react-msaview 5.4.1 → 5.6.0

package/dist/model.d.ts

@@ -6,6 +6,14 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
 /**
  * #stateModel MsaView
+ *
+ * The main MSAView state model. Holds the loaded alignment, tree, and optional
+ * InterProScan domain annotations, plus all display state (color scheme, zoom,
+ * scroll, collapsed clades). It composes in members from `DialogQueueSessionMixin`,
+ * `Tree`, and `MSAModel` (see Inherited members below). Data is loaded reactively
+ * from the `msaFilehandle` / `treeFilehandle` / `gffFilehandle` properties, or set
+ * directly with `setData`. Most state is persisted into the shareable URL.
+ *
  * #example
  * ```js
  * import { MSAModelF } from 'react-msaview'
@@ -16,41 +24,109 @@ import type { Theme } from '@mui/material';
  * root.view.setData({ msa: '>seq1\nACGT\n>seq2\nACGT' })
  * ```
  */
-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>;
+declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "autoTreeAreaWidth"> & {
+    drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "bgColor" | "colorSchemeName" | "msaFormat"> & {
-    bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "bgColor" | "colorSchemeName" | "showColumnStats" | "msaFormat"> & {
+    bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
+}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "height" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "currentAlignment" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
+    /**
+     * #property
+     * id of view, randomly generated if not provided
+     */
     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>;
+    /**
+     * #property
+     */
+    showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     */
+    hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     */
+    allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     */
+    subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * hardcoded view type
+     */
     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>;
+    /**
+     * #property
+     */
+    drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * zoom in/out on plain mouse-wheel without holding ctrl
+     */
+    scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * height of the div containing the view, px
+     */
     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, {
+    /**
+     * #property
+     * height of each row, px
+     */
+    rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     * scroll position, Y-offset, px
+     */
+    scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     * scroll position, X-offset, px
+     */
+    scrollX: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     * width of columns, px
+     */
+    colWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     * filehandle object for the tree
+     */
+    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").ModelSnapshotType<{
-            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
         }> | undefined;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -58,11 +134,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
@@ -70,7 +142,90 @@ 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;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    }, ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>) | ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>)>, 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>>;
+    /**
+     * #property
+     * filehandle object for the MSA (which could contain a tree e.g. with
+     * stockholm files)
+     */
+    msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -78,11 +233,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
@@ -90,7 +241,89 @@ 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;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    }, ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>) | ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>)>, 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>>;
+    /**
+     * #property
+     * filehandle object for tree metadata
+     */
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -98,11 +331,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
@@ -110,7 +339,89 @@ 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;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    }, ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>) | ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>)>, 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>>;
+    /**
+     * #property
+     * filehandle object for InterProScan GFF file
+     */
+    gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -118,14 +429,94 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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>>;
+    }> | {
+        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;
+    }, ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>) | ({
+        blobId: string;
+        locationType: "BlobLocation";
+        name: string;
+    } & Partial<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }>) | ({
+        handleId: string;
+        locationType: "FileHandleLocation";
+        name: string;
+    } & Partial<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }>) | ({
+        localPath: string;
+        locationType: "LocalPathLocation";
+    } & Partial<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }>)>, 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>>;
+    /**
+     * #property
+     */
+    currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     * array of tree parent nodes that are 'collapsed' (all children are
+     * hidden)
+     */
+    collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    /**
+     * #property
+     * focus on particular subtree
+     */
     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>>;
+    /**
+     * #property
+     * turned off tracks
+     */
+    turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    /**
+     * #property
+     * data from the loaded tree/msa/treeMetadata, generally loaded by
+     * autorun
+     */
     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>>;
@@ -142,8 +533,22 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         treeMetadata: string | undefined;
         gff: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    /**
+     * #property
+     */
+    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    /**
+     * #property
+     */
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     * declarative seed for the highlighted-columns overlay (visible column
+     * indices). Unlike the volatile `highlightedColumns` (driven by
+     * transient genome-hover sync), this persists in the snapshot/URL so a
+     * shared link can open with specific columns highlighted. Applied once
+     * in afterCreate.
+     */
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
@@ -158,12 +563,14 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setTreeWidth(n: number): void;
     setLabelsAlignRight(arg: boolean): void;
     setDrawTree(arg: boolean): void;
+    setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
+    setShowColumnStats(arg: boolean): void;
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     /**
@@ -263,10 +670,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
 } & {
     /**
      * #action
+     * draw the alignment with positions numbered relative to the given row's
+     * sequence (its node id), instead of in raw MSA-column coordinates
      */
     drawRelativeTo(id: string | undefined): void;
     /**
      * #action
+     * hide columns that are entirely (or mostly, see allowedGappyness) gaps
      */
     setHideGaps(arg: boolean): void;
     /**
@@ -321,6 +731,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setHighlightedColumns(columns?: number[]): void;
     /**
      * #action
+     * toggle the InterProScan protein-domain overlay on the alignment
      */
     setShowDomains(arg: boolean): void;
     /**
@@ -354,14 +765,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setCurrentAlignment(n: number): void;
     /**
      * #action
+     * collapse or un-collapse the subtree rooted at the given tree node id
      */
     toggleCollapsed(node: string): void;
     /**
      * #action
+     * show only the subtree rooted at the given node id (pass undefined to
+     * show the whole tree again)
      */
     setShowOnly(node?: string): void;
     /**
      * #action
+     * set the alignment/tree/metadata/domain data directly from strings,
+     * bypassing the filehandle loaders
      */
     setData(data: {
         msa?: string;
@@ -576,6 +992,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * Returns values 0-1 where 1 = fully conserved, 0 = no conservation.
      */
     readonly conservation: number[];
+    /**
+     * #getter
+     * Per-column conservation of physicochemical property class (amino acids
+     * only). Surfaces conservative-substitution sites that identity-based
+     * conservation misses. Empty for nucleotide alignments.
+     */
+    readonly propertyConservation: number[];
     /**
      * #getter
      * generates a new tree that is clustered with x,y positions
@@ -675,6 +1098,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     calculateNeighborJoiningTreeFromMSA(): void;
     /**
      * #action
+     * restore the default column width and row height
      */
     resetZoom(): void;
     /**
@@ -853,32 +1277,40 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[]>;
 } & {
     /**
@@ -890,12 +1322,99 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly verticalScrollbarWidth: 0 | 20;
+    /**
+     * #getter
+     * ordinal segment types (exons etc.), ordered by sequence position so
+     * exon-1..exon-14 read left-to-right; colored by alternating shade and
+     * labeled by number rather than each getting a distinct hue + legend row
+     */
+    readonly segmentDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    /**
+     * #getter
+     * categorical feature types (InterPro domains and the like) that each get
+     * their own color and a legend entry
+     */
+    readonly categoricalDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     readonly fillPalette: {
-        [k: string]: string;
+        [x: string]: string;
     };
     readonly strokePalette: {
         [k: string]: string;
     };
+    /**
+     * #getter
+     * accession -> number drawn on each segment band: the trailing number of
+     * the feature name ("exon-3" -> "3"), else its 1-based position
+     */
+    readonly segmentLabels: Map<string, string>;
+    /**
+     * #getter
+     * the domain types currently drawn on the alignment (filtered-on), shared
+     * by the on-screen legend and the SVG export legend. Ordinal segments
+     * (exons) are excluded — they read as a numbered gene model, not a color
+     * key — so this is the categorical types ordered by sequence position
+     */
+    readonly visibleDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    /**
+     * #getter
+     * domain annotations under the mouse, hit-tested against the exact visible
+     * column span each box is drawn at (so it matches the overlay across gaps)
+     */
+    readonly mouseOverDomains: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    /**
+     * #getter
+     * per-column summary statistics for the hovered column: consensus residue
+     * and its identity fraction, conservation score, gap fraction, and the
+     * sorted non-gap residue distribution. undefined when nothing is hovered.
+     */
+    readonly mouseOverColumnStats: {
+        col: number;
+        total: number;
+        gaps: number;
+        gapFraction: number;
+        conservation: number;
+        propertyConservation: number | undefined;
+        consensusLetter: string;
+        consensusCount: number;
+        consensusFraction: number;
+        distribution: [string, number][];
+    } | undefined;
     /**
      * #method
      */
@@ -944,41 +1463,41 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     fitHorizontally(): void;
     afterCreate(): void;
-}, 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" | "msaFormat"> & {
-    bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
-    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
-    drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
-        locationType: "UriLocation";
-        uri: string;
-        internetAccountId: string | undefined;
-        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").ModelSnapshotType<{
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+    data: {
+        treeMetadata?: string | undefined;
+        msa?: string | undefined;
+        tree?: string | undefined;
+    };
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number;
+    treeWidth: number;
+    showBranchLen: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    autoTreeAreaWidth: boolean;
+    bgColor: boolean;
+    colorSchemeName: string;
+    showColumnStats: boolean;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    id: string;
+    showDomains: boolean;
+    hideGaps: boolean;
+    allowedGappyness: number;
+    subFeatureRows: boolean;
+    type: "MsaView";
+    drawMsaLetters: boolean;
+    scrollZoom: boolean;
+    height: number;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -986,11 +1505,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
@@ -998,7 +1513,11 @@ 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;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    } | undefined;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -1006,11 +1525,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
@@ -1018,7 +1533,11 @@ 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;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    } | undefined;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -1026,11 +1545,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
@@ -1038,7 +1553,11 @@ 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;
-    } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    } | undefined;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
         locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -1046,34 +1565,23 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         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;
-    }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
-    relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
-}>, symbol>>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    currentAlignment: number;
+    collapsed: string[];
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    relativeTo: string | undefined;
+    highlightColumns: number[] | undefined;
+}>;
 export default stateModelFactory;
 export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type MsaViewModel = Instance<MsaViewStateModel>;