react-msaview 6.2.3 → 6.3.0

package/dist/svgTestUtil.d.ts

@@ -0,0 +1,1662 @@
+import MSAModelF from './model.ts';
+type Snapshot = NonNullable<Parameters<ReturnType<typeof MSAModelF>['create']>[0]>;
+export declare function installSvgTestEnv(contextExtras?: Partial<CanvasRenderingContext2D>): void;
+export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?: number): import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<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]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats"> & {
+    bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    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>>;
+}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+    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]>;
+    hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    scrollX: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    colWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    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("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec, import("./types.ts").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>>;
+        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, {
+        [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("./types.ts").Highlight, import("./types.ts").Highlight, import("./types.ts").Highlight>>, [undefined]>;
+}> & {
+    queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
+} & {
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
+    readonly DialogProps: any;
+} & {
+    removeActiveDialog(): void;
+    queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
+} & {
+    setTreeAreaWidth(n: number): void;
+    setTreeWidth(n: number): void;
+    setLabelsAlignRight(arg: boolean): void;
+    setDrawTree(arg: boolean): void;
+    setAutoTreeAreaWidth(arg: boolean): void;
+    setShowBranchLen(arg: boolean): void;
+    setDrawNodeBubbles(arg: boolean): void;
+    setDrawLabels(arg: boolean): void;
+} & {
+    setColorSchemeName(name: string): void;
+    setBgColor(arg: boolean): void;
+    setShowColumnStats(arg: boolean): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+} & {
+    headerHeight: number;
+    status: {
+        msg: string;
+        url?: string;
+        onCancel?: () => void;
+    } | undefined;
+    highResScaleFactor: number;
+    loadingMSA: boolean;
+    loadingTree: boolean;
+    volatileWidth: number | undefined;
+    resizeHandleWidth: number;
+    blockSize: number;
+    mouseRow: number | undefined;
+    mouseCol: number | undefined;
+    mouseClickRow: number | undefined;
+    mouseClickCol: number | undefined;
+    hoveredTreeNode: {
+        nodeId: string;
+        descendantNames: string[];
+    } | undefined;
+    highlightedColumns: number[] | undefined;
+    minimapHeight: number;
+    conservationTrackHeight: number;
+    sequenceLogoTrackHeight: number;
+    marginLeft: number;
+    error: unknown;
+    annotations: import("msa-parsers").Annotation[];
+} & {
+    drawRelativeTo(id: string | undefined): void;
+    setHideGaps(arg: boolean): void;
+    setAllowedGappyness(arg: number): void;
+    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;
+    setHighlightedColumns(columns?: number[]): void;
+    setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    setShowDomains(arg: boolean): void;
+    setShowDomainLegend(arg: boolean): void;
+    setSubFeatureRows(arg: boolean): void;
+    setMouseClickPos(col?: number, row?: number): void;
+    setRowHeight(n: number): void;
+    setColWidth(n: number): void;
+    setCurrentAlignment(n: number): void;
+    toggleCollapsed(node: string): void;
+    setShowOnly(node?: string): void;
+    setData(data: {
+        msa?: string;
+        tree?: string;
+        treeMetadata?: string;
+        gff?: string;
+    }): 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;
+    setTreeMetadata(result: string): void;
+} & {
+    readonly hideGapsEffective: boolean;
+    readonly realAllowedGappyness: number;
+    readonly actuallyShowDomains: boolean;
+    readonly viewInitialized: boolean;
+    readonly width: number;
+} & {
+    extraViewMenuItems(): never[];
+    readonly colorScheme: Record<string, string>;
+    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: Record<string, Record<string, string> | undefined>;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly numColumns: number;
+    readonly tree: import("./types.ts").NodeWithIds;
+    readonly rowNames: string[];
+    readonly rowNamesSet: Map<string, number>;
+    readonly mouseOverRowName: string | undefined;
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
+    readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly msaAreaWidth: number;
+    readonly treeAreaWidthMinusMargin: number;
+    readonly blanks: number[];
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
+    readonly rows: [string, string][];
+    readonly numRows: number;
+    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    readonly rowMap: Map<string, string>;
+    readonly columns: Map<string, string>;
+    readonly columns2d: string[];
+    readonly fontSize: number;
+    readonly colStats: import("./columnCounts.ts").ColumnCounts;
+    readonly sequenceType: 'dna' | 'rna' | 'amino';
+    readonly colConsensus: {
+        letter: string;
+        color: string | undefined;
+    }[];
+    readonly colClustalX: Record<string, string>[];
+    readonly conservation: number[];
+    readonly alphabetMaxBits: number;
+    readonly propertyConservation: number[];
+    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
+    readonly totalHeight: number;
+    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly maxBranchLength: number;
+    readonly maxDepthToLeaf: number;
+    readonly allBranchesLength0: boolean;
+    readonly showBranchLenEffective: boolean;
+} & {
+    readonly totalWidth: number;
+} & {
+    readonly dataInitialized: boolean;
+    readonly blocksX: number[];
+    readonly blocksY: number[];
+    readonly visibleMsaHeight: 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;
+    zoomInHorizontal(): void;
+    zoomInVertical(): void;
+    zoomOutVertical(): void;
+    zoomIn(): void;
+    zoomOut(): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    doScrollY(deltaY: number): void;
+    setScrollY(n: number): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
+    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
+    applyGFFText(gffText: string): void;
+    doScrollX(deltaX: number): void;
+    setScrollX(n: number): void;
+    setColumnTracks(tracks: import("./types.ts").ColumnTrackSpec[]): void;
+    toggleTrack(id: string): void;
+    setStatus(status?: {
+        msg: string;
+        url?: string;
+        onCancel?: () => void;
+    }): void;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+    }>;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
+    readonly tracks: import("./types.ts").BasicTrack[];
+    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+} & {
+    readonly msaAreaHeight: number;
+    readonly totalTrackAreaHeight: number;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
+} & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
+    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
+    readonly fillPalette: {
+        [x: string]: string;
+    };
+    readonly strokePalette: {
+        [k: string]: string;
+    };
+    readonly segmentLabels: Map<string, string>;
+    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly domainBands: Map<string, import("./types.ts").DomainBand[]>;
+    readonly domainBandsByStart: Map<string, import("./types.ts").DomainBand[]>;
+    readonly mouseOverDomains: import("msa-parsers").Annotation[];
+    readonly referenceRowIndex: number | undefined;
+    readonly hoveredRowIndices: number[];
+    readonly highlightedColumnRuns: {
+        start: number;
+        end: number;
+    }[];
+    readonly resolvedHighlights: import("./types.ts").ResolvedHighlight[];
+    readonly mouseOverColumnStats: {
+        col: number;
+        total: number;
+        gaps: number;
+        gapFraction: number;
+        conservation: number;
+        propertyConservation: number | undefined;
+        consensusLetter: string;
+        consensusCount: number;
+        consensusFraction: number;
+        distribution: [string, number][];
+    } | undefined;
+    getRowData(name: string): {
+        data: {
+            name?: string;
+            accession?: string;
+            dbxref?: string;
+        } | undefined;
+        treeMetadata: Record<string, string> | undefined;
+    };
+} & {
+    setHeaderHeight(arg: number): void;
+    setConservationTrackHeight(arg: number): void;
+    setSequenceLogoTrackHeight(arg: number): void;
+    reset(): void;
+    exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    initFilter(arg: string): void;
+    setFilter(arg: string, flag: boolean): void;
+    fit(): void;
+    fitVertically(): void;
+    fitHorizontally(): void;
+    afterCreate(): void;
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<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]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats"> & {
+    bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    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>>;
+}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+    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]>;
+    hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    scrollX: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    colWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, 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;
+    }, ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    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("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec, import("./types.ts").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>>;
+        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, {
+        [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("./types.ts").Highlight, import("./types.ts").Highlight, import("./types.ts").Highlight>>, [undefined]>;
+}, {
+    queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
+} & {
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
+    readonly DialogProps: any;
+} & {
+    removeActiveDialog(): void;
+    queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
+} & {
+    setTreeAreaWidth(n: number): void;
+    setTreeWidth(n: number): void;
+    setLabelsAlignRight(arg: boolean): void;
+    setDrawTree(arg: boolean): void;
+    setAutoTreeAreaWidth(arg: boolean): void;
+    setShowBranchLen(arg: boolean): void;
+    setDrawNodeBubbles(arg: boolean): void;
+    setDrawLabels(arg: boolean): void;
+} & {
+    setColorSchemeName(name: string): void;
+    setBgColor(arg: boolean): void;
+    setShowColumnStats(arg: boolean): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+} & {
+    headerHeight: number;
+    status: {
+        msg: string;
+        url?: string;
+        onCancel?: () => void;
+    } | undefined;
+    highResScaleFactor: number;
+    loadingMSA: boolean;
+    loadingTree: boolean;
+    volatileWidth: number | undefined;
+    resizeHandleWidth: number;
+    blockSize: number;
+    mouseRow: number | undefined;
+    mouseCol: number | undefined;
+    mouseClickRow: number | undefined;
+    mouseClickCol: number | undefined;
+    hoveredTreeNode: {
+        nodeId: string;
+        descendantNames: string[];
+    } | undefined;
+    highlightedColumns: number[] | undefined;
+    minimapHeight: number;
+    conservationTrackHeight: number;
+    sequenceLogoTrackHeight: number;
+    marginLeft: number;
+    error: unknown;
+    annotations: import("msa-parsers").Annotation[];
+} & {
+    drawRelativeTo(id: string | undefined): void;
+    setHideGaps(arg: boolean): void;
+    setAllowedGappyness(arg: number): void;
+    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;
+    setHighlightedColumns(columns?: number[]): void;
+    setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    setShowDomains(arg: boolean): void;
+    setShowDomainLegend(arg: boolean): void;
+    setSubFeatureRows(arg: boolean): void;
+    setMouseClickPos(col?: number, row?: number): void;
+    setRowHeight(n: number): void;
+    setColWidth(n: number): void;
+    setCurrentAlignment(n: number): void;
+    toggleCollapsed(node: string): void;
+    setShowOnly(node?: string): void;
+    setData(data: {
+        msa?: string;
+        tree?: string;
+        treeMetadata?: string;
+        gff?: string;
+    }): 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;
+    setTreeMetadata(result: string): void;
+} & {
+    readonly hideGapsEffective: boolean;
+    readonly realAllowedGappyness: number;
+    readonly actuallyShowDomains: boolean;
+    readonly viewInitialized: boolean;
+    readonly width: number;
+} & {
+    extraViewMenuItems(): never[];
+    readonly colorScheme: Record<string, string>;
+    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: Record<string, Record<string, string> | undefined>;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly numColumns: number;
+    readonly tree: import("./types.ts").NodeWithIds;
+    readonly rowNames: string[];
+    readonly rowNamesSet: Map<string, number>;
+    readonly mouseOverRowName: string | undefined;
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
+    readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly msaAreaWidth: number;
+    readonly treeAreaWidthMinusMargin: number;
+    readonly blanks: number[];
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
+    readonly rows: [string, string][];
+    readonly numRows: number;
+    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    readonly rowMap: Map<string, string>;
+    readonly columns: Map<string, string>;
+    readonly columns2d: string[];
+    readonly fontSize: number;
+    readonly colStats: import("./columnCounts.ts").ColumnCounts;
+    readonly sequenceType: 'dna' | 'rna' | 'amino';
+    readonly colConsensus: {
+        letter: string;
+        color: string | undefined;
+    }[];
+    readonly colClustalX: Record<string, string>[];
+    readonly conservation: number[];
+    readonly alphabetMaxBits: number;
+    readonly propertyConservation: number[];
+    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
+    readonly totalHeight: number;
+    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly maxBranchLength: number;
+    readonly maxDepthToLeaf: number;
+    readonly allBranchesLength0: boolean;
+    readonly showBranchLenEffective: boolean;
+} & {
+    readonly totalWidth: number;
+} & {
+    readonly dataInitialized: boolean;
+    readonly blocksX: number[];
+    readonly blocksY: number[];
+    readonly visibleMsaHeight: 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;
+    zoomInHorizontal(): void;
+    zoomInVertical(): void;
+    zoomOutVertical(): void;
+    zoomIn(): void;
+    zoomOut(): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    doScrollY(deltaY: number): void;
+    setScrollY(n: number): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
+    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
+    applyGFFText(gffText: string): void;
+    doScrollX(deltaX: number): void;
+    setScrollX(n: number): void;
+    setColumnTracks(tracks: import("./types.ts").ColumnTrackSpec[]): void;
+    toggleTrack(id: string): void;
+    setStatus(status?: {
+        msg: string;
+        url?: string;
+        onCancel?: () => void;
+    }): void;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+    }>;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
+    readonly tracks: import("./types.ts").BasicTrack[];
+    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+} & {
+    readonly msaAreaHeight: number;
+    readonly totalTrackAreaHeight: number;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
+} & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
+    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
+    readonly fillPalette: {
+        [x: string]: string;
+    };
+    readonly strokePalette: {
+        [k: string]: string;
+    };
+    readonly segmentLabels: Map<string, string>;
+    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly domainBands: Map<string, import("./types.ts").DomainBand[]>;
+    readonly domainBandsByStart: Map<string, import("./types.ts").DomainBand[]>;
+    readonly mouseOverDomains: import("msa-parsers").Annotation[];
+    readonly referenceRowIndex: number | undefined;
+    readonly hoveredRowIndices: number[];
+    readonly highlightedColumnRuns: {
+        start: number;
+        end: number;
+    }[];
+    readonly resolvedHighlights: import("./types.ts").ResolvedHighlight[];
+    readonly mouseOverColumnStats: {
+        col: number;
+        total: number;
+        gaps: number;
+        gapFraction: number;
+        conservation: number;
+        propertyConservation: number | undefined;
+        consensusLetter: string;
+        consensusCount: number;
+        consensusFraction: number;
+        distribution: [string, number][];
+    } | undefined;
+    getRowData(name: string): {
+        data: {
+            name?: string;
+            accession?: string;
+            dbxref?: string;
+        } | undefined;
+        treeMetadata: Record<string, string> | undefined;
+    };
+} & {
+    setHeaderHeight(arg: number): void;
+    setConservationTrackHeight(arg: number): void;
+    setSequenceLogoTrackHeight(arg: number): void;
+    reset(): void;
+    exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    initFilter(arg: string): void;
+    setFilter(arg: string, flag: boolean): void;
+    fit(): void;
+    fitVertically(): void;
+    fitHorizontally(): void;
+    afterCreate(): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+    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("./types.ts").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("./types.ts").Highlight[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+} | {
+    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?: undefined;
+    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("./types.ts").Highlight[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+}>>;
+export declare function syntheticProteinMsa(rows: number, cols: number): string;
+export {};