react-msaview 8.4.1 → 9.1.0

package/dist/components/MSAViewer.d.ts

@@ -10,6 +10,12 @@ export interface MSAViewerProps {
     msaFilehandle?: FileLocationType;
     treeFilehandle?: FileLocationType;
     gffFilehandle?: FileLocationType;
+    /** a URL the viewer fetches the alignment from; `msaFilehandle` wins */
+    msaUrl?: string;
+    /** a URL the viewer fetches the Newick tree from; `treeFilehandle` wins */
+    treeUrl?: string;
+    /** a URL the viewer fetches the GFF from; `gffFilehandle` wins */
+    gffUrl?: string;
     /**
      * a scheme name from the built-in table, or `{map}`, a color per residue
      * letter that leaves every other letter uncolored
@@ -24,7 +30,10 @@ export interface MSAViewerProps {
      * hide columns at least this percent gaps (default 100, i.e. hide nothing)
      */
     allowedGappyness?: number;
-    /** alignment columns (0-based) to highlight with a persistent overlay */
+    /**
+     * alignment columns, 1-based like `highlights`, drawn as one `{start, end}`
+     * highlight per run of adjacent columns
+     */
     highlightColumns?: number[];
     /**
      * labeled highlights in 1-based inclusive coordinates: `{start, end}` for
@@ -67,10 +76,8 @@ export interface MSAViewerProps {
     rowPanels?: RowPanelSpec[];
     /** draw the phylogenetic tree (default true); false leaves a labels-only gutter */
     drawTree?: boolean;
-    /** fixed width (px) of the tree/label area */
+    /** fixed width (px) of the tree/label area; unset fits it to the labels and the tree */
     treeAreaWidth?: number;
-    /** auto-size the tree/label area to the labels (used when drawTree is false) */
-    autoTreeAreaWidth?: boolean;
     /** draw branch lengths (default true); false draws a cladogram */
     showBranchLen?: boolean;
     /**
@@ -122,13 +129,1891 @@ export interface MSAViewerProps {
     onSelectionChange?: (selection: MsaSelection | undefined) => void;
     /**
      * the model the viewer built, for the model API; called again with the new
-     * model when msa, tree, msaFilehandle or treeFilehandle changes
+     * model when msa, tree, msaUrl, treeUrl, msaFilehandle or treeFilehandle
+     * changes
      */
     onModel?: (model: MsaViewModel) => void;
 }
 /**
  * A new alignment or tree needs a new model, so the viewer remounts when one
  * of those props changes and keeps its model across every other change,
- * including a new annotation file.
+ * including a new annotation file. A `ref` holds the current model.
  */
-export default function MSAViewer(props: MSAViewerProps): React.JSX.Element;
+declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "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").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<TreeOrder>, [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]>;
+    drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, "bgColor" | "colorSchemeName" | "customColorScheme" | "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]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, 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" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "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").ILiteralType<"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]>;
+    scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<TreeRoot | undefined, TreeRoot | undefined, TreeRoot | 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]>;
+    trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ColumnTrackSpec, ColumnTrackSpec, ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ResidueMapping, ResidueMapping, ResidueMapping>>, [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]>;
+    turnedOffFeatures: 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<Highlight, Highlight, Highlight>>, [undefined]>;
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Feature, Feature, Feature>>, [undefined]>;
+    selection: import("@jbrowse/mobx-state-tree").IType<MsaSelection | undefined, MsaSelection | undefined, MsaSelection | undefined>;
+    region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
+    clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Clade, Clade, Clade>>, [undefined]>;
+    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Encoding, Encoding, Encoding>>, [undefined]>;
+    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<RowPanelSpec, RowPanelSpec, RowPanelSpec>>, [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 | undefined): void;
+    setTreeWidth(n: number | undefined): void;
+    setLabelsAlignRight(arg: boolean): void;
+    setDrawTree(arg: boolean): void;
+    setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: TreeOrder): void;
+    setDrawNodeBubbles(arg: boolean): void;
+    setDrawNodeLabels(arg: boolean): void;
+    setShowTreeOverview(arg: boolean): void;
+    setDrawLabels(arg: boolean): void;
+} & {
+    setColorSchemeName(name: string): void;
+    setCustomColorScheme(map?: Record<string, string>): void;
+    setBgColor(arg: boolean): void;
+    setShowColumnStats(arg: boolean): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+} & {
+    headerHeight: number;
+    hideHeader: boolean;
+    importForm: boolean;
+    status: {
+        msg: 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;
+    transientHighlights: Record<string, Highlight[]>;
+    minimapHeight: number;
+    marginLeft: number;
+    error: unknown;
+    loadWarnings: string[];
+    dismissedWarnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
+    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;
+    addWarning(warning: string): void;
+    setHostCarriesData(arg: boolean): void;
+    setMousePos(col?: number, row?: number): void;
+    setHighlightedColumns(columns?: number[]): void;
+    setRegion(region?: Region): void;
+    setHighlights(highlights: Highlight[]): void;
+    setFeatures(features: Feature[]): void;
+    setSelection(selection?: MsaSelection): void;
+    clearSelection(): void;
+    setClades(clades: Clade[]): void;
+    applyHighlight(owner: string, highlights: Highlight[]): void;
+    clearHighlight(owner: string): 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;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: TreeRoot): void;
+    setShowOnly(node?: string): void;
+    setData(data: {
+        msa?: string;
+        tree?: string;
+        treeMetadata?: string;
+        gff?: string;
+    }): void;
+    setMSAFilehandle(msaFilehandle?: FileLocationType): void;
+    setTreeFilehandle(treeFilehandle?: FileLocationType): void;
+    setTreeMetadataFilehandle(treeMetadataFilehandle?: FileLocationType): void;
+    setGFFFilehandle(gffFilehandle?: FileLocationType): void;
+    setMSA(result: string): void;
+    setTree(result: string): void;
+    setTreeMetadata(result: string): void;
+    setGFF(result?: string): void;
+} & {
+    readonly hideGapsEffective: boolean;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
+    readonly viewInitialized: boolean;
+    readonly width: number;
+} & {
+    readonly colorScheme: Record<string, string>;
+    readonly dynamicColorSchemeName: string | undefined;
+    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;
+    readonly unshareableData: import("../types.ts").UnshareableData[];
+    menuItems(): never[];
+    readonly rowData: Record<string, Record<string, string> | undefined>;
+    rowDataOf(name: string): Record<string, string> | undefined;
+    readonly rowFields: string[];
+    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly numColumns: number;
+    readonly inputTree: import("../types.ts").NodeWithIds;
+    readonly tree: import("../types.ts").NodeWithIds;
+    readonly rowNames: string[];
+    readonly rowNamesSet: Map<string, number>;
+    readonly resolvedClades: import("../types.ts").ResolvedClade[];
+    readonly cladeGutterWidth: number;
+    readonly treeDrawn: boolean;
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    readonly maxTipLabelWidth: number;
+    readonly labelColumnWidth: number;
+    readonly fittedTreeAreaWidth: number;
+    readonly effectiveTreeAreaWidth: number;
+    readonly effectiveTreeWidth: number;
+    readonly showTreeText: boolean;
+    readonly mouseOverRowName: string | undefined;
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
+    readonly root: import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIds>;
+    readonly treeNewick: string;
+    readonly treeOverviewHeight: number;
+    readonly treeOverviewLayout: {
+        root: import("../hierarchy.ts").LaidOutNode<import("../types.ts").NodeWithIds>;
+        numTips: number;
+        maxDepthToLeaf: number;
+        showBranchLen: boolean;
+    } | undefined;
+    readonly treeOverviewClades: import("../types.ts").ResolvedClade[];
+    readonly treeOverviewFocusRows: [number, number] | undefined;
+    treeOverviewHit(y: number): {
+        id: string;
+        rows: [number, number];
+    } | undefined;
+    readonly rowPanelsWidth: number;
+    readonly rowPanelsHeaderHeight: 0 | 56;
+    readonly msaAreaWidth: number;
+    readonly treeAreaWidthMinusMargin: number;
+    readonly blanks: number[];
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
+    readonly rows: [string, string][];
+    readonly numRows: number;
+    seqPosIndex(rowName: string): Int32Array | undefined;
+    rowSequence(name: string): string | undefined;
+    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 treeLayout: {
+        root: import("../hierarchy.ts").LaidOutNode<import("../types.ts").NodeWithIds>;
+        leaves: import("../hierarchy.ts").LaidOutNode<import("../types.ts").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIds>;
+    readonly totalHeight: number;
+    readonly leaves: import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIds>[];
+    readonly rootToTipLength: number;
+    readonly pxPerBranchLength: number;
+    readonly maxDepthToLeaf: number;
+    readonly allBranchesLength0: boolean;
+    readonly showBranchLenEffective: boolean;
+} & {
+    readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+} & {
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("../types.ts").Arc[];
+    }>;
+    trackHeight(kind: import("../types.ts").TrackKind, heightKey?: string, given?: number): number;
+    columnTrackModel(track: ColumnTrackSpec): import("../types.ts").BasicTrack;
+    readonly columnTrackModels: import("../types.ts").BasicTrack[];
+} & {
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("../types.ts").Arc[] | undefined;
+    readonly adapterTrackModels: import("../types.ts").BasicTrack[];
+    readonly basePairTrackModels: import("../types.ts").BasicTrack[];
+    readonly computedTrackModels: 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;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    visibleSpan({ row, start: rawStart, end: rawEnd }: Region): {
+        startCol: number;
+        endCol: number;
+    } | undefined;
+    readonly residueMappingProblems: import("../types.ts").ResidueMappingProblem[];
+    readonly usableResidueMappings: ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("../types.ts").MappedStructure;
+    }[];
+    structureResidue(rowName: string, seqPos: number, structureId?: string): import("../types.ts").StructureResidue | undefined;
+    rowResidue(structureId: string, position: number, asymId?: string): import("../types.ts").RowResidue | undefined;
+} & {
+    readonly treeScaleBar: {
+        step: number;
+        px: number;
+        label: string;
+    } | undefined;
+    readonly topBandHeight: number;
+    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 dataInitialized: boolean;
+    readonly blocksX: number[];
+    readonly blocksY: number[];
+} & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
+    readonly blocks2d: (readonly [number, number])[];
+    readonly isLoading: boolean;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
+    readonly maxScrollY: number;
+    readonly wheelZoomAxis: import("../constants.ts").ScrollZoomAxis;
+} & {
+    setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
+    setScrollZoom(arg: boolean): void;
+    setScrollZoomAxis(arg: import("../constants.ts").ScrollZoomAxis): void;
+    setHoveredTreeNode(nodeId?: string): void;
+    calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
+    replaceTree(newick: string): void;
+    resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: import("../constants.ts").ScrollZoomAxis): void;
+    zoomIn(): void;
+    zoomOut(): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("../constants.ts").ScrollZoomAxis): void;
+    doScrollY(deltaY: number): void;
+    setScrollY(n: number): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
+    applyGFFText(gffText: string): void;
+    doScrollX(deltaX: number): void;
+    setScrollX(n: number): void;
+    setColumnTracks(tracks: ColumnTrackSpec[]): void;
+    setRowData(rowData: RowDataInput): void;
+    setEncodings(encodings: Encoding[]): void;
+    setRowPanels(panels: RowPanelSpec[]): void;
+    setResidueMappings(mappings: ResidueMapping[]): void;
+    toggleTrack(id: string): void;
+    setStatus(status?: {
+        msg: string;
+        onCancel?: () => void;
+    }): void;
+} & {
+    cellAt(visibleCol: number, rowIndex?: number): Cell;
+    readonly hoveredCell: Cell | undefined;
+    readonly clickedCell: Cell | undefined;
+    readonly viewport: Viewport | undefined;
+    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
+    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
+    readonly fillPalette: {
+        [x: string]: string;
+    };
+    readonly featureFillEncoding: import("../types.ts").ResolvedEncoding | undefined;
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
+    readonly segmentLabels: Map<string, string>;
+    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly legends: import("../types.ts").Legend[];
+    readonly domainUnderline: boolean;
+    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;
+    }[];
+    fillHighlightLabel(label: string, row?: string, start?: number): string;
+    readonly resolvedHighlights: import("../types.ts").ResolvedHighlight[];
+    readonly resolvedSelection: import("../types.ts").ResolvedSelection | undefined;
+    readonly selectionSize: {
+        columns: number;
+        rows: number;
+    } | undefined;
+    readonly selectionFileSpan: {
+        start: number;
+        end: number;
+    } | undefined;
+    readonly selectionFasta: string;
+    columnStatsAt(col: number): import("../columnStats.ts").ColumnStats | undefined;
+    getRowData(name: string): {
+        data: {
+            name?: string;
+            accession?: string;
+            dbxref?: string;
+        } | undefined;
+        rowData: Record<string, string> | undefined;
+    };
+    readonly resolvedEncodings: import("../types.ts").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        legend: import("../types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'strip';
+        field: string;
+        colors: Map<string, string>;
+    } | {
+        header: string;
+        legend: import("../types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'features';
+        x: 'column' | 'position';
+        field?: string;
+        colors: Map<import("msa-parsers").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        labels?: Map<import("msa-parsers").Annotation, string>;
+    })[];
+    readonly resolvedRowPanels: import("../types.ts").ResolvedRowPanel[];
+    readonly featureAlignShifts: Map<string, Map<string, number>>;
+    readonly tipLabelColors: Map<string, string> | undefined;
+    readonly rowTints: (string | undefined)[] | undefined;
+    readonly branchColors: Map<string, string> | undefined;
+} & {
+    setHeaderHeight(arg: number): void;
+    setHideHeader(arg: boolean): void;
+    setImportForm(arg: boolean): void;
+    treeOverviewClick(y: number): void;
+    setTrackHeight(heightKey: string, height: number): void;
+    reset(): void;
+    exportSVG(opts: import("../exportLayout.ts").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
+    setFilter(accession: string, shown: boolean): void;
+    fit(): void;
+    fitVertically(): void;
+    zoomToRegion(region: Region): void;
+    revealRegion(region: Region): void;
+    zoomToSelection(): void;
+    selectBlock(anchor: {
+        col: number;
+        row?: number;
+    }, head: {
+        col: number;
+        row?: number;
+    }): void;
+    fitHorizontally(): void;
+    afterCreate(): void;
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "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").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<TreeOrder>, [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]>;
+    drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, "bgColor" | "colorSchemeName" | "customColorScheme" | "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]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, 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" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "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").ILiteralType<"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]>;
+    scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, 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]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<TreeRoot | undefined, TreeRoot | undefined, TreeRoot | 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]>;
+    trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ColumnTrackSpec, ColumnTrackSpec, ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ResidueMapping, ResidueMapping, ResidueMapping>>, [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]>;
+    turnedOffFeatures: 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<Highlight, Highlight, Highlight>>, [undefined]>;
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Feature, Feature, Feature>>, [undefined]>;
+    selection: import("@jbrowse/mobx-state-tree").IType<MsaSelection | undefined, MsaSelection | undefined, MsaSelection | undefined>;
+    region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
+    clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Clade, Clade, Clade>>, [undefined]>;
+    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Encoding, Encoding, Encoding>>, [undefined]>;
+    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<RowPanelSpec, RowPanelSpec, RowPanelSpec>>, [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 | undefined): void;
+    setTreeWidth(n: number | undefined): void;
+    setLabelsAlignRight(arg: boolean): void;
+    setDrawTree(arg: boolean): void;
+    setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: TreeOrder): void;
+    setDrawNodeBubbles(arg: boolean): void;
+    setDrawNodeLabels(arg: boolean): void;
+    setShowTreeOverview(arg: boolean): void;
+    setDrawLabels(arg: boolean): void;
+} & {
+    setColorSchemeName(name: string): void;
+    setCustomColorScheme(map?: Record<string, string>): void;
+    setBgColor(arg: boolean): void;
+    setShowColumnStats(arg: boolean): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+} & {
+    headerHeight: number;
+    hideHeader: boolean;
+    importForm: boolean;
+    status: {
+        msg: 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;
+    transientHighlights: Record<string, Highlight[]>;
+    minimapHeight: number;
+    marginLeft: number;
+    error: unknown;
+    loadWarnings: string[];
+    dismissedWarnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
+    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;
+    addWarning(warning: string): void;
+    setHostCarriesData(arg: boolean): void;
+    setMousePos(col?: number, row?: number): void;
+    setHighlightedColumns(columns?: number[]): void;
+    setRegion(region?: Region): void;
+    setHighlights(highlights: Highlight[]): void;
+    setFeatures(features: Feature[]): void;
+    setSelection(selection?: MsaSelection): void;
+    clearSelection(): void;
+    setClades(clades: Clade[]): void;
+    applyHighlight(owner: string, highlights: Highlight[]): void;
+    clearHighlight(owner: string): 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;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: TreeRoot): void;
+    setShowOnly(node?: string): void;
+    setData(data: {
+        msa?: string;
+        tree?: string;
+        treeMetadata?: string;
+        gff?: string;
+    }): void;
+    setMSAFilehandle(msaFilehandle?: FileLocationType): void;
+    setTreeFilehandle(treeFilehandle?: FileLocationType): void;
+    setTreeMetadataFilehandle(treeMetadataFilehandle?: FileLocationType): void;
+    setGFFFilehandle(gffFilehandle?: FileLocationType): void;
+    setMSA(result: string): void;
+    setTree(result: string): void;
+    setTreeMetadata(result: string): void;
+    setGFF(result?: string): void;
+} & {
+    readonly hideGapsEffective: boolean;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
+    readonly viewInitialized: boolean;
+    readonly width: number;
+} & {
+    readonly colorScheme: Record<string, string>;
+    readonly dynamicColorSchemeName: string | undefined;
+    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;
+    readonly unshareableData: import("../types.ts").UnshareableData[];
+    menuItems(): never[];
+    readonly rowData: Record<string, Record<string, string> | undefined>;
+    rowDataOf(name: string): Record<string, string> | undefined;
+    readonly rowFields: string[];
+    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly numColumns: number;
+    readonly inputTree: import("../types.ts").NodeWithIds;
+    readonly tree: import("../types.ts").NodeWithIds;
+    readonly rowNames: string[];
+    readonly rowNamesSet: Map<string, number>;
+    readonly resolvedClades: import("../types.ts").ResolvedClade[];
+    readonly cladeGutterWidth: number;
+    readonly treeDrawn: boolean;
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    readonly maxTipLabelWidth: number;
+    readonly labelColumnWidth: number;
+    readonly fittedTreeAreaWidth: number;
+    readonly effectiveTreeAreaWidth: number;
+    readonly effectiveTreeWidth: number;
+    readonly showTreeText: boolean;
+    readonly mouseOverRowName: string | undefined;
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
+    readonly root: import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIds>;
+    readonly treeNewick: string;
+    readonly treeOverviewHeight: number;
+    readonly treeOverviewLayout: {
+        root: import("../hierarchy.ts").LaidOutNode<import("../types.ts").NodeWithIds>;
+        numTips: number;
+        maxDepthToLeaf: number;
+        showBranchLen: boolean;
+    } | undefined;
+    readonly treeOverviewClades: import("../types.ts").ResolvedClade[];
+    readonly treeOverviewFocusRows: [number, number] | undefined;
+    treeOverviewHit(y: number): {
+        id: string;
+        rows: [number, number];
+    } | undefined;
+    readonly rowPanelsWidth: number;
+    readonly rowPanelsHeaderHeight: 0 | 56;
+    readonly msaAreaWidth: number;
+    readonly treeAreaWidthMinusMargin: number;
+    readonly blanks: number[];
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
+    readonly rows: [string, string][];
+    readonly numRows: number;
+    seqPosIndex(rowName: string): Int32Array | undefined;
+    rowSequence(name: string): string | undefined;
+    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 treeLayout: {
+        root: import("../hierarchy.ts").LaidOutNode<import("../types.ts").NodeWithIds>;
+        leaves: import("../hierarchy.ts").LaidOutNode<import("../types.ts").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIds>;
+    readonly totalHeight: number;
+    readonly leaves: import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIds>[];
+    readonly rootToTipLength: number;
+    readonly pxPerBranchLength: number;
+    readonly maxDepthToLeaf: number;
+    readonly allBranchesLength0: boolean;
+    readonly showBranchLenEffective: boolean;
+} & {
+    readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+} & {
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("../types.ts").Arc[];
+    }>;
+    trackHeight(kind: import("../types.ts").TrackKind, heightKey?: string, given?: number): number;
+    columnTrackModel(track: ColumnTrackSpec): import("../types.ts").BasicTrack;
+    readonly columnTrackModels: import("../types.ts").BasicTrack[];
+} & {
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("../types.ts").Arc[] | undefined;
+    readonly adapterTrackModels: import("../types.ts").BasicTrack[];
+    readonly basePairTrackModels: import("../types.ts").BasicTrack[];
+    readonly computedTrackModels: 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;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    visibleSpan({ row, start: rawStart, end: rawEnd }: Region): {
+        startCol: number;
+        endCol: number;
+    } | undefined;
+    readonly residueMappingProblems: import("../types.ts").ResidueMappingProblem[];
+    readonly usableResidueMappings: ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("../types.ts").MappedStructure;
+    }[];
+    structureResidue(rowName: string, seqPos: number, structureId?: string): import("../types.ts").StructureResidue | undefined;
+    rowResidue(structureId: string, position: number, asymId?: string): import("../types.ts").RowResidue | undefined;
+} & {
+    readonly treeScaleBar: {
+        step: number;
+        px: number;
+        label: string;
+    } | undefined;
+    readonly topBandHeight: number;
+    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 dataInitialized: boolean;
+    readonly blocksX: number[];
+    readonly blocksY: number[];
+} & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
+    readonly blocks2d: (readonly [number, number])[];
+    readonly isLoading: boolean;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
+    readonly maxScrollY: number;
+    readonly wheelZoomAxis: import("../constants.ts").ScrollZoomAxis;
+} & {
+    setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
+    setScrollZoom(arg: boolean): void;
+    setScrollZoomAxis(arg: import("../constants.ts").ScrollZoomAxis): void;
+    setHoveredTreeNode(nodeId?: string): void;
+    calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
+    replaceTree(newick: string): void;
+    resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: import("../constants.ts").ScrollZoomAxis): void;
+    zoomIn(): void;
+    zoomOut(): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("../constants.ts").ScrollZoomAxis): void;
+    doScrollY(deltaY: number): void;
+    setScrollY(n: number): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
+    applyGFFText(gffText: string): void;
+    doScrollX(deltaX: number): void;
+    setScrollX(n: number): void;
+    setColumnTracks(tracks: ColumnTrackSpec[]): void;
+    setRowData(rowData: RowDataInput): void;
+    setEncodings(encodings: Encoding[]): void;
+    setRowPanels(panels: RowPanelSpec[]): void;
+    setResidueMappings(mappings: ResidueMapping[]): void;
+    toggleTrack(id: string): void;
+    setStatus(status?: {
+        msg: string;
+        onCancel?: () => void;
+    }): void;
+} & {
+    cellAt(visibleCol: number, rowIndex?: number): Cell;
+    readonly hoveredCell: Cell | undefined;
+    readonly clickedCell: Cell | undefined;
+    readonly viewport: Viewport | undefined;
+    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
+    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
+    readonly fillPalette: {
+        [x: string]: string;
+    };
+    readonly featureFillEncoding: import("../types.ts").ResolvedEncoding | undefined;
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
+    readonly segmentLabels: Map<string, string>;
+    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly legends: import("../types.ts").Legend[];
+    readonly domainUnderline: boolean;
+    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;
+    }[];
+    fillHighlightLabel(label: string, row?: string, start?: number): string;
+    readonly resolvedHighlights: import("../types.ts").ResolvedHighlight[];
+    readonly resolvedSelection: import("../types.ts").ResolvedSelection | undefined;
+    readonly selectionSize: {
+        columns: number;
+        rows: number;
+    } | undefined;
+    readonly selectionFileSpan: {
+        start: number;
+        end: number;
+    } | undefined;
+    readonly selectionFasta: string;
+    columnStatsAt(col: number): import("../columnStats.ts").ColumnStats | undefined;
+    getRowData(name: string): {
+        data: {
+            name?: string;
+            accession?: string;
+            dbxref?: string;
+        } | undefined;
+        rowData: Record<string, string> | undefined;
+    };
+    readonly resolvedEncodings: import("../types.ts").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        legend: import("../types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'strip';
+        field: string;
+        colors: Map<string, string>;
+    } | {
+        header: string;
+        legend: import("../types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'features';
+        x: 'column' | 'position';
+        field?: string;
+        colors: Map<import("msa-parsers").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        labels?: Map<import("msa-parsers").Annotation, string>;
+    })[];
+    readonly resolvedRowPanels: import("../types.ts").ResolvedRowPanel[];
+    readonly featureAlignShifts: Map<string, Map<string, number>>;
+    readonly tipLabelColors: Map<string, string> | undefined;
+    readonly rowTints: (string | undefined)[] | undefined;
+    readonly branchColors: Map<string, string> | undefined;
+} & {
+    setHeaderHeight(arg: number): void;
+    setHideHeader(arg: boolean): void;
+    setImportForm(arg: boolean): void;
+    treeOverviewClick(y: number): void;
+    setTrackHeight(heightKey: string, height: number): void;
+    reset(): void;
+    exportSVG(opts: import("../exportLayout.ts").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
+    setFilter(accession: string, shown: boolean): void;
+    fit(): void;
+    fitVertically(): void;
+    zoomToRegion(region: Region): void;
+    revealRegion(region: Region): void;
+    zoomToSelection(): void;
+    selectBlock(anchor: {
+        col: number;
+        row?: number;
+    }, head: {
+        col: number;
+        row?: number;
+    }): void;
+    fitHorizontally(): void;
+    afterCreate(): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+    bgColor: boolean;
+    colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
+    showColumnStats: boolean;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
+    showBranchLen: boolean;
+    treeOrder: TreeOrder;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    drawNodeLabels: boolean;
+    showTreeOverview: boolean;
+    overviewHeight: number;
+    columnTracks: ColumnTrackSpec[];
+    id: string;
+    showDomains: boolean;
+    showDomainLegend: boolean;
+    hideGaps: boolean;
+    allowedGappyness: number;
+    subFeatureRows: boolean;
+    type: "MsaView";
+    drawMsaLetters: boolean;
+    scrollZoom: boolean;
+    scrollZoomAxis: "both" | "horizontal" | "vertical";
+    height: number;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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[];
+    rotated: string[];
+    treeRoot: TreeRoot | undefined;
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    trackHeights: import("mobx").IKeyValueMap<number>;
+    residueMappings: ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
+    relativeTo: string | undefined;
+    highlightColumns: number[] | undefined;
+    highlights: Highlight[];
+    features: Feature[];
+    selection: MsaSelection | undefined;
+    region: Region | undefined;
+    clades: Clade[];
+    encodings: Encoding[];
+    rowPanels: RowPanelSpec[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+} | {
+    bgColor: boolean;
+    colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
+    showColumnStats: boolean;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
+    showBranchLen: boolean;
+    treeOrder: TreeOrder;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    drawNodeLabels: boolean;
+    showTreeOverview: boolean;
+    overviewHeight: number;
+    columnTracks?: undefined;
+    id: string;
+    showDomains: boolean;
+    showDomainLegend: boolean;
+    hideGaps: boolean;
+    allowedGappyness: number;
+    subFeatureRows: boolean;
+    type: "MsaView";
+    drawMsaLetters: boolean;
+    scrollZoom: boolean;
+    scrollZoomAxis: "both" | "horizontal" | "vertical";
+    height: number;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"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").ILiteralType<"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[];
+    rotated: string[];
+    treeRoot: TreeRoot | undefined;
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    trackHeights: import("mobx").IKeyValueMap<number>;
+    residueMappings: ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
+    relativeTo: string | undefined;
+    highlightColumns: number[] | undefined;
+    highlights: Highlight[];
+    features: Feature[];
+    selection: MsaSelection | undefined;
+    region: Region | undefined;
+    clades: Clade[];
+    encodings: Encoding[];
+    rowPanels: RowPanelSpec[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+}>>>>;
+export default MSAViewer;