetadata?: string): void;
         setGFF(gff?: string): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-        tree: string | undefined;
-        msa: string | undefined;
-        treeMetadata: string | undefined;
-        gff: string | undefined;
+        [k: string]: string | undefined;
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -550,6 +575,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     highlightedColumns: number[] | undefined;
     minimapHeight: number;
     conservationTrackHeight: number;
+    sequenceLogoTrackHeight: number;
     marginLeft: number;
     error: unknown;
     annotations: import("msa-parsers").Annotation[];
@@ -646,6 +672,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }[];
     readonly colClustalX: Record<string, string>[];
     readonly conservation: number[];
+    readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
     readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
     readonly totalHeight: number;
@@ -660,6 +687,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
+    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
@@ -695,6 +723,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }): void;
 } & {
     readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
@@ -761,6 +790,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     setHeaderHeight(arg: number): void;
     setConservationTrackHeight(arg: number): void;
+    setSequenceLogoTrackHeight(arg: number): void;
     reset(): void;
     exportSVG(opts: {
         theme: import("@mui/material").Theme;

package/dist/MsaViewPanel/model.js

@@ -6,6 +6,12 @@ import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
 import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
+/**
+ * Where the ortholog set comes from. NCBI's sets cover vertebrates and
+ * insects; PANTHER's span its 144 reference proteomes, human to yeast to
+ * Arabidopsis, so a gene from outside NCBI's scope aligns only through it.
+ */
+export const orthologSources = ['ncbi', 'panther'];
 /**
  * #stateModel MsaViewPlugin
  * extends

package/dist/MsaViewPanel/observeProteinHighlights.test.js

@@ -18,6 +18,7 @@ function makeModel({ highlightColumns } = {}) {
     const calls = [];
     const model = {
         querySeqName: 'query',
+        rows: [['query', 'MKVLTAEEK']],
         connectedViewId: CONNECTED,
         // g2p is indexed by genome coord; identity keeps the arithmetic out of the way
         transcriptToMsaMap: {
@@ -195,6 +196,16 @@ describe('scope and redundant writes', () => {
         run();
         expect(calls).toEqual([]);
     });
+    // seqPosToGlobalCol answers 0 for a row name it does not know, so without a
+    // guard a structure hover would light column 0 of whatever row is first
+    test('a query row this alignment does not have contributes no column', () => {
+        const { model, calls } = makeModel();
+        Object.assign(model, { rows: [['some_other_row', 'MKVLTAEEK']] });
+        const run = observeProteinHighlights(model);
+        session({ hover: [{ start: 10, end: 12 }] });
+        run();
+        expect(calls).toEqual([]);
+    });
     test('nothing happens until the view is connected and mapped', () => {
         const { calls } = makeModel();
         const bare = {

package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js

@@ -21,6 +21,7 @@ function makeModel() {
     const calls = [];
     const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion,
         connectedView: { initialized: true, assemblyNames: ['hg38'] },

package/dist/MsaViewPanel/util.d.ts

@@ -1,3 +1,21 @@
+/**
+ * Whether `querySeqName` names a row this alignment actually has.
+ *
+ * react-msaview's `seqPosToGlobalCol` answers 0 for a name it does not know, so
+ * without this every genome position maps to the first column and hovering the
+ * genome — or a connected structure — lights column 0 of an unrelated row. The
+ * name is wrong more often than it looks: it defaults to `QUERY`, which an
+ * uploaded alignment has no reason to carry, and the manual panel leaves it
+ * empty when it cannot match the protein to a row.
+ *
+ * The other direction has no such hole: msaCoordToGenomeRegions needs the query
+ * row's sequence to map a column at all, so a missing row is already nothing
+ * there.
+ */
+export declare function hasQueryRow(model: {
+    rows: string[][];
+    querySeqName: string;
+}): boolean;
 export declare function hasHoverPosition(hovered: unknown): hovered is {
     hoverPosition: {
         coord: number;

package/dist/MsaViewPanel/util.js

@@ -1,3 +1,20 @@
+/**
+ * Whether `querySeqName` names a row this alignment actually has.
+ *
+ * react-msaview's `seqPosToGlobalCol` answers 0 for a name it does not know, so
+ * without this every genome position maps to the first column and hovering the
+ * genome — or a connected structure — lights column 0 of an unrelated row. The
+ * name is wrong more often than it looks: it defaults to `QUERY`, which an
+ * uploaded alignment has no reason to carry, and the manual panel leaves it
+ * empty when it cannot match the protein to a row.
+ *
+ * The other direction has no such hole: msaCoordToGenomeRegions needs the query
+ * row's sequence to map a column at all, so a missing row is already nothing
+ * there.
+ */
+export function hasQueryRow(model) {
+    return model.rows.some(r => r[0] === model.querySeqName);
+}
 export function hasHoverPosition(hovered) {
     return (!!hovered &&
         typeof hovered === 'object' &&