jbrowse-plugin-msaview 3.9.0 → 4.0.0

package/dist/MsaViewPanel/model.d.ts

@@ -111,24 +111,26 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
+}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats"> & {
+}, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
+}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -165,14 +167,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: any;
         }> | undefined;
     }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -183,41 +185,27 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    }, ({
-        blobId: string;
-        locationType: "BlobLocation";
-        name: string;
-    } & Partial<{
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    }>) | ({
-        handleId: string;
-        locationType: "FileHandleLocation";
-        name: string;
-    } & Partial<{
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    }>) | ({
-        localPath: string;
-        locationType: "LocalPathLocation";
-    } & Partial<{
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }>) | ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
     }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
@@ -259,14 +247,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: any;
         }> | undefined;
     }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -277,41 +265,27 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    }, ({
-        blobId: string;
-        locationType: "BlobLocation";
-        name: string;
-    } & Partial<{
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    }>) | ({
-        handleId: string;
-        locationType: "FileHandleLocation";
-        name: string;
-    } & Partial<{
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    }>) | ({
-        localPath: string;
-        locationType: "LocalPathLocation";
-    } & Partial<{
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }>) | ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
     }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
@@ -353,14 +327,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: any;
         }> | undefined;
     }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -371,41 +345,27 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    }, ({
-        blobId: string;
-        locationType: "BlobLocation";
-        name: string;
-    } & Partial<{
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    }>) | ({
-        handleId: string;
-        locationType: "FileHandleLocation";
-        name: string;
-    } & Partial<{
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    }>) | ({
-        localPath: string;
-        locationType: "LocalPathLocation";
-    } & Partial<{
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }>) | ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
     }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
@@ -447,14 +407,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: any;
         }> | undefined;
     }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -465,41 +425,27 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
-    }, ({
-        blobId: string;
-        locationType: "BlobLocation";
-        name: string;
-    } & Partial<{
-        locationType: "BlobLocation";
-        name: string;
-        blobId: string;
-    }>) | ({
-        handleId: string;
-        locationType: "FileHandleLocation";
-        name: string;
-    } & Partial<{
-        locationType: "FileHandleLocation";
-        name: string;
-        handleId: string;
-    }>) | ({
-        localPath: string;
-        locationType: "LocalPathLocation";
-    } & Partial<{
-        locationType: "LocalPathLocation";
-        localPath: string;
-    }>) | ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
     }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
@@ -522,6 +468,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
@@ -544,6 +492,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Highlight, import("react-msaview").Highlight, import("react-msaview").Highlight>>, [undefined]>;
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Feature, import("react-msaview").Feature, import("react-msaview").Feature>>, [undefined]>;
+    selection: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined>;
     region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
@@ -566,6 +516,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     width: number;
     bodyMounted: boolean;
 } & {
+    readonly rendersDisplays: boolean;
     readonly effectiveBodyMounted: boolean;
     menuItems(): MenuItem[];
     readonly ownTracks: import("@jbrowse/core/util").AbstractTrackModel[];
@@ -590,6 +541,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setDrawTree(arg: boolean): void;
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: import("react-msaview").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
@@ -597,9 +549,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
+    setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
 } & {
     headerHeight: number;
     hideHeader: boolean;
@@ -626,10 +579,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     minimapHeight: number;
     marginLeft: number;
     error: unknown;
-    warnings: string[];
+    loadWarnings: string[];
+    dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
-    annotations: import("msa-parsers").Annotation[];
+    annotations: import("react-msaview").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -641,12 +595,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setHeight(height: number): void;
     setError(error?: unknown): void;
     addWarning(warning: string): void;
-    clearWarnings(): void;
     setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setRegion(region?: import("react-msaview").Region): void;
     setHighlights(highlights: import("react-msaview").Highlight[]): void;
+    setFeatures(features: import("react-msaview").Feature[]): void;
+    setSelection(selection?: import("react-msaview").MsaSelection): void;
+    clearSelection(): void;
     setClades(clades: import("react-msaview").Clade[]): void;
     applyHighlight(owner: string, highlights: import("react-msaview").Highlight[]): void;
     clearHighlight(owner: string): void;
@@ -658,6 +614,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColWidth(n: number): void;
     setCurrentAlignment(n: number): void;
     toggleCollapsed(node: string): void;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: import("react-msaview").TreeRoot): void;
     setShowOnly(node?: string): void;
     setData(data: {
         msa?: string;
@@ -672,16 +631,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
-    setGFF(result: string): void;
+    setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
+    readonly allAnnotations: import("react-msaview").Annotation[];
     readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
     readonly colorScheme: Record<string, string>;
+    readonly dynamicColorSchemeName: string | undefined;
     readonly header: Record<string, unknown> | {
         info: string;
         version: string | undefined;
@@ -702,8 +663,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rowData: Record<string, Record<string, string> | undefined>;
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
-    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
+    readonly inputTree: import("react-msaview").NodeWithIds;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
@@ -716,6 +678,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         letters: string;
     } | undefined;
     readonly root: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
+    readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
         root: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
@@ -755,9 +718,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
-    readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
+    readonly treeLayout: {
+        root: import("react-msaview").LaidOutNode<import("react-msaview").NodeWithIds>;
+        leaves: import("react-msaview").LaidOutNode<import("react-msaview").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
     readonly totalHeight: number;
-    readonly leaves: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>[];
+    readonly leaves: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>[];
     readonly rootToTipLength: number;
     readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
@@ -783,7 +751,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly labelWidthScale: number;
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
     readonly secondaryStructureArcs: import("react-msaview").Arc[] | undefined;
     readonly adapterTrackModels: import("react-msaview").BasicTrack[];
     readonly basePairTrackModels: import("react-msaview").BasicTrack[];
@@ -797,6 +764,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     globalColToVisibleCol(globalCol: number): number | undefined;
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(rowName: string, seqPos: number): number | undefined;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
     visibleSpan({ row, start: rawStart, end: rawEnd }: import("react-msaview").Region): {
         startCol: number;
@@ -819,9 +787,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly topBandHeight: number;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
-    readonly filteredAnnotations: import("msa-parsers").Annotation[];
-    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+    readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
+    readonly filteredAnnotations: import("react-msaview").Annotation[];
+    readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
@@ -829,19 +797,26 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
-    readonly maxScrollX: number;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
     readonly maxScrollY: number;
     readonly wheelZoomAxis: "both" | "horizontal" | "vertical";
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
     setScrollZoom(arg: boolean): void;
     setScrollZoomAxis(arg: "both" | "horizontal" | "vertical"): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
     replaceTree(newick: string): void;
     resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: "both" | "horizontal" | "vertical"): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -851,13 +826,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: "both" | "horizontal" | "vertical"): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
-    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
-    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
+    setAnnotations(annotations: import("react-msaview").Annotation[]): void;
+    setDomains(data?: Record<string, import("react-msaview").InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
     setColumnTracks(tracks: import("react-msaview").ColumnTrackSpec[]): void;
-    setRowData(rowData: Record<string, Record<string, string>>): void;
+    setRowData(rowData: import("react-msaview").RowDataInput): void;
     setEncodings(encodings: import("react-msaview").Encoding[]): void;
     setRowPanels(panels: import("react-msaview").RowPanelSpec[]): void;
     setResidueMappings(mappings: import("react-msaview").ResidueMapping[]): void;
@@ -867,30 +842,28 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         onCancel?: () => void;
     }): void;
 } & {
-    readonly verticalScrollbarWidth: 0 | 20;
-    readonly msaCanvasWidth: number;
     cellAt(visibleCol: number, rowIndex?: number): import("react-msaview").Cell;
     readonly hoveredCell: import("react-msaview").Cell | undefined;
     readonly clickedCell: import("react-msaview").Cell | undefined;
     readonly viewport: import("react-msaview").Viewport | undefined;
-    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
-    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
+    readonly segmentDomainTypes: import("react-msaview").Annotation[];
+    readonly categoricalDomainTypes: import("react-msaview").Annotation[];
     readonly fillPalette: {
         [x: string]: string;
     };
     readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
-    readonly featureColors: Map<import("msa-parsers").Annotation, {
+    readonly featureColors: Map<import("react-msaview").Annotation, {
         fill: string;
         stroke: string;
     }>;
-    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
+    readonly featureLabels: Map<import("react-msaview").Annotation, string> | undefined;
     readonly segmentLabels: Map<string, string>;
-    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly visibleDomainTypes: import("react-msaview").Annotation[];
     readonly legends: import("react-msaview").Legend[];
     readonly domainUnderline: boolean;
     readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
     readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
-    readonly mouseOverDomains: import("msa-parsers").Annotation[];
+    readonly mouseOverDomains: import("react-msaview").Annotation[];
     readonly referenceRowIndex: number | undefined;
     readonly hoveredRowIndices: number[];
     readonly highlightedColumnRuns: {
@@ -899,6 +872,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }[];
     fillHighlightLabel(label: string, row?: string, start?: number): string;
     readonly resolvedHighlights: import("react-msaview").ResolvedHighlight[];
+    readonly resolvedSelection: import("react-msaview").ResolvedSelection | undefined;
+    readonly selectionSize: {
+        columns: number;
+        rows: number;
+    } | undefined;
+    readonly selectionFileSpan: {
+        start: number;
+        end: number;
+    } | undefined;
+    readonly selectionFasta: string;
     columnStatsAt(col: number): import("react-msaview").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
@@ -909,6 +892,26 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         rowData: Record<string, string> | undefined;
     };
     readonly resolvedEncodings: import("react-msaview").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        kind: "strip";
+        field: string;
+        colors: Map<string, string>;
+        legend: import("react-msaview").LegendEntry[];
+        legendTitle?: string | undefined;
+    } | {
+        header: string;
+        x: "column" | "position";
+        kind: "features";
+        field?: string | undefined;
+        colors: Map<import("react-msaview").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        legend: import("react-msaview").LegendEntry[];
+        legendTitle?: string | undefined;
+        labels?: Map<import("react-msaview").Annotation, string> | undefined;
+    })[];
     readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
     readonly tipLabelColors: Map<string, string> | undefined;
@@ -921,10 +924,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("react-msaview").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     zoomToRegion(region: import("react-msaview").Region): void;
+    zoomToSelection(): void;
+    selectBlock(anchor: {
+        col: number;
+        row?: number;
+    }, head: {
+        col: number;
+        row?: number;
+    }): void;
     fitHorizontally(): void;
     afterCreate(): void;
 } & {
@@ -1106,16 +1118,423 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     menuItems(): MenuItem[];
 } & {
     afterCreate(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, ({
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<{
+    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").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+    drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").TreeOrder>, [undefined]>;
+    drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
+    bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
+    showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
+}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
+    drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
+    height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    scrollX: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    colWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    }, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"UriLocation">;
+        uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        baseUri: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IModelType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }>>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "LocalPathLocation";
+        localPath: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "BlobLocation";
+        name: string;
+        blobId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "FileHandleLocation";
+        name: string;
+        handleId: string;
+    }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
+    }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined>;
+    showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping>>, [undefined]>;
+    data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    }, {
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
+        setTreeMetadata(treeMetadata?: string): void;
+        setGFF(gff?: string): void;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
+        [k: string]: string | undefined;
+    }>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Highlight, import("react-msaview").Highlight, import("react-msaview").Highlight>>, [undefined]>;
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Feature, import("react-msaview").Feature, import("react-msaview").Feature>>, [undefined]>;
+    selection: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined>;
+    region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
+    clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
+    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
+    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
+}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+    connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+    connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
+    orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
+    querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    querySeqOffset: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    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>;
+    dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
+}>, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
     bgColor: boolean;
     colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
     treeWidth: number;
     showBranchLen: boolean;
+    treeOrder: import("react-msaview").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
@@ -1139,14 +1558,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     scrollX: number;
     colWidth: number;
     treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1159,14 +1578,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         }> | undefined;
     } | undefined;
     msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1179,14 +1598,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         }> | undefined;
     } | undefined;
     treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1199,14 +1618,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         }> | undefined;
     } | undefined;
     gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1220,6 +1639,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     } | undefined;
     currentAlignment: number;
     collapsed: string[];
+    rotated: string[];
+    treeRoot: import("react-msaview").TreeRoot | undefined;
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
@@ -1228,6 +1649,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("react-msaview").Highlight[];
+    features: import("react-msaview").Feature[];
+    selection: import("react-msaview").MsaSelection | undefined;
     region: import("react-msaview").Region | undefined;
     clades: import("react-msaview").Clade[];
     encodings: import("react-msaview").Encoding[];
@@ -1238,16 +1661,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         treeMetadata?: string | undefined;
         gff?: string | undefined;
     };
-} & import("@jbrowse/mobx-state-tree")._NotCustomized) | ({
+} | {
     bgColor: boolean;
     colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
     treeWidth: number;
     showBranchLen: boolean;
+    treeOrder: import("react-msaview").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
@@ -1271,14 +1696,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     scrollX: number;
     colWidth: number;
     treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1291,14 +1716,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         }> | undefined;
     } | undefined;
     msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1311,14 +1736,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         }> | undefined;
     } | undefined;
     treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1331,14 +1756,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         }> | undefined;
     } | undefined;
     gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"LocalPathLocation">;
         localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"BlobLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        locationType: import("@jbrowse/mobx-state-tree").ILiteralType<"FileHandleLocation">;
         name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     }> | {
@@ -1352,6 +1777,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     } | undefined;
     currentAlignment: number;
     collapsed: string[];
+    rotated: string[];
+    treeRoot: import("react-msaview").TreeRoot | undefined;
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
@@ -1360,6 +1787,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("react-msaview").Highlight[];
+    features: import("react-msaview").Feature[];
+    selection: import("react-msaview").MsaSelection | undefined;
     region: import("react-msaview").Region | undefined;
     clades: import("react-msaview").Clade[];
     encodings: import("react-msaview").Encoding[];
@@ -1370,10 +1799,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         treeMetadata?: string | undefined;
         gff?: string | undefined;
     };
-} & import("@jbrowse/mobx-state-tree")._NotCustomized)>;
+})>;
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
 export { type MafRegion, type MsaViewInitState } from './types';
-export declare function isMsaView(view: {
-    type: string;
-}): view is JBrowsePluginMsaViewModel;