jbrowse-plugin-msaview 1.0.18 → 2.0.0

package/dist/MsaViewPanel/model.d.ts

@@ -0,0 +1,596 @@
+import { Instance } from 'mobx-state-tree';
+import { Feature } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+type MaybeLGV = LGV | undefined;
+export interface IRegion {
+    refName: string;
+    start: number;
+    end: number;
+}
+export interface BlastParams {
+    blastDatabase: string;
+    msaAlgorithm: string;
+    blastProgram: string;
+    selectedTranscript: Feature;
+    proteinSequence: string;
+}
+/**
+ * #stateModel MsaViewPlugin
+ * extends
+ * - MSAModel from https://github.com/GMOD/react-msaview
+ */
+export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    bgColor: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
+} & {
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    featureMode: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    type: import("mobx-state-tree").ISimpleType<"MsaView">;
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
+    scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
+    scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
+    colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
+    treeFilehandle: import("mobx-state-tree" /**
+     * #getter
+     */).IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    treeMetadataFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
+    collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
+    collapsed2: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
+    showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    data: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }, {
+        setTree(tree?: string | undefined): void;
+        setMSA(msa?: string | undefined): void;
+        setTreeMetadata(treeMetadata?: string | undefined): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+} & {
+    connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    connectedFeature: import("mobx-state-tree").IType<any, any, any>;
+    connectedHighlights: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    blastParams: import("mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
+    zoomToBaseLevel: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+}, {
+    width: number;
+} & {
+    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    setDisplayName(name: string): void;
+    setWidth(newWidth: number): void;
+    setMinimized(flag: boolean): void;
+} & {
+    queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
+} & {
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType;
+    readonly DialogProps: any;
+} & {
+    removeActiveDialog(): void;
+    queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
+} & {
+    setTreeWidthMatchesArea(arg: boolean): void;
+    setTreeAreaWidth(n: number): void;
+    setTreeWidth(n: number): void;
+    setLabelsAlignRight(arg: boolean): void;
+    setDrawTree(arg: boolean): void;
+    setShowBranchLen(arg: boolean): void;
+    setDrawNodeBubbles(arg: boolean): void;
+    setDrawLabels(arg: boolean): void;
+} & {
+    setColorSchemeName(name: string): void;
+    setBgColor(arg: boolean): void;
+} & {
+    status: {
+        msg: string;
+        url?: string | undefined;
+    } | undefined;
+    highResScaleFactor: number;
+    loadingMSA: boolean;
+    loadingTree: boolean;
+    width: number;
+    resizeHandleWidth: number;
+    blockSize: number;
+    mouseRow: number | undefined;
+    mouseCol: number | undefined;
+    mouseClickRow: number | undefined;
+    mouseClickCol: number | undefined;
+    nref: number;
+    minimapHeight: number;
+    marginLeft: number;
+    error: unknown;
+    annotPos: {
+        left: number;
+        right: number;
+    } | undefined;
+    loadedInterProAnnotations: Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults> | undefined;
+    interProScanJobIds: {
+        jobId: string;
+        date: number;
+    }[];
+} & {
+    setLoadingMSA(arg: boolean): void;
+    setLoadingTree(arg: boolean): void;
+    setWidth(arg: number): void;
+    setHeight(height: number): void;
+    setError(error?: unknown): void;
+    setMousePos(col?: number, row?: number): void;
+    setFeatureMode(arg: boolean): void;
+    setSubFeatureRows(arg: boolean): void;
+    setMouseClickPos(col?: number, row?: number): void;
+    setRowHeight(n: number): void;
+    setColWidth(n: number): void;
+    setScrollY(n: number): void;
+    setCurrentAlignment(n: number): void;
+    toggleCollapsed(node: string): void;
+    toggleCollapsed2(node: string): void;
+    setShowOnly(node?: string): void;
+    setData(data: {
+        msa?: string;
+        tree?: string;
+    }): void;
+    setMSAFilehandle(msaFilehandle?: import("@jbrowse/core/util").FileLocation): void;
+    setTreeFilehandle(treeFilehandle?: import("@jbrowse/core/util").FileLocation): void;
+    setMSA(result: string): void;
+    setTree(result: string): void;
+    setTreeMetadata(result: string): void;
+} & {
+    extraViewMenuItems(): never[];
+    readonly colorScheme: Record<string, string>;
+    readonly header: {};
+    getRowData(name: string): {
+        data: {
+            name: string;
+            accession: string;
+            dbxref: string;
+        } | undefined;
+    };
+    readonly alignmentNames: string[];
+    readonly noTree: boolean;
+    readonly noAnnotations: boolean;
+    readonly menuItems: never[];
+    readonly treeMetadata: any;
+    readonly MSA: import("react-msaview/dist/parsers/StockholmMSA").default | import("react-msaview/dist/parsers/FastaMSA").default | import("react-msaview/dist/parsers/ClustalMSA").default | null;
+    readonly numColumns: number;
+    readonly _tree: import("react-msaview/dist/util").NodeWithIds;
+    readonly rowNames: string[];
+    readonly mouseOverRowName: string | undefined;
+    readonly root: HierarchyNode<import("react-msaview/dist/util").NodeWithIds>;
+    readonly msaAreaWidth: number;
+    readonly treeAreaWidthMinusMargin: number;
+    readonly blanks: number[];
+    readonly rows: [string, string][];
+    readonly columns: {
+        [k: string]: string;
+    };
+    readonly columns2d: string[];
+    readonly fontSize: number;
+    readonly colStats: Record<string, number>[];
+    readonly hierarchy: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>;
+    readonly totalHeight: number;
+} & {
+    readonly totalWidth: number;
+} & {
+    readonly initialized: boolean | "" | undefined;
+    readonly blocksX: number[];
+    readonly blocksY: number[];
+} & {
+    readonly blocks2d: number[][];
+    readonly isLoading: boolean;
+    readonly maxScrollX: number;
+} & {
+    zoomIn(): void;
+    zoomOut(): void;
+    setLoadedInterProAnnotations(data: Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>): void;
+    doScrollY(deltaY: number): void;
+    doScrollX(deltaX: number): void;
+    setScrollX(n: number): void;
+    toggleTrack(id: string): void;
+    addInterProScanJobId(arg: string): void;
+    setStatus(status?: {
+        msg: string;
+        url?: string;
+    }): void;
+} & {
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly conservation: string[];
+    readonly adapterTrackModels: import("react-msaview/dist/model").ITextTrack[];
+    readonly tracks: import("react-msaview/dist/model").ITextTrack[];
+    readonly turnedOnTracks: import("react-msaview/dist/model").ITextTrack[];
+    globalCoordToRowSpecificSeqCoord(rowName: string, position: number): number;
+    seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
+} & {
+    readonly totalTrackAreaHeight: number;
+    readonly tidyTypes: Map<string, import("react-msaview/dist/model").Accession>;
+    readonly tidyAnnotations: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }[];
+    readonly tidyFilteredAnnotations: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }[];
+    readonly tidyFilteredGatheredAnnotations: Record<string, {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }[] | undefined>;
+} & {
+    readonly fillPalette: Record<string, string>;
+    readonly strokePalette: {
+        [k: string]: string;
+    };
+} & {
+    loadInterProScanResults(jobId: string): Promise<void>;
+    queryInterProScan(programs: string[]): Promise<void>;
+    reset(): void;
+    exportSVG(opts: {
+        theme: import("@mui/material").Theme;
+        includeMinimap?: boolean;
+        exportType: string;
+    }): Promise<void>;
+    incrementRef(): void;
+    initFilter(arg: string): void;
+    setFilter(arg: string, flag: boolean): void;
+    afterCreate(): void;
+} & {
+    rid: string | undefined;
+    progress: string;
+    error: unknown;
+} & {
+    /**
+     * #method
+     */
+    ungappedCoordMap(rowName: string, position: number): number | undefined;
+} & {
+    /**
+     * #getter
+     */
+    readonly transcriptToMsaMap: {
+        g2p: Record<number, number | undefined>;
+        p2g: Record<number, number | undefined>;
+        refName: string;
+        strand: number;
+    } | undefined;
+} & {
+    /**
+     * #getter
+     */
+    readonly mouseCol2: number | undefined;
+    /**
+     * #getter
+     */
+    readonly clickCol2: undefined;
+} & {
+    /**
+     * #getter
+     */
+    readonly processing: boolean;
+    /**
+     * #getter
+     */
+    readonly connectedView: MaybeLGV;
+} & {
+    /**
+     * #action
+     */
+    setZoomToBaseLevel(arg: boolean): void;
+    /**
+     * #action
+     */
+    setError(e: unknown): void;
+    /**
+     * #action
+     */
+    setProgress(arg: string): void;
+    /**
+     * #action
+     */
+    setRid(arg: string): void;
+    /**
+     * #action
+     */
+    setConnectedHighlights(r: IRegion[]): void;
+    /**
+     * #action
+     */
+    addToConnectedHighlights(r: IRegion): void;
+    /**
+     * #action
+     */
+    clearConnectedHighlights(): void;
+    /**
+     * #action
+     */
+    setBlastParams(args?: BlastParams): void;
+} & {
+    /**
+     * #method
+     * overrides base
+     */
+    extraViewMenuItems(): {
+        label: string;
+        checked: boolean;
+        type: string;
+        onClick: () => void;
+    }[];
+    /**
+     * #getter
+     */
+    readonly processing: boolean;
+    /**
+     * #getter
+     */
+    readonly connectedView: MaybeLGV;
+} & {
+    afterCreate(): void;
+}, import("mobx-state-tree")._NotCustomized, {
+    height: number;
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number;
+    treeWidth: number;
+    treeWidthMatchesArea: boolean;
+    showBranchLen: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    bgColor: boolean;
+    colorSchemeName: string;
+    id: string;
+    featureMode: boolean;
+    subFeatureRows: boolean;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    currentAlignment: number;
+    type: "MsaView";
+    treeFilehandle: {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | undefined;
+    msaFilehandle: {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | undefined;
+    treeMetadataFilehandle: {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }> | undefined;
+    collapsed: string[];
+    collapsed2: string[];
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    data: {
+        treeMetadata?: string | undefined;
+        msa?: string | undefined;
+        tree?: string | undefined;
+    };
+} & import("mobx-state-tree")._NotCustomized>;
+export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
+export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
+export {};