jbrowse-plugin-msaview 3.4.0 → 3.4.1

package/dist/MsaViewPanel/doLaunchOrthologs.test.js

@@ -33,10 +33,24 @@ const setQuerySeqName = vi.fn();
 function makeModel(orthologParams) {
     return {
         orthologParams,
-        setProgress: () => { },
         setQuerySeqName,
     };
 }
+// a scope that never cancels, so these tests see the launch's own behaviour --
+// what the scope does when it IS cancelled is runLaunch.test.ts's subject
+function launch({ self }) {
+    return doLaunchOrthologs({
+        self,
+        scope: {
+            signal: new AbortController().signal,
+            act: fn => {
+                fn();
+            },
+            onProgress: () => { },
+            onRid: () => { },
+        },
+    });
+}
 function params(extra = {}) {
     return {
         taxId: HUMAN,
@@ -79,11 +93,11 @@ beforeEach(() => {
 });
 describe('which species become rows', () => {
     test('omitted taxa asks for no restriction at all, which is every ortholog NCBI has', async () => {
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(rowRequest().taxa).toBeUndefined();
     });
     test('given taxa is taken as written', async () => {
-        await doLaunchOrthologs({
+        await launch({
             self: makeModel(params({ taxa: [HUMAN, 10090, 9615] })),
         });
         expect(rowRequest().taxa).toEqual([9606, 9615, 10090]);
@@ -92,20 +106,20 @@ describe('which species become rows', () => {
     // and "the query row already covers this one" stay separable -- an unrestricted
     // launch still has to drop the query species.
     test('the query species is excluded whether or not taxa was given', async () => {
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(rowRequest().exclude).toBe(HUMAN);
         vi.clearAllMocks();
         mockResolveGeneId.mockResolvedValue({ geneId: GENE_ID, matched: 'NLRP1' });
         mockFetchProtein.mockResolvedValue(REPRESENTATIVE);
         mockFetchRows.mockResolvedValue([]);
         mockLaunchMSA.mockResolvedValue({ msa: '', tree: '' });
-        await doLaunchOrthologs({
+        await launch({
             self: makeModel(params({ taxa: [HUMAN, 10090] })),
         });
         expect(rowRequest().exclude).toBe(HUMAN);
     });
     test('an empty list is a request for no rows, not a request for all of them', async () => {
-        await doLaunchOrthologs({ self: makeModel(params({ taxa: [] })) });
+        await launch({ self: makeModel(params({ taxa: [] })) });
         expect(rowRequest().taxa).toEqual([]);
     });
 });
@@ -114,11 +128,11 @@ describe('which species become rows', () => {
 // second a row.
 describe('the row cap', () => {
     test('is passed through when given', async () => {
-        await doLaunchOrthologs({ self: makeModel(params({ maxSpecies: 12 })) });
+        await launch({ self: makeModel(params({ maxSpecies: 12 })) });
         expect(rowRequest().limit).toBe(12);
     });
     test('omitted leaves the default to fetchOrthologGenes rather than sending Infinity', async () => {
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(rowRequest().limit).toBeUndefined();
         expect(defaultMaxSpecies).toBeGreaterThan(2);
     });
@@ -129,7 +143,7 @@ describe('the row cap', () => {
 // model's querySeqName and the header have to be the same string.
 describe('the query row name', () => {
     test('is the species, marked, rather than a bare QUERY among named rows', async () => {
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(queryRowName()).toBe('human_query');
         expect(setQuerySeqName).toHaveBeenCalledWith('human_query');
     });
@@ -137,41 +151,41 @@ describe('the query row name', () => {
         mockFetchRows.mockResolvedValue([
             { label: 'human_query', sequence: 'MM' },
         ]);
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(queryRowName()).toBe('human_query_2');
         expect(setQuerySeqName).toHaveBeenCalledWith('human_query_2');
     });
     test('falls back rather than throwing when NCBI cannot name the taxon', async () => {
         vi.spyOn(console, 'warn').mockImplementation(() => { });
         mockFetchTaxonomy.mockRejectedValue(new Error('429'));
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(queryRowName()).toBe('query_query');
     });
     test('the metadata that drives the domain overlay is keyed to that same name', async () => {
-        const result = await doLaunchOrthologs({ self: makeModel(params()) });
+        const result = await launch({ self: makeModel(params()) });
         expect(Object.keys(JSON.parse(result.treeMetadata))).toContain('human_query');
     });
 });
 describe('the query row sequence', () => {
     test('omitted proteinSequence falls back to the representative protein', async () => {
-        await doLaunchOrthologs({ self: makeModel(params()) });
+        await launch({ self: makeModel(params()) });
         expect(queryRowSent()).toBe(REPRESENTATIVE.sequence);
     });
     test('a supplied sequence is used, and is cleaned first', async () => {
-        await doLaunchOrthologs({
+        await launch({
             self: makeModel(params({ proteinSequence: 'MAGG*AWGR&' })),
         });
         expect(queryRowSent()).toBe('MAGGAWGR');
     });
     test('throws when neither a sequence nor a representative is available', async () => {
         mockFetchProtein.mockResolvedValue(undefined);
-        await expect(doLaunchOrthologs({ self: makeModel(params()) })).rejects.toThrow(/No query protein/);
+        await expect(launch({ self: makeModel(params()) })).rejects.toThrow(/No query protein/);
         expect(mockLaunchMSA).not.toHaveBeenCalled();
     });
     test('a failed representative lookup does not take down a launch that brought its own sequence', async () => {
         vi.spyOn(console, 'warn').mockImplementation(() => { });
         mockFetchProtein.mockRejectedValue(new Error('429'));
-        await doLaunchOrthologs({
+        await launch({
             self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
         });
         expect(queryRowSent()).toBe(REPRESENTATIVE.sequence);
@@ -183,14 +197,14 @@ describe('the query row sequence', () => {
 // here, in both directions.
 describe('the Accession that drives the domain overlay', () => {
     test('is attached when the query row IS the representative protein', async () => {
-        const result = await doLaunchOrthologs({ self: makeModel(params()) });
+        const result = await launch({ self: makeModel(params()) });
         expect(queryMetadata(result)).toMatchObject({
             'Gene ID': GENE_ID,
             Accession: REPRESENTATIVE.accession,
         });
     });
     test('is withheld from a non-representative isoform', async () => {
-        const result = await doLaunchOrthologs({
+        const result = await launch({
             self: makeModel(params({ proteinSequence: 'MDIFFERENTISOFORM' })),
         });
         expect(queryMetadata(result).Accession).toBeUndefined();
@@ -198,7 +212,7 @@ describe('the Accession that drives the domain overlay', () => {
     test('is withheld when the representative lookup failed', async () => {
         vi.spyOn(console, 'warn').mockImplementation(() => { });
         mockFetchProtein.mockRejectedValue(new Error('429'));
-        const result = await doLaunchOrthologs({
+        const result = await launch({
             self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
         });
         expect(queryMetadata(result).Accession).toBeUndefined();
@@ -235,12 +249,12 @@ describe('the PANTHER source', () => {
         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()) });
+        await launch({ 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({
+        await launch({
             self: makeModel({
                 taxId: YEAST,
                 source: 'panther',
@@ -260,7 +274,7 @@ describe('the PANTHER source', () => {
         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({
+        const result = await launch({
             self: makeModel({
                 taxId: YEAST,
                 source: 'panther',
@@ -280,7 +294,7 @@ describe('the PANTHER source', () => {
         });
     });
     test('a supplied sequence still wins, and a different isoform earns no Accession', async () => {
-        const result = await doLaunchOrthologs({
+        const result = await launch({
             self: makeModel({
                 taxId: YEAST,
                 source: 'panther',
@@ -294,7 +308,7 @@ describe('the PANTHER source', () => {
     });
     test('names PANTHER when it has no protein for the query row', async () => {
         mockFetchPanther.mockResolvedValue({ ...found, query: undefined });
-        await expect(doLaunchOrthologs({
+        await expect(launch({
             self: makeModel({
                 taxId: YEAST,
                 source: 'panther',

package/dist/MsaViewPanel/model.d.ts

@@ -1,5 +1,6 @@
 export type { MSAFormat } from 'msa-parsers';
 import type { BlastDatabase, MsaAlgorithm, PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts';
+import type { MsaDataPayload } from './msaDataStore';
 import type { MafRegion, MsaViewInitState } from './types';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
@@ -85,7 +86,7 @@ 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>;
-}, "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"> & {
+}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "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]>;
@@ -99,7 +100,7 @@ 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>>;
-}, "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" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "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]>;
@@ -494,6 +495,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -510,6 +512,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Highlight, import("react-msaview").Highlight, import("react-msaview").Highlight>>, [undefined]>;
 }, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "orthologParams" | "uniprotId" | "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>;
@@ -591,6 +594,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setError(error?: unknown): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
+    setHighlights(highlights: import("react-msaview").Highlight[]): void;
     setShowDomains(arg: boolean): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -608,6 +612,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }): void;
     setMSAFilehandle(msaFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setTreeFilehandle(treeFilehandle?: import("@jbrowse/core/util").FileLocation): void;
+    setTreeMetadataFilehandle(treeMetadataFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setGFFFilehandle(gffFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setMSA(result: string): void;
     setTree(result: string): void;
@@ -715,6 +720,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
+    setColumnTracks(tracks: import("react-msaview").ColumnTrackSpec[]): void;
     toggleTrack(id: string): void;
     setStatus(status?: {
         msg: string;
@@ -728,6 +734,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
     readonly adapterTrackModels: import("react-msaview").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+    }>;
+    readonly columnTrackModels: import("react-msaview").BasicTrack[];
     readonly tracks: import("react-msaview").BasicTrack[];
     readonly turnedOnTracks: import("react-msaview").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
@@ -767,6 +778,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         start: number;
         end: number;
     }[];
+    readonly resolvedHighlights: import("react-msaview").ResolvedHighlight[];
     readonly mouseOverColumnStats: {
         col: number;
         total: number;
@@ -792,12 +804,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setConservationTrackHeight(arg: number): void;
     setSequenceLogoTrackHeight(arg: number): void;
     reset(): void;
-    exportSVG(opts: {
-        theme: import("@mui/material").Theme;
-        includeMinimap?: boolean;
-        includeTracks?: boolean;
-        exportType: "entire" | "viewport";
-    }): Promise<void>;
+    exportSVG(opts: import("react-msaview").ExportSvgOptions): Promise<void>;
     initFilter(arg: string): void;
     setFilter(arg: string, flag: boolean): void;
     fit(): void;
@@ -810,6 +817,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     error: unknown;
     loadingStoredData: boolean;
     isStoringData: boolean;
+    lastStoredData: MsaDataPayload | undefined;
+    launchController: AbortController | undefined;
     domainsRequested: boolean;
 } & {
     /**
@@ -908,6 +917,23 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setIsStoringData(arg: boolean): void;
+    /**
+     * #action
+     */
+    setLastStoredData(arg?: MsaDataPayload): void;
+    /**
+     * #action
+     */
+    setLaunchController(arg?: AbortController): void;
+    /**
+     * #action
+     * Abandon the launch in flight. The EBI job keeps running on their side —
+     * nothing here can recall it, and its JobLink stays valid — so this only
+     * stops the polling and the writes it would make. Dropping the params is
+     * what keeps the request from refiring; the view falls back to the import
+     * form, which is where react-msaview's own cancel leaves it too.
+     */
+    cancelLaunch(): void;
     /**
      * #action
      */
@@ -937,7 +963,129 @@ 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>;
-}> & {
+}> & (({
+    bgColor: boolean;
+    colorSchemeName: string;
+    showColumnStats: boolean;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number;
+    treeWidth: number;
+    showBranchLen: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    autoTreeAreaWidth: boolean;
+    columnTracks: import("react-msaview").ColumnTrackSpec[];
+    id: string;
+    showDomains: boolean;
+    showDomainLegend: boolean;
+    hideGaps: boolean;
+    allowedGappyness: number;
+    subFeatureRows: boolean;
+    type: "MsaView";
+    drawMsaLetters: boolean;
+    scrollZoom: boolean;
+    height: number;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    currentAlignment: number;
+    collapsed: string[];
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    relativeTo: string | undefined;
+    highlightColumns: number[] | undefined;
+    highlights: import("react-msaview").Highlight[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+} & import("@jbrowse/mobx-state-tree")._NotCustomized) | ({
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
@@ -950,6 +1098,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawTree: boolean;
     drawNodeBubbles: boolean;
     autoTreeAreaWidth: boolean;
+    columnTracks?: undefined;
     id: string;
     showDomains: boolean;
     showDomainLegend: boolean;
@@ -1051,13 +1200,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     featureFilters: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
+    highlights: import("react-msaview").Highlight[];
     data: {
         tree?: string | undefined;
         msa?: string | undefined;
         treeMetadata?: string | undefined;
         gff?: string | undefined;
     };
-} & import("@jbrowse/mobx-state-tree")._NotCustomized>;
+} & import("@jbrowse/mobx-state-tree")._NotCustomized))>;
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
 export { type MafRegion, type MsaViewInitState } from './types';

package/dist/MsaViewPanel/model.js

@@ -88,6 +88,21 @@ export default function stateModelFactory() {
          * #volatile
          */
         isStoringData: false,
+        /**
+         * #volatile
+         * what IndexedDB was last known to hold for this view, so an edit made
+         * after the first write (react-msaview replacing data.tree with a
+         * neighbor-joining tree, say) is recognized as needing a new one
+         */
+        lastStoredData: undefined,
+        /**
+         * #volatile
+         * aborts the launch currently in flight -- from the Cancel button, and
+         * from the disposer afterCreate registers, so a closed view stops
+         * polling EBI instead of running to completion and writing to a node
+         * that is gone
+         */
+        launchController: undefined,
         /**
          * #volatile
          * guards the one-shot auto-fetch of protein domains so it doesn't refire
@@ -106,7 +121,7 @@ export default function stateModelFactory() {
          * #method
          */
         getSequenceByRowName(rowName) {
-            return self.rows.find(r => r[0] === rowName)?.[1];
+            return this.getRowByName(rowName)?.[1];
         },
     }))
         .views(self => ({
@@ -241,6 +256,35 @@ export default function stateModelFactory() {
         setIsStoringData(arg) {
             self.isStoringData = arg;
         },
+        /**
+         * #action
+         */
+        setLastStoredData(arg) {
+            self.lastStoredData = arg;
+        },
+        /**
+         * #action
+         */
+        setLaunchController(arg) {
+            self.launchController = arg;
+        },
+        /**
+         * #action
+         * Abandon the launch in flight. The EBI job keeps running on their side —
+         * nothing here can recall it, and its JobLink stays valid — so this only
+         * stops the polling and the writes it would make. Dropping the params is
+         * what keeps the request from refiring; the view falls back to the import
+         * form, which is where react-msaview's own cancel leaves it too.
+         */
+        cancelLaunch() {
+            self.launchController?.abort();
+            self.launchController = undefined;
+            self.blastParams = undefined;
+            self.orthologParams = undefined;
+            self.progress = '';
+            self.rid = undefined;
+            self.error = undefined;
+        },
         /**
          * #action
          */
@@ -301,6 +345,12 @@ export default function stateModelFactory() {
         .actions(self => ({
         afterCreate() {
             runCleanup();
+            // ties the launch to the view: closing one mid-BLAST used to leave the
+            // poller running for the job's lifetime and then call actions on a
+            // destroyed node, which surfaced as an unhandled rejection
+            addDisposer(self, () => {
+                self.launchController?.abort();
+            });
             for (const fn of [
                 loadStoredData,
                 storeDataToIndexedDB,

package/dist/MsaViewPanel/msaDataStore.d.ts

@@ -1,9 +1,11 @@
-export declare function generateDataStoreId(): string;
-export declare function storeMsaData(id: string, data: {
+/** the documents a view keeps in IndexedDB rather than in its session snapshot */
+export interface MsaDataPayload {
     msa?: string;
     tree?: string;
     treeMetadata?: string;
-}): Promise<boolean>;
+}
+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;

package/dist/MsaViewPanel/msaDataStore.js

@@ -33,14 +33,23 @@ export async function retrieveMsaData(id) {
     try {
         const db = await getDB();
         const result = await db.get(STORE_NAME, id);
-        if (result) {
-            return {
-                msa: result.msa,
-                tree: result.tree,
-                treeMetadata: result.treeMetadata,
-            };
+        if (!result) {
+            return undefined;
         }
-        return undefined;
+        // reading counts as use, which is what makes cleanupOldData's policy
+        // "unused for 7 days" rather than "written 7 days ago" -- a session opened
+        // every day used to lose its alignment on the eighth
+        try {
+            await db.put(STORE_NAME, { ...result, timestamp: Date.now() });
+        }
+        catch (e) {
+            console.warn('Failed to refresh MSA data timestamp:', e);
+        }
+        return {
+            msa: result.msa,
+            tree: result.tree,
+            treeMetadata: result.treeMetadata,
+        };
     }
     catch (e) {
         console.warn('Failed to retrieve MSA data:', e);

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

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