jbrowse-plugin-msaview 2.5.0 → 2.5.2

package/dist/MsaViewPanel/model.d.ts

@@ -1,3 +1,4 @@
+export type { MSAFormat } from 'msa-parsers';
 import type { ProteinView, StructureConnection } from './structureConnection';
 import type { MafRegion, MsaViewInitState } from './types';
 import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
@@ -25,11 +26,11 @@ export interface BlastParams {
  * extends
  * - MSAModel from https://github.com/GMOD/react-msaview
  */
-export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
+export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
     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" | "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "bgColor" | "colorSchemeName" | "msaFormat" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -37,10 +38,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
+}, "bgColor" | "colorSchemeName" | "msaFormat"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-} & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -48,6 +50,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
@@ -61,18 +64,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
@@ -81,18 +84,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
@@ -101,18 +104,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
@@ -121,18 +124,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -155,7 +158,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     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>;
+}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "connectedStructures" | "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>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
@@ -193,6 +197,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
     status: {
@@ -215,7 +220,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         descendantNames: string[];
     } | undefined;
     highlightedColumns: number[] | undefined;
-    nref: number;
     minimapHeight: number;
     conservationTrackHeight: number;
     marginLeft: number;
@@ -228,10 +232,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setLoadingMSA(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
+    setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
     setMousePos(col?: number, row?: number): void;
-    setHoveredTreeNode(nodeId?: string): void;
     setHighlightedColumns(columns?: number[]): void;
     setShowDomains(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -263,16 +267,28 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
-    readonly header: Record<string, unknown>;
+    readonly header: Record<string, unknown> | {
+        info: string;
+        version: string | undefined;
+    } | {
+        General: Record<string, string[]>;
+        Accessions: {
+            [k: string]: string | undefined;
+        };
+        Dbxref: {
+            [k: string]: string;
+        };
+    };
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly noDomains: boolean;
     menuItems(): never[];
     readonly treeMetadata: any;
-    readonly MSA: import("react-msaview").MSAParserType | null;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
+    readonly rowNamesSet: Map<string, number>;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -291,9 +307,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rows: [string, string][];
     readonly numRows: number;
     readonly rowMap: Map<string, string>;
-    readonly columns: {
-        [k: string]: string;
-    };
+    readonly columns: Map<string, string>;
     readonly columns2d: string[];
     readonly fontSize: number;
     readonly colStats: Record<string, number>[];
@@ -315,17 +329,20 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     readonly totalWidth: number;
 } & {
-    readonly dataInitialized: boolean | "" | undefined;
+    readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
+    readonly maxScrollY: number;
     readonly showMsaLetters: boolean;
     readonly showTreeText: boolean;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    setScrollZoom(arg: boolean): void;
+    setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
@@ -334,8 +351,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
     doScrollY(deltaY: number): void;
-    setInterProAnnotations(data: Record<string, import("react-msaview").InterProScanResults>): void;
+    setDomains(data?: Record<string, import("react-msaview").InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -346,6 +364,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         onCancel?: () => void;
     }): void;
 } & {
+    readonly labelWidthMap: Map<string, number>;
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
@@ -353,7 +372,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly tracks: import("react-msaview").BasicTrack[];
     readonly turnedOnTracks: import("react-msaview").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
-    readonly rowNamesSet: Map<string, number>;
     visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
     visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
     visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
@@ -361,12 +379,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     seqPosToGlobalCol(rowName: string, seqPos: number): number;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
-    readonly hoveredCell: {
-        rowName: string;
-        col: number;
-        base: string | undefined;
-        seqPos: number | undefined;
-    } | undefined;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly tidyInterProAnnotationTypes: Map<string, {
@@ -427,9 +439,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         theme: import("@mui/material").Theme;
         includeMinimap?: boolean;
         includeTracks?: boolean;
-        exportType: string;
+        exportType: "entire" | "viewport";
     }): Promise<void>;
-    incrementRef(): void;
     initFilter(arg: string): void;
     setFilter(arg: string, flag: boolean): void;
     fit(): void;
@@ -442,6 +453,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     error: unknown;
     loadingStoredData: boolean;
     isStoringData: boolean;
+    domainsRequested: boolean;
 } & {
     /**
      * #method
@@ -526,6 +538,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setIsStoringData(arg: boolean): void;
+    /**
+     * #action
+     */
+    setDomainsRequested(arg: boolean): void;
     /**
      * #action
      */
@@ -564,33 +580,37 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     })[];
 } & {
     afterCreate(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    id: string;
-    displayName: string | undefined;
-    minimized: boolean;
-} & Omit<{
-    drawLabels: boolean;
-    labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
-    showBranchLen: boolean;
-    drawTree: boolean;
-    drawNodeBubbles: boolean;
-    bgColor: boolean;
-    colorSchemeName: string;
-    id: string;
-    showDomains: boolean;
-    hideGaps: boolean;
-    allowedGappyness: number;
-    subFeatureRows: boolean;
-    type: "MsaView";
-    drawMsaLetters: boolean;
-    height: number;
-    rowHeight: number;
-    scrollY: number;
-    scrollX: number;
-    colWidth: number;
-    treeFilehandle: {
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    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>;
+}> & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
+    drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+}, "bgColor" | "colorSchemeName" | "msaFormat"> & {
+    bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -598,19 +618,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    msaFilehandle: {
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -618,19 +638,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    treeMetadataFilehandle: {
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -638,19 +658,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    gffFilehandle: {
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -658,31 +678,42 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    currentAlignment: number;
-    collapsed: string[];
-    showOnly: string | undefined;
-    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    data: {
+    } | 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>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    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>>;
+        treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    }, {
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
+        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;
-    };
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
-    relativeTo: string | undefined;
-}, symbol> & import("@jbrowse/mobx-state-tree")._NotCustomized>;
+    }>, [undefined]>;
+    featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    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>;
+}>, symbol> & 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

@@ -5,7 +5,7 @@ import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
-import { autoConnectStructures, highlightConnectedStructures, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { autoConnectStructures, autoLoadProteinDomains, highlightConnectedStructures, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
 import { getProteinViews } from './structureConnection';
@@ -27,9 +27,6 @@ export default function stateModelFactory() {
          * #property
          */
         connectedFeature: types.frozen(),
-        /**
-         * #property
-         */
         /**
          * #property
          */
@@ -84,6 +81,12 @@ export default function stateModelFactory() {
          * #volatile
          */
         isStoringData: false,
+        /**
+         * #volatile
+         * guards the one-shot auto-fetch of protein domains so it doesn't refire
+         * when NCBI returns no domains (leaving interProAnnotations undefined)
+         */
+        domainsRequested: false,
     }))
         .views(self => ({
         /**
@@ -219,6 +222,12 @@ export default function stateModelFactory() {
         setIsStoringData(arg) {
             self.isStoringData = arg;
         },
+        /**
+         * #action
+         */
+        setDomainsRequested(arg) {
+            self.domainsRequested = arg;
+        },
         /**
          * #action
          */
@@ -353,13 +362,16 @@ export default function stateModelFactory() {
                 processInit,
                 highlightConnectedStructures,
                 autoConnectStructures,
-                observeProteinHighlights,
+                autoLoadProteinDomains,
             ]) {
                 addDisposer(self, autorun(() => {
                     fn(self);
                 }));
             }
+            // these two keep per-reaction state across runs (a "did I set it?" flag),
+            // so they're factories returning the autorun body rather than plain fns
             addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)));
+            addDisposer(self, autorun(observeProteinHighlights(self)));
         },
     }));
 }