jbrowse-plugin-msaview 3.3.0 → 3.4.1

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,7 @@
 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 { 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';
@@ -11,12 +12,31 @@ 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
@@ -66,7 +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>;
-}, "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" | "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]>;
@@ -80,7 +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>>;
-}, "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" | "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]>;
@@ -475,6 +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>>;
@@ -486,14 +507,12 @@ 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>>;
     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>;
@@ -559,6 +578,7 @@ 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[];
@@ -574,6 +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;
@@ -591,6 +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;
@@ -655,6 +677,7 @@ 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;
@@ -669,6 +692,7 @@ 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;
@@ -696,6 +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;
@@ -704,10 +729,16 @@ 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;
     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;
@@ -747,6 +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;
@@ -770,13 +802,9 @@ 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;
-        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;
@@ -789,6 +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;
 } & {
     /**
@@ -887,6 +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
      */
@@ -916,7 +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;
@@ -929,6 +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;
@@ -1030,13 +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 {};

package/dist/MsaViewPanel/msaDataStore.test.js

@@ -0,0 +1,44 @@
+import { beforeEach, expect, test, vi } from 'vitest';
+import { retrieveMsaData } 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(() => ({
+    rows: new Map(),
+    state: { putFails: false },
+}));
+vi.mock('../utils/idb', () => ({
+    createDbOpener: () => () => Promise.resolve({
+        get: (_store, id) => Promise.resolve(rows.get(id)),
+        put: (_store, value) => {
+            if (state.putFails) {
+                return Promise.reject(new Error('QuotaExceededError'));
+            }
+            rows.set(value.id, value);
+            return Promise.resolve(value.id);
+        },
+    }),
+}));
+beforeEach(() => {
+    rows.clear();
+    state.putFails = false;
+});
+// cleanupOldData deletes by timestamp, so without this a session opened every
+// single day still lost its alignment on the eighth
+test('reading a row refreshes its timestamp, making the expiry "unused for 7 days"', async () => {
+    rows.set('msa-1', { id: 'msa-1', msa: '>a\nMK', timestamp: 1000 });
+    const before = Date.now();
+    expect((await retrieveMsaData('msa-1'))?.msa).toBe('>a\nMK');
+    expect(rows.get('msa-1').timestamp).toBeGreaterThanOrEqual(before);
+});
+test('a row that is no longer there reads as undefined and writes nothing', async () => {
+    expect(await retrieveMsaData('msa-gone')).toBeUndefined();
+    expect(rows.size).toBe(0);
+});
+// the refresh is housekeeping; failing it must not turn a readable alignment
+// into a missing one, which is what the caller reports as expired
+test('a refresh that fails still hands back the data it read', async () => {
+    vi.spyOn(console, 'warn').mockImplementation(() => { });
+    rows.set('msa-1', { id: 'msa-1', msa: '>a\nMK', timestamp: 1000 });
+    state.putFails = true;
+    expect((await retrieveMsaData('msa-1'))?.msa).toBe('>a\nMK');
+});

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/runLaunch.d.ts

@@ -0,0 +1,38 @@
+import type { JBrowsePluginMsaViewModel } from './model';
+/**
+ * What a launch is allowed to do to the model and to the network while it runs.
+ *
+ * Every write a launch makes goes through `act`, so "nothing touches the model
+ * once the launch has been abandoned" is one rule in one place. Spreading that
+ * guard across the call sites only takes one omission to undo: an abandoned
+ * launch keeps running until its next network hop rejects, and an action on a
+ * destroyed mobx-state-tree node throws where nothing is catching.
+ */
+export interface LaunchScope {
+    /** aborts when the user cancels, and when the view is destroyed */
+    signal: AbortSignal;
+    act: (fn: () => void) => void;
+    onProgress: (arg: string) => void;
+    /** the EBI job id, published before the first poll so the view can link out */
+    onRid: (arg: string) => void;
+}
+interface LaunchedData {
+    msa: string;
+    tree: string;
+    treeMetadata: string;
+}
+/**
+ * Run one launch attempt, owning the AbortController that ties it to the view.
+ *
+ * The controller lives on the model because two things end a launch and neither
+ * is here: the Cancel button, and the disposer `afterCreate` registers. Before
+ * it existed, closing a view mid-BLAST left the poller checking EBI for the
+ * job's lifetime and then writing to a node that was gone.
+ */
+export declare function runLaunch({ self, message, launch, onLaunched, }: {
+    self: JBrowsePluginMsaViewModel;
+    message: string;
+    launch: (scope: LaunchScope) => Promise<LaunchedData>;
+    onLaunched: () => void;
+}): void;
+export {};