react-msaview 5.1.1 → 5.2.1

package/dist/model.d.ts

@@ -6,12 +6,17 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
 /**
  * #stateModel MsaView
- * extends
- * - [DialogQueueSessionMixin](../dialogqueuesessionmixin)
- * - [MSAModel](../msamodel)
- * - [Tree](../tree)
+ * #example
+ * ```js
+ * import { MSAModelF } from 'react-msaview'
+ * import { types } from '@jbrowse/mobx-state-tree'
+ *
+ * const RootModel = types.model({ view: types.optional(MSAModelF(), {}) })
+ * const root = RootModel.create({})
+ * root.view.setData({ msa: '>seq1\nACGT\n>seq2\nACGT' })
+ * ```
  */
-declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
+declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -19,10 +24,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
+}, "bgColor" | "colorSchemeName"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-} & {
+}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -30,6 +35,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
@@ -43,18 +49,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
@@ -63,18 +69,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
@@ -83,18 +89,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
@@ -103,18 +109,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -172,7 +178,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #volatile
      * high resolution scale factor, helps make canvas look better on hi-dpi
-     * screens
+     * screens. derived from the device pixel ratio so canvases are crisp on
+     * retina/4k displays and not needlessly oversized on standard ones
      */
     highResScaleFactor: number;
     /**
@@ -230,12 +237,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * array of column indices to highlight
      */
     highlightedColumns: number[] | undefined;
-    /**
-     * #volatile
-     * a dummy variable that is incremented when ref changes so autorun for
-     * drawing canvas commands will run
-     */
-    nref: number;
     /**
      * #volatile
      */
@@ -281,6 +282,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setWidth(arg: number): void;
+    /**
+     * #action
+     * high-res scale factor, tracks the device pixel ratio so canvases stay
+     * crisp when the window moves between monitors or the browser zooms
+     */
+    setHighResScaleFactor(arg: number): void;
     /**
      * #action
      * set the height of the view in px
@@ -294,16 +301,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #action
      * set mouse position (row, column) in the MSA
+     *
+     * CROSS-REPO CONTRACT: jbrowse-plugin-protein3d calls this (and reads the
+     * `mouseCol` volatile) to sync MSA<->3D-structure hover. Keep the name and
+     * signature stable; see that repo's ProteinToMsaHoverSync.tsx.
      */
     setMousePos(col?: number, row?: number): void;
-    /**
-     * #action
-     * set hovered tree node and its descendants
-     */
-    setHoveredTreeNode(nodeId?: string): void;
     /**
      * #action
      * set highlighted columns
+     *
+     * CROSS-REPO CONTRACT: called by jbrowse-plugin-msaview
+     * (afterCreateAutoruns.ts) to highlight alignment columns. It has no
+     * in-repo caller, so do not flag it as dead code — it is public API.
      */
     setHighlightedColumns(columns?: number[]): void;
     /**
@@ -412,7 +422,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly header: Record<string, unknown>;
+    readonly header: Record<string, unknown> | {
+        info: string;
+        version: string | undefined;
+    } | {
+        General: Record<string, string[]>;
+        Accessions: {
+            [k: string]: string | undefined;
+        };
+        Dbxref: {
+            [k: string]: string;
+        };
+    };
     /**
      * #getter
      */
@@ -441,8 +462,14 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     readonly tree: NodeWithIds;
     /**
      * #getter
+     * Returns the list of row (sequence) names in display order.
+     * Part of the public API used by downstream consumers (e.g. jbrowse plugins).
      */
     readonly rowNames: string[];
+    /**
+     * #getter
+     */
+    readonly rowNamesSet: Map<string, number>;
     /**
      * #getter
      */
@@ -500,9 +527,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly columns: {
-        [k: string]: string;
-    };
+    readonly columns: Map<string, string>;
     /**
      * #getter
      */
@@ -589,7 +614,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly dataInitialized: boolean | "" | undefined;
+    readonly dataInitialized: boolean;
     /**
      * #getter
      */
@@ -611,6 +636,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly maxScrollX: number;
+    /**
+     * #getter
+     * most-negative allowed scrollY, keeping the last row in view rather than
+     * letting the whole alignment scroll off the top. visible MSA height is
+     * computed inline here because msaAreaHeight is defined later in the chain.
+     */
+    readonly maxScrollY: number;
     /**
      * #getter
      */
@@ -624,6 +656,15 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     */
+    setScrollZoom(arg: boolean): void;
+    /**
+     * #action
+     * set hovered tree node and its descendants
+     */
+    setHoveredTreeNode(nodeId?: string): void;
     /**
      * #action
      * Calculate a neighbor joining tree from the current MSA using BLOSUM62 distances
@@ -657,11 +698,28 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     zoomOut(): void;
+    /**
+     * #action
+     * Smoothly zoom by a continuous scaleFactor. The column under the cursor
+     * (offsetX/offsetY, px relative to the MSA area) stays anchored
+     * horizontally. Vertically the anchor is biased toward the top: when the
+     * alignment nearly fits the viewport, snap to y=0 rather than pinning a
+     * random row under the cursor, with the bias fading out as the alignment
+     * grows taller than the viewport (where cursor-anchoring is useful).
+     * Drives wheel/trackpad-pinch zoom.
+     */
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
     /**
      * #action
      */
     doScrollY(deltaY: number): void;
-    setInterProAnnotations(data: Record<string, InterProScanResults>): void;
+    /**
+     * #action
+     * Set domain annotations and reveal the overlay in a single step (or clear
+     * both when passed undefined). Shared by every domain source: InterProScan,
+     * GFF, user-provided uploads, and NCBI CDD.
+     */
+    setDomains(data?: Record<string, InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     /**
      * #action
@@ -687,6 +745,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
+    readonly labelWidthMap: Map<string, number>;
     readonly labelsWidth: number;
     /**
      * #getter
@@ -712,10 +771,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly showHorizontalScrollbar: boolean;
-    /**
-     * #getter
-     */
-    readonly rowNamesSet: Map<string, number>;
     /**
      * #method
      * Return a row-specific letter at a visible column, or undefined if gap.
@@ -730,6 +785,11 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * Convert a visible column to a row-specific sequence position (0-based).
      * Returns undefined if the position is a gap in the sequence.
      *
+     * CROSS-REPO CONTRACT: this and the sibling coordinate converters
+     * (seqPosToVisibleCol, globalColToVisibleCol, seqPosToGlobalCol) are used
+     * by jbrowse-plugin-protein3d to translate between alignment columns and
+     * structure/sequence residue positions across gaps. Keep them stable.
+     *
      * @param rowName - The name of the row
      * @param visibleCol - The visible column index
      * @returns The sequence position (0-based), or undefined if it's a gap
@@ -775,16 +835,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
-    /**
-     * #getter
-     * Returns information about the currently hovered cell
-     */
-    readonly hoveredCell: {
-        rowName: string;
-        col: number;
-        base: string | undefined;
-        seqPos: number | undefined;
-    } | undefined;
     /**
      * #getter
      * widget width minus the tree area gives the space for the MSA
@@ -874,13 +924,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         theme: Theme;
         includeMinimap?: boolean;
         includeTracks?: boolean;
-        exportType: string;
+        exportType: "entire" | "viewport";
     }): Promise<void>;
-    /**
-     * #action
-     * internal, used for drawing to canvas
-     */
-    incrementRef(): void;
     initFilter(arg: string): void;
     setFilter(arg: string, flag: boolean): void;
     /**
@@ -896,29 +941,32 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     fitHorizontally(): void;
     afterCreate(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<{
-    drawLabels: boolean;
-    labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
-    showBranchLen: boolean;
-    drawTree: boolean;
-    drawNodeBubbles: boolean;
-    bgColor: boolean;
-    colorSchemeName: string;
-    id: string;
-    showDomains: boolean;
-    hideGaps: boolean;
-    allowedGappyness: number;
-    subFeatureRows: boolean;
-    type: "MsaView";
-    drawMsaLetters: boolean;
-    height: number;
-    rowHeight: number;
-    scrollY: number;
-    scrollX: number;
-    colWidth: number;
-    treeFilehandle: {
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
+    drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+}, "bgColor" | "colorSchemeName"> & {
+    bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo"> & {
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -926,19 +974,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    msaFilehandle: {
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -946,19 +994,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    treeMetadataFilehandle: {
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -966,19 +1014,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    gffFilehandle: {
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
@@ -986,31 +1034,41 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    } | {
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    } | {
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    } | {
-        locationType: "LocalPathLocation";
-        localPath: string;
-    } | undefined;
-    currentAlignment: number;
-    collapsed: string[];
-    showOnly: string | undefined;
-    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    data: {
+    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    }, {
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
+        setTreeMetadata(treeMetadata?: string): void;
+        setGFF(gff?: string): void;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         tree: string | undefined;
         msa: string | undefined;
         treeMetadata: string | undefined;
         gff: string | undefined;
-    };
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
-    relativeTo: string | undefined;
-}, symbol>>;
+    }>, [undefined]>;
+    featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+}>, symbol>>;
 export default stateModelFactory;
 export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type MsaViewModel = Instance<MsaViewStateModel>;