jbrowse-plugin-msaview 3.6.0 → 3.7.0

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -47,7 +47,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
-            rows: [['hg38.chr1', 'ACGTACGTAC']],
+            rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -67,7 +67,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
-            rows: [['hg38.chr1', 'ACGTACGTAC']],
+            rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -92,7 +92,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(5);
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -105,6 +105,7 @@ describe('genomeToMSA', () => {
                     assemblyNames: ['hg38'],
                 },
                 seqPosToVisibleCol: mockSeqPosToVisibleCol,
+                visibleColToSeqPos: () => 4,
             };
             const result = genomeToMSA({ model });
             // hover coord 1005 is 1-based, so the 0-based genome position is 1004,
@@ -112,6 +113,34 @@ describe('genomeToMSA', () => {
             expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4);
             expect(result).toBe(5);
         });
+        test('a position past the end of the row lights nothing', () => {
+            mockSession({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1009, refName: 'chr1' },
+                },
+            });
+            // react-msaview answers one column past the end for a residue the row
+            // does not have, and that column maps back to no residue
+            const model = {
+                querySeqName: 'hg38.chr1',
+                rowMap: new Map([['hg38.chr1', 'ACGTACG']]),
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['hg38'],
+                },
+                seqPosToVisibleCol: () => 7,
+                visibleColToSeqPos: () => undefined,
+            };
+            expect(genomeToMSA({ model })).toBeUndefined();
+        });
         test('returns undefined when hover refName does not match mafRegion', () => {
             mockSession({
                 hovered: {
@@ -121,7 +150,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -148,7 +177,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -175,7 +204,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -201,7 +230,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -231,7 +260,7 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 0,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     // g2p is keyed by 0-based genome position, the hover coord is 1-based
@@ -258,7 +287,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn();
             const model = {
                 querySeqName: 'QUERY',
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1004: 10 },
@@ -283,7 +312,7 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 4,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -304,7 +333,7 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 20,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -326,7 +355,7 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 0,
-                rows: [['QUERY', 'MKV']],
+                rowMap: new Map([['QUERY', 'MKV']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -344,7 +373,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'QUERY',
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1000: 0 }, // No entry for 1004
@@ -366,7 +395,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'QUERY',
-            rows: [['QUERY', 'MKVLTAEEK']],
+            rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
             transcriptToMsaMap: undefined,
             mafRegion: undefined,
             connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -375,10 +404,6 @@ 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', () => {
         mockSession({
             hovered: {
@@ -389,7 +414,7 @@ describe('genomeToMSA', () => {
         const seqPosToVisibleCol = vi.fn(() => 0);
         const model = {
             querySeqName: 'QUERY',
-            rows: [['some_other_row', 'MKVLTAEEK']],
+            rowMap: new Map([['some_other_row', 'MKVLTAEEK']]),
             transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
             mafRegion: undefined,
             connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -398,6 +423,26 @@ describe('genomeToMSA', () => {
         expect(genomeToMSA({ model })).toBeUndefined();
         expect(seqPosToVisibleCol).not.toHaveBeenCalled();
     });
+    test('a query row folded into a collapsed clade still maps', () => {
+        mockSession({
+            hovered: {
+                hoverFeature: {},
+                hoverPosition: { coord: 1005, refName: 'chr1' },
+            },
+        });
+        const model = {
+            querySeqName: 'QUERY',
+            querySeqOffset: 0,
+            rows: [['collapsed_clade', 'MKVLTAEEK']],
+            rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
+            transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
+            mafRegion: undefined,
+            connectedView: { initialized: true, assemblyNames: ['hg38'] },
+            seqPosToVisibleCol: (_name, pos) => pos,
+            visibleColToSeqPos: (_name, col) => col,
+        };
+        expect(genomeToMSA({ model })).toBe(3);
+    });
     // A hover names the chromosome the assembly's way and the transcript names it
     // the annotation file's way, so on GENCODE-on-hg38 -- jbrowse.org's own
     // config -- the two are '1' and 'chr1' and pointing at a codon lit nothing.
@@ -416,7 +461,7 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 0,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -438,7 +483,7 @@ describe('genomeToMSA', () => {
             const seqPosToVisibleCol = vi.fn();
             const model = {
                 querySeqName: 'QUERY',
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -462,7 +507,7 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 0,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
@@ -483,7 +528,7 @@ describe('genomeToMSA', () => {
             const seqPosToVisibleCol = vi.fn().mockReturnValue(5);
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -493,6 +538,7 @@ describe('genomeToMSA', () => {
                 },
                 connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol,
+                visibleColToSeqPos: () => 4,
             };
             expect(genomeToMSA({ model })).toBe(5);
             expect(seqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4);

package/dist/MsaViewPanel/launchAutoruns.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/launchAutoruns.test.js

@@ -0,0 +1,36 @@
+import { expect, test, vi } from 'vitest';
+import { doLaunchBlast } from './doLaunchBlast';
+import stateModelFactory from './model';
+vi.mock('@jbrowse/core/util', async (importOriginal) => ({
+    ...(await importOriginal()),
+    getSession: () => ({ views: [], hovered: undefined }),
+}));
+vi.mock('./doLaunchBlast', () => ({ doLaunchBlast: vi.fn() }));
+vi.mock('./msaDataStore', () => ({
+    cleanupOldData: vi.fn(async () => { }),
+    deleteMsaData: vi.fn(async () => { }),
+    generateDataStoreId: vi.fn(),
+    retrieveMsaData: vi.fn(),
+    storeMsaData: vi.fn(),
+}));
+// the real launch reads querySeqName before its first await, as resolveQuery
+// does, which used to make that name a reason to launch again
+test('a write the launch body read does not start a second launch', () => {
+    vi.mocked(doLaunchBlast).mockImplementation(({ self }) => {
+        void self.querySeqName;
+        return new Promise(() => { });
+    });
+    const model = stateModelFactory().create({
+        type: 'MsaView',
+        id: 'msa1',
+        blastParams: {
+            searchProgram: 'blastp',
+            blastDatabase: 'uniprotkb_swissprot',
+            msaAlgorithm: 'clustalo',
+            proteinSequence: 'MKV',
+        },
+    });
+    expect(doLaunchBlast).toHaveBeenCalledTimes(1);
+    model.setQuerySeqName('P53_HUMAN_query');
+    expect(doLaunchBlast).toHaveBeenCalledTimes(1);
+});

package/dist/MsaViewPanel/model.d.ts

@@ -7,6 +7,7 @@ import type { TranscriptRef } from './util';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Region } from 'react-msaview';
 type LGV = LinearGenomeViewModel;
 type MaybeLGV = LGV | undefined;
 export interface IRegion {
@@ -547,7 +548,7 @@ 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" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion" | "region"> & {
     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>>;
@@ -561,6 +562,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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>;
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
+    region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
 }, {
     width: number;
     bodyMounted: boolean;
@@ -768,20 +770,22 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly showMsaLetters: boolean;
     readonly showTreeText: boolean;
 } & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
-    readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
-    readonly secondaryStructureArcs: import("react-msaview").Arc[] | undefined;
-    readonly adapterTrackModels: import("react-msaview").BasicTrack[];
     readonly columnTrackContent: Map<string, {
         values?: number[];
         data?: string;
         arcs?: import("react-msaview").Arc[];
     }>;
     trackHeight(kind: import("react-msaview").TrackKind, heightKey?: string, given?: number): number;
+    columnTrackModel(track: import("react-msaview").ColumnTrackSpec): import("react-msaview").BasicTrack;
     readonly columnTrackModels: import("react-msaview").BasicTrack[];
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("react-msaview").Arc[] | undefined;
+    readonly adapterTrackModels: import("react-msaview").BasicTrack[];
     readonly basePairTrackModels: import("react-msaview").BasicTrack[];
     readonly computedTrackModels: import("react-msaview").BasicTrack[];
     readonly tracks: import("react-msaview").BasicTrack[];
@@ -794,7 +798,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-    visibleSpan({ row, start: rawStart, end: rawEnd }: import("react-msaview").Region): {
+    visibleSpan({ row, start: rawStart, end: rawEnd }: Region): {
         startCol: number;
         endCol: number;
     } | undefined;
@@ -874,9 +878,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly fillPalette: {
         [x: string]: string;
     };
-    readonly strokePalette: {
-        [k: string]: string;
-    };
     readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
     readonly featureColors: Map<import("msa-parsers").Annotation, {
         fill: string;
@@ -898,7 +899,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }[];
     readonly resolvedHighlights: import("react-msaview").ResolvedHighlight[];
     columnStatsAt(col: number): import("react-msaview").ColumnStats | undefined;
-    readonly mouseOverColumnStats: import("react-msaview").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
             name?: string;
@@ -923,7 +923,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
-    zoomToRegion(region: import("react-msaview").Region): void;
+    zoomToRegion(region: Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
 } & {
@@ -1035,6 +1035,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setMafRegion(arg?: MafRegion): void;
+    /**
+     * #action
+     */
+    setRegion(arg?: Region): void;
     /**
      * #action
      */

package/dist/MsaViewPanel/model.js

@@ -5,6 +5,7 @@ import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
 import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { applyRegion } from './applyRegion';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { deleteMsaData } from './msaDataStore';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
@@ -107,6 +108,13 @@ export default function stateModelFactory() {
          * #property
          */
         mafRegion: types.frozen(),
+        /**
+         * #property
+         * where the view opens: 1-based residues of `row`, or alignment
+         * columns without one. Zoomed onto once and then cleared, so a
+         * reloaded session keeps the reader's own scroll.
+         */
+        region: types.frozen(),
     }))
         .volatile(() => ({
         /**
@@ -299,6 +307,12 @@ export default function stateModelFactory() {
         setMafRegion(arg) {
             self.mafRegion = arg;
         },
+        /**
+         * #action
+         */
+        setRegion(arg) {
+            self.region = arg;
+        },
         /**
          * #action
          */
@@ -493,6 +507,9 @@ export default function stateModelFactory() {
             // so they're factories returning the autorun body rather than plain fns
             addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)));
             addDisposer(self, autorun(observeProteinHighlights(self)));
+            addDisposer(self, autorun(() => {
+                applyRegion(self);
+            }));
         },
     }));
 }

package/dist/MsaViewPanel/msaDataStore.d.ts

@@ -3,13 +3,15 @@ export interface MsaDataPayload {
     msa?: string;
     tree?: string;
     treeMetadata?: string;
+    gff?: string;
 }
 export declare function generateDataStoreId(): string;
 export declare function storeMsaData(id: string, data: MsaDataPayload): Promise<boolean>;
 export declare function retrieveMsaData(id: string): Promise<{
-    msa: string | undefined;
-    tree: string | undefined;
-    treeMetadata: string | undefined;
+    msa?: string;
+    tree?: string;
+    treeMetadata?: string;
+    gff?: string;
 } | undefined>;
 /** drop one view's row, for a reset that just orphaned it */
 export declare function deleteMsaData(id: string): Promise<void>;

package/dist/MsaViewPanel/msaDataStore.js

@@ -14,13 +14,7 @@ export function generateDataStoreId() {
 export async function storeMsaData(id, data) {
     try {
         const db = await getDB();
-        const storedData = {
-            id,
-            msa: data.msa,
-            tree: data.tree,
-            treeMetadata: data.treeMetadata,
-            timestamp: Date.now(),
-        };
+        const storedData = { ...data, id, timestamp: Date.now() };
         await db.put(STORE_NAME, storedData);
         return true;
     }
@@ -45,11 +39,8 @@ export async function retrieveMsaData(id) {
         catch (e) {
             console.warn('Failed to refresh MSA data timestamp:', e);
         }
-        return {
-            msa: result.msa,
-            tree: result.tree,
-            treeMetadata: result.treeMetadata,
-        };
+        const { id: _id, timestamp: _timestamp, ...payload } = result;
+        return payload;
     }
     catch (e) {
         console.warn('Failed to retrieve MSA data:', e);

package/dist/MsaViewPanel/msaDataStore.test.js

@@ -1,5 +1,5 @@
 import { beforeEach, expect, test, vi } from 'vitest';
-import { retrieveMsaData } from './msaDataStore';
+import { retrieveMsaData, storeMsaData } from './msaDataStore';
 // An in-memory stand-in for the one object store this module opens, with a
 // switch for the write half so a browser that refuses writes can be played back.
 const { rows, state } = vi.hoisted(() => ({
@@ -42,3 +42,10 @@ test('a refresh that fails still hands back the data it read', async () => {
     state.putFails = true;
     expect((await retrieveMsaData('msa-1'))?.msa).toBe('>a\nMK');
 });
+test('every document a view keeps comes back, and nothing else', async () => {
+    await storeMsaData('msa-1', { msa: '>a\nMK', gff: 'a\t.\tdomain\t1\t2' });
+    expect(await retrieveMsaData('msa-1')).toEqual({
+        msa: '>a\nMK',
+        gff: 'a\t.\tdomain\t1\t2',
+    });
+});

package/dist/MsaViewPanel/observeProteinHighlights.test.js

@@ -19,7 +19,7 @@ function makeModel({ highlightColumns, querySeqOffset = 0, } = {}) {
     const model = {
         querySeqName: 'query',
         querySeqOffset,
-        rows: [['query', 'MKVLTAEEK']],
+        rowMap: new Map([['query', 'MKVLTAEEK']]),
         connectedViewId: CONNECTED,
         // g2p is indexed by genome coord; identity keeps the arithmetic out of the way
         transcriptToMsaMap: {
@@ -213,11 +213,11 @@ 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']] });
+        Object.assign(model, {
+            rowMap: new Map([['some_other_row', 'MKVLTAEEK']]),
+        });
         const run = observeProteinHighlights(model);
         session({ hover: [{ start: 10, end: 12 }] });
         run();

package/dist/MsaViewPanel/regionSnapshot.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/regionSnapshot.test.js

@@ -0,0 +1,29 @@
+import { expect, test, vi } from 'vitest';
+import stateModelFactory from './model';
+vi.mock('@jbrowse/core/util', async (importOriginal) => ({
+    ...(await importOriginal()),
+    getSession: () => ({ views: [], hovered: undefined }),
+}));
+vi.mock('./msaDataStore', () => ({
+    cleanupOldData: vi.fn(async () => { }),
+    deleteMsaData: vi.fn(async () => { }),
+    generateDataStoreId: vi.fn(),
+    retrieveMsaData: vi.fn(),
+    storeMsaData: vi.fn(async () => true),
+}));
+const MSA = `>Human\n${'MEEPQSDPSV'.repeat(20)}\n>Mouse\n${'MEE-QSDPSV'.repeat(20)}`;
+test('a spec region waits for the view to have a width, zooms, and is dropped', () => {
+    const region = { row: 'Human', start: 150, end: 160 };
+    const model = stateModelFactory().create({
+        type: 'MsaView',
+        id: 'msaview1',
+        data: { msa: MSA },
+        region,
+        gffFilehandle: { uri: 'http://example.com/a.gff' },
+    });
+    expect(model.region).toEqual(region);
+    expect(model.gffFilehandle).toMatchObject({ locationType: 'UriLocation' });
+    model.setWidth(800);
+    expect(model.region).toBeUndefined();
+    expect(model.scrollX).toBeLessThan(0);
+});

package/dist/MsaViewPanel/resolveConnectedTranscript.d.ts

@@ -1,9 +1,46 @@
 import type { JBrowsePluginMsaViewModel } from './model';
+interface Region {
+    assemblyName: string;
+    refName: string;
+    start: number;
+    end: number;
+}
+interface GenomeView {
+    tracks: {
+        type: string;
+    }[];
+    displayedRegions: Region[];
+    dynamicBlocks?: {
+        contentBlocks?: Region[];
+    };
+}
+/**
+ * The part of the genome on screen, then everything the view can scroll to.
+ * `displayedRegions` is usually whole chromosomes -- navigating to a locus
+ * displays its parent region -- so it is the fallback, not the first ask.
+ */
+export declare function searchWindows(view: GenomeView): {
+    assemblyName: string;
+    refName: string;
+    start: number;
+    end: number;
+}[][];
+/**
+ * Gene models live on feature tracks. Asking an alignments, variant or
+ * quantitative track for a chromosome's worth of features to look for a
+ * transcript among them is the slowest possible way to find nothing.
+ */
+export declare function transcriptTracks<T extends {
+    type: string;
+}>(tracks: T[]): T[];
 /**
  * Resolve `connectedTranscript` into `connectedFeature` once the connected
- * genome view has its assembly, regions and tracks, then hand the translation
- * to whichever launch is waiting for a query. Left in place on failure so the
- * error stays attributable; the autorun's tracked reads are the view's
- * readiness, so nothing refires until that changes.
+ * genome view has its assembly and tracks, then hand the translation to
+ * whichever launch is waiting for a query.
+ *
+ * The autorun re-fires on the view's readiness (a track opened after a miss)
+ * and on the request itself, which is what `retryLaunch` re-states. The lookup
+ * runs untracked, so scrolling the genome view is not a reason to look again.
  */
 export declare function resolveConnectedTranscriptIfNeeded(self: JBrowsePluginMsaViewModel): void;
+export {};