jbrowse-plugin-msaview 2.2.3 → 2.2.5

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,8 @@
+import type { StructureConnection } from './structureConnection';
+import type { MafRegion, MsaViewInitState } from './types';
 import type { Feature } from '@jbrowse/core/util';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { Instance } from 'mobx-state-tree';
 type LGV = LinearGenomeViewModel;
 type MaybeLGV = LGV | undefined;
 export interface IRegion {
@@ -13,7 +15,7 @@ export interface BlastParams {
     blastDatabase: string;
     msaAlgorithm: string;
     blastProgram: string;
-    selectedTranscript: Feature;
+    selectedTranscript?: Feature;
     proteinSequence: string;
 }
 /**
@@ -21,220 +23,324 @@ export interface BlastParams {
  * extends
  * - MSAModel from https://github.com/GMOD/react-msaview
  */
-export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
-    drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-} & {
-    bgColor: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
-} & {
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
-    contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    type: import("mobx-state-tree").ISimpleType<"MsaView">;
-    drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
-    scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
-    scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
-    colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
-    treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
-        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    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]>;
+    treeWidthMatchesArea: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+} & {
+    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>;
+    contrastLettering: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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>;
+    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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }>>, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        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("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }>, import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+    } | 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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
-    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
-        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
-        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }>>, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        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("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }>, import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+    } | 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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
-    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
-        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    treeMetadataFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
-        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }>>, {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        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("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }>, import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+    } | 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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
-    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
-        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
-    collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
-    collapsedLeaves: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
-    showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
-    data: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: 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").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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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>>;
+    collapsedLeaves: 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>>;
     }, {
         setTree(tree?: string): void;
         setMSA(msa?: string): void;
         setTreeMetadata(treeMetadata?: string): void;
-    }, import("mobx-state-tree")._NotCustomized, {
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         tree: string | undefined;
         msa: string | undefined;
         treeMetadata: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
-    relativeTo: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    connectedFeature: import("mobx-state-tree").IType<any, any, any>;
-    connectedHighlights: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        refName: import("mobx-state-tree").ISimpleType<string>;
-        start: import("mobx-state-tree").ISimpleType<number>;
-        end: import("mobx-state-tree").ISimpleType<number>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    blastParams: import("mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
-    querySeqName: import("mobx-state-tree").IType<string | undefined, string, string>;
-    zoomToBaseLevel: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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>>;
+} & {
+    connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+    connectedHighlights: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+        refName: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        start: import("@jbrowse/mobx-state-tree").ISimpleType<number>;
+        end: import("@jbrowse/mobx-state-tree").ISimpleType<number>;
+    }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
+    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
+    connectedStructures: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<StructureConnection, StructureConnection, StructureConnection>>;
+    dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
 }, {
     width: number;
 } & {
@@ -284,15 +390,17 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         nodeId: string;
         descendantNames: string[];
     } | undefined;
+    highlightedColumns: number[] | undefined;
     nref: number;
     minimapHeight: number;
+    conservationTrackHeight: number;
     marginLeft: number;
     error: unknown;
     annotPos: {
         left: number;
         right: number;
     } | undefined;
-    interProAnnotations: undefined | Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>;
+    interProAnnotations: undefined | Record<string, import("react-msaview").InterProScanResults>;
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -306,6 +414,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setError(error?: unknown): void;
     setMousePos(col?: number, row?: number): void;
     setHoveredTreeNode(nodeId?: string): void;
+    setHighlightedColumns(columns?: number[]): void;
     setShowDomains(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
@@ -314,7 +423,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setScrollY(n: number): void;
     setCurrentAlignment(n: number): void;
     toggleCollapsed(node: string): void;
-    toggleCollapsed2(node: string): void;
+    toggleCollapsedLeaf(node: string): void;
     setShowOnly(node?: string): void;
     setData(data: {
         msa?: string;
@@ -323,10 +432,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     }): void;
     setMSAFilehandle(msaFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setTreeFilehandle(treeFilehandle?: import("@jbrowse/core/util").FileLocation): void;
+    setGFFFilehandle(gffFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
 } & {
+    readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
     readonly actuallyShowDomains: boolean;
     readonly viewInitialized: boolean;
@@ -340,16 +451,25 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly noDomains: boolean;
     menuItems(): never[];
     readonly treeMetadata: any;
-    readonly MSA: import("react-msaview/dist/parsers/StockholmMSA").default | import("react-msaview/dist/parsers/FastaMSA").default | import("react-msaview/dist/parsers/EmfMSA").default | import("react-msaview/dist/parsers/ClustalMSA").default | null;
+    readonly MSA: import("msa-parsers").StockholmMSA | import("msa-parsers").A3mMSA | import("msa-parsers").FastaMSA | import("msa-parsers").EmfMSA | import("msa-parsers").ClustalMSA | null;
     readonly numColumns: number;
-    readonly tree: import("react-msaview/dist/types").NodeWithIds;
+    readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
     readonly mouseOverRowName: string | undefined;
-    readonly root: HierarchyNode<import("react-msaview/dist/types").NodeWithIds>;
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
+    readonly root: HierarchyNode<import("react-msaview").NodeWithIds>;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
     readonly blanksSet: Set<number>;
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
     readonly rowMap: Map<string, string>;
@@ -360,10 +480,18 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly fontSize: number;
     readonly colStats: Record<string, number>[];
     readonly colStatsSums: number[];
-    readonly hierarchy: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>;
+    readonly sequenceType: "dna" | "rna" | "amino";
+    readonly colConsensus: {
+        letter: string;
+        color: string | undefined;
+    }[];
+    readonly colClustalX: Record<string, string>[];
+    readonly conservation: number[];
+    readonly hierarchy: HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
     readonly totalHeight: number;
-    readonly leaves: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>[];
+    readonly leaves: HierarchyNode<import("react-msaview").NodeWithIdsAndLength>[];
     readonly allBranchesLength0: boolean;
+    readonly showBranchLenEffective: boolean;
 } & {
     readonly totalWidth: number;
 } & {
@@ -378,6 +506,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly showTreeText: boolean;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    calculateNeighborJoiningTreeFromMSA(): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -385,7 +514,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
-    setInterProAnnotations(data: Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>): void;
+    setInterProAnnotations(data: Record<string, import("react-msaview").InterProScanResults>): void;
     doScrollY(deltaY: number): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -398,20 +527,21 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
-    readonly conservation: string[];
-    readonly adapterTrackModels: import("react-msaview/dist/types").BasicTrack[];
-    readonly tracks: import("react-msaview/dist/types").BasicTrack[];
-    readonly turnedOnTracks: import("react-msaview/dist/types").ITextTrack[];
+    readonly adapterTrackModels: import("react-msaview").BasicTrack[];
+    readonly tracks: import("react-msaview").BasicTrack[];
+    readonly turnedOnTracks: import("react-msaview").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
     readonly rowNamesSet: Map<string, number>;
-    mouseOverCoordToRowLetter(rowName: string, pos: number): string | undefined;
-    mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
-    mouseOverCoordToGapRemovedRowCoordOneBased(rowName: string, position: number): number | undefined;
-    seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview/dist/types").Accession>;
+    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview").Accession>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
@@ -440,7 +570,9 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
-    readonly fillPalette: Record<string, string>;
+    readonly fillPalette: {
+        [k: string]: string;
+    };
     readonly strokePalette: {
         [k: string]: string;
     };
@@ -454,10 +586,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     };
 } & {
     setHeaderHeight(arg: number): void;
+    setConservationTrackHeight(arg: number): void;
     reset(): void;
     exportSVG(opts: {
         theme: import("@mui/material").Theme;
         includeMinimap?: boolean;
+        includeTracks?: boolean;
         exportType: string;
     }): Promise<void>;
     incrementRef(): void;
@@ -480,11 +614,22 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
      * #volatile
      */
     error: unknown;
+    /**
+     * #volatile
+     * True when loading MSA data from IndexedDB
+     */
+    loadingStoredData: boolean;
 } & {
     /**
      * #method
+     * Get a row by name, returns [name, sequence] or undefined
+     */
+    getRowByName(rowName: string): [string, string] | undefined;
+    /**
+     * #method
+     * Get the sequence for a row by name
      */
-    ungappedCoordMap(rowName: string, position: number): number | undefined;
+    getSequenceByRowName(rowName: string): string | undefined;
 } & {
     /**
      * #getter
@@ -495,24 +640,40 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         refName: string;
         strand: number;
     } | undefined;
-} & {
     /**
      * #getter
      */
-    readonly mouseCol2: number | undefined;
+    readonly processing: boolean;
     /**
      * #getter
      */
-    readonly clickCol2: undefined;
+    readonly connectedView: MaybeLGV;
+    /**
+     * #getter
+     * Get connected protein views with their full model references
+     */
+    readonly connectedProteinViews: (StructureConnection & {
+        proteinView: any;
+    })[];
 } & {
     /**
      * #getter
+     * Get the MSA column that corresponds to the currently hovered structure position
+     * Returns the first match from any connected structure
      */
-    readonly processing: boolean;
+    readonly structureHoverCol: number | undefined;
+} & {
     /**
      * #getter
+     * Returns a secondary highlight column from either:
+     * 1. Structure hover (from connected protein 3D view)
+     * 2. Genome hover (from connected linear genome view)
      */
-    readonly connectedView: MaybeLGV;
+    readonly mouseCol2: number | undefined;
+    /**
+     * #getter
+     */
+    readonly clickCol2: undefined;
 } & {
     /**
      * #action
@@ -546,10 +707,49 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
      * #action
      */
     setBlastParams(args?: BlastParams): void;
+    /**
+     * #action
+     */
+    setInit(arg?: MsaViewInitState): void;
+    /**
+     * #action
+     */
+    setQuerySeqName(arg: string): void;
+    /**
+     * #action
+     */
+    setUniprotId(arg?: string): void;
+    /**
+     * #action
+     */
+    setDataStoreId(arg?: string): void;
+    /**
+     * #action
+     */
+    setMafRegion(arg?: MafRegion): void;
+    /**
+     * #action
+     */
+    setLoadingStoredData(arg: boolean): void;
     /**
      * #action
      */
     handleMsaClick(coord: number): void;
+    /**
+     * #action
+     * Connect to a protein structure for synchronized highlighting
+     */
+    connectToStructure(proteinViewId: string, structureIdx: number, msaRowName?: string): void;
+    /**
+     * #action
+     * Disconnect from a protein structure
+     */
+    disconnectFromStructure(proteinViewId: string, structureIdx: number): void;
+    /**
+     * #action
+     * Disconnect from all protein structures
+     */
+    disconnectAllStructures(): void;
 } & {
     /**
      * #action
@@ -561,29 +761,322 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
      * #method
      * overrides base
      */
-    extraViewMenuItems(): {
+    extraViewMenuItems(): ({
         label: string;
         checked: boolean;
         type: string;
         onClick: () => void;
-    }[];
-    /**
-     * #getter
-     */
-    readonly processing: boolean;
-    /**
-     * #getter
-     */
-    readonly connectedView: MaybeLGV;
+    } | {
+        label: string;
+        onClick: () => void;
+        checked?: undefined;
+        type?: undefined;
+    })[];
 } & {
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, {
-    data: {
-        treeMetadata?: string | undefined;
-        msa?: string | undefined;
-        tree?: string | undefined;
-    };
-} & import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+    id: string;
+    displayName: string | undefined;
+    minimized: boolean;
+} & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    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]>;
+    treeWidthMatchesArea: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+} & {
+    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>;
+    contrastLettering: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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>;
+    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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: 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").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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: 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").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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: 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").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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: 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").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>;
+    }>, import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+        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").ModelInstanceType<{
+        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").ModelInstanceType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"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/mobx-state-tree/dist/internal").NonEmptyObject)>, 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>>;
+    collapsedLeaves: 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>>;
+    }, {
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
+        setTreeMetadata(treeMetadata?: string): void;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+        tree: string | undefined;
+        msa: string | undefined;
+        treeMetadata: 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>>;
+}>, symbol> & import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
-export {};
+export { type MafRegion, type MsaViewInitState } from './types';