react-msaview 3.1.7 → 3.1.8

package/dist/model.d.ts

@@ -7,13 +7,11 @@ import { NodeWithIds, NodeWithIdsAndLength } from './util';
 import ClustalMSA from './parsers/ClustalMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
-export interface RowDetails {
-    [key: string]: unknown;
+import { InterProScanResults } from './launchInterProScan';
+interface Accession {
+    accession: string;
     name: string;
-    range?: {
-        start: number;
-        end: number;
-    };
+    description: string;
 }
 export interface BasicTrackModel {
     id: string;
@@ -21,63 +19,44 @@ export interface BasicTrackModel {
     associatedRowName?: string;
     height: number;
 }
-export interface Structure {
-    pdb: string;
-    startPos: number;
-    endPos: number;
-}
 export interface TextTrackModel extends BasicTrackModel {
     customColorScheme?: Record<string, string>;
     data: string;
 }
-export interface BoxTrackModel extends BasicTrackModel {
-    features: {
-        start: number;
-        end: number;
-    }[];
-}
 export interface ITextTrack {
     ReactComponent: React.FC<any>;
     model: TextTrackModel;
 }
-export interface IBoxTrack {
-    ReactComponent: React.FC<any>;
-    model: BoxTrackModel;
-}
-export type BasicTrack = IBoxTrack | ITextTrack;
-export type DialogComponentType = React.LazyExoticComponent<React.FC<any>> | React.FC<any>;
-declare const model: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+export type BasicTrack = ITextTrack;
+/**
+ * #stateModel MsaView
+ * extends
+ * - DialogQueueSessionMixin
+ * - MSAModel
+ * - Tree
+ */
+declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
+    drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 } & {
-    selectedStructures: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        structure: import("mobx-state-tree").IModelType<{
-            pdb: import("mobx-state-tree").ISimpleType<string>;
-            startPos: import("mobx-state-tree").ISimpleType<number>;
-            endPos: import("mobx-state-tree").ISimpleType<number>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    bgColor: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    featureMode: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
     height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
     scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
-    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
-    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    bgColor: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    highResScaleFactor: import("mobx-state-tree").IType<number | undefined, number, number>;
-    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
     treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -86,10 +65,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-         * #property
-         * filehandle object for the tree
-         */
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -101,10 +77,17 @@ declare const model: import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
+        /**
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
+         */
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
+        }> | undefined; /**
+         * #volatile
+         */
     } | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -117,11 +100,10 @@ declare const model: import("mobx-state-tree").IModelType<{
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">; /**
-         * #volatile
-         * the currently mouse-hovered column
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
          */
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
@@ -132,9 +114,6 @@ declare const model: import("mobx-state-tree").IModelType<{
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            /**
-             * #volatile
-             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -146,10 +125,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-         * #property
-         * filehandle object for the tree
-         */
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -161,10 +137,17 @@ declare const model: import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
+        /**
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
+         */
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
+        }> | undefined; /**
+         * #volatile
+         */
     } | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -177,11 +160,10 @@ declare const model: import("mobx-state-tree").IModelType<{
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">; /**
-         * #volatile
-         * the currently mouse-hovered column
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
          */
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
@@ -192,9 +174,6 @@ declare const model: import("mobx-state-tree").IModelType<{
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            /**
-             * #volatile
-             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -206,10 +185,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-         * #property
-         * filehandle object for the tree
-         */
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -221,10 +197,17 @@ declare const model: import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
+        /**
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
+         */
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
+        }> | undefined; /**
+         * #volatile
+         */
     } | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -237,11 +220,10 @@ declare const model: import("mobx-state-tree").IModelType<{
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">; /**
-         * #volatile
-         * the currently mouse-hovered column
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
          */
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
         uri: string;
@@ -252,9 +234,6 @@ declare const model: import("mobx-state-tree").IModelType<{
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            /**
-             * #volatile
-             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -262,33 +241,6 @@ declare const model: import("mobx-state-tree").IModelType<{
     collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     collapsed2: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    boxTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        accession: import("mobx-state-tree").ISimpleType<string>;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        associatedRowName: import("mobx-state-tree").ISimpleType<string>;
-        height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    }, {
-        error: unknown;
-        data: string | undefined;
-    } & {
-        setError(error: unknown): void;
-        setData(data: string): void;
-    } & {
-        afterCreate(): void;
-    } & {
-        readonly loading: boolean;
-        readonly features: {
-            seq_id: string;
-            source: string;
-            type: string;
-            start: number;
-            end: number;
-            score: number;
-            strand: string;
-            phase: string;
-        }[] | undefined;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
     data: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -299,15 +251,8 @@ declare const model: import("mobx-state-tree").IModelType<{
         setMSA(msa?: string | undefined): void;
         setTreeMetadata(treeMetadata?: string | undefined): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
 }, {
-    width: number;
-} & {
-    menuItems(): import("@jbrowse/core/ui").MenuItem[];
-} & {
-    setDisplayName(name: string): void;
-    setWidth(newWidth: number): void;
-    setMinimized(flag: boolean): void;
-} & {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
     readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType;
@@ -316,34 +261,40 @@ declare const model: import("mobx-state-tree").IModelType<{
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
 } & {
-    addStructureToSelection(elt: import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        structure: import("mobx-state-tree").IModelType<{
-            pdb: import("mobx-state-tree").ISimpleType<string>;
-            startPos: import("mobx-state-tree").ISimpleType<number>;
-            endPos: import("mobx-state-tree").ISimpleType<number>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }>>): void;
-    removeStructureFromSelection(elt: import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        structure: import("mobx-state-tree").IModelType<{
-            pdb: import("mobx-state-tree").ISimpleType<string>;
-            startPos: import("mobx-state-tree").ISimpleType<number>;
-            endPos: import("mobx-state-tree").ISimpleType<number>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }>>): void;
-    toggleStructureSelection(elt: {
-        id: string;
-        structure: {
-            startPos: number;
-            endPos: number;
-            pdb: string;
-        };
-    }): void;
-    clearSelectedStructures(): void;
+    setTreeWidthMatchesArea(arg: boolean): void;
+    setTreeAreaWidth(n: number): void;
+    setTreeWidth(n: number): void;
+    setLabelsAlignRight(arg: boolean): void;
+    setDrawTree(arg: boolean): void;
+    setShowBranchLen(arg: boolean): void;
+    setDrawNodeBubbles(arg: boolean): void;
+    setDrawLabels(arg: boolean): void;
 } & {
+    setColorSchemeName(name: string): void;
+    setBgColor(arg: boolean): void;
+} & {
+    status: {
+        msg: string;
+        url?: string | undefined;
+    } | undefined;
+    /**
+     * #volatile
+     * high resolution scale factor, helps make canvas look better on hi-dpi
+     * screens
+     */
+    highResScaleFactor: number;
+    /**
+     * #volatile
+     */
+    loadingMSA: boolean;
+    /**
+     * #volatile
+     */
+    loadingTree: boolean;
+    /**
+     * #volatile
+     */
+    width: number;
     /**
      * #volatile
      * resize handle width between tree and msa area, px
@@ -399,75 +350,79 @@ declare const model: import("mobx-state-tree").IModelType<{
         left: number;
         right: number;
     } | undefined;
-} & {
     /**
-     * #action
-     * set the height of the view in px
+     * #volatile
+     *
      */
-    setHeight(height: number): void;
+    loadedInterProAnnotations: Record<string, InterProScanResults> | undefined;
+    /**
+     * #volatile
+     */
+    interProScanJobIds: {
+        jobId: string;
+        date: number;
+    }[];
+} & {
     /**
      * #action
-     * set error state
      */
-    setError(error?: unknown): void;
+    setLoadingMSA(arg: boolean): void;
     /**
      * #action
-     * set mouse position (row, column) in the MSA
      */
-    setMousePos(col?: number, row?: number): void;
+    setLoadingTree(arg: boolean): void;
     /**
      * #action
-     * set mouse click position (row, column) in the MSA
      */
-    setMouseClickPos(col?: number, row?: number): void;
+    setWidth(arg: number): void;
     /**
      * #action
-     * set row height (px)
+     * set the height of the view in px
      */
-    setRowHeight(n: number): void;
+    setHeight(height: number): void;
     /**
      * #action
-     * set col width (px)
+     * set error state
      */
-    setColWidth(n: number): void;
+    setError(error?: unknown): void;
     /**
      * #action
-     * set color scheme name
+     * set mouse position (row, column) in the MSA
      */
-    setColorSchemeName(name: string): void;
+    setMousePos(col?: number, row?: number): void;
     /**
      * #action
-     * synchronize the treewidth and treeareawidth
      */
-    setTreeWidthMatchesArea(arg: boolean): void;
+    setFeatureMode(arg: boolean): void;
     /**
      * #action
-     * set scroll Y-offset (px)
      */
-    setScrollY(n: number): void;
+    setSubFeatureRows(arg: boolean): void;
     /**
      * #action
-     * set tree area width (px)
+     * set mouse click position (row, column) in the MSA
      */
-    setTreeAreaWidth(n: number): void;
+    setMouseClickPos(col?: number, row?: number): void;
     /**
      * #action
-     * set tree width (px)
+     * set row height (px)
      */
-    setTreeWidth(n: number): void;
+    setRowHeight(n: number): void;
     /**
      * #action
-     *
+     * set col width (px)
      */
-    setCurrentAlignment(n: number): void;
+    setColWidth(n: number): void;
     /**
      * #action
+     * set scroll Y-offset (px)
      */
-    setLabelsAlignRight(arg: boolean): void;
+    setScrollY(n: number): void;
     /**
      * #action
+     *
      */
-    setDrawTree(arg: boolean): void;
+    setCurrentAlignment(n: number): void;
     /**
      * #action
      */
@@ -480,18 +435,6 @@ declare const model: import("mobx-state-tree").IModelType<{
      * #action
      */
     setShowOnly(node?: string): void;
-    /**
-     * #action
-     */
-    setShowBranchLen(arg: boolean): void;
-    /**
-     * #action
-     */
-    setBgColor(arg: boolean): void;
-    /**
-     * #action
-     */
-    setDrawNodeBubbles(arg: boolean): void;
     /**
      * #action
      */
@@ -502,11 +445,11 @@ declare const model: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setMSAFilehandle(msaFilehandle?: FileLocationType): Promise<void>;
+    setMSAFilehandle(msaFilehandle?: FileLocationType): void;
     /**
      * #action
      */
-    setTreeFilehandle(treeFilehandle?: FileLocationType): Promise<void>;
+    setTreeFilehandle(treeFilehandle?: FileLocationType): void;
     /**
      * #action
      */
@@ -520,6 +463,11 @@ declare const model: import("mobx-state-tree").IModelType<{
      */
     setTreeMetadata(result: string): void;
 } & {
+    /**
+     * #method
+     * unused here, but can be used by derived classes to add extra items
+     */
+    extraViewMenuItems(): never[];
     /**
      * #getter
      */
@@ -532,28 +480,24 @@ declare const model: import("mobx-state-tree").IModelType<{
      * #method
      */
     getRowData(name: string): {
-        range?: {
-            start: number;
-            end: number;
-        } | undefined;
         data: {
             name: string;
             accession: string;
             dbxref: string;
-        } | Record<string, unknown>;
+        } | undefined;
     };
     /**
      * #getter
      */
-    readonly currentAlignmentName: string;
+    readonly alignmentNames: string[];
     /**
      * #getter
      */
-    readonly alignmentNames: string[];
+    readonly noTree: boolean;
     /**
      * #getter
      */
-    readonly noTree: boolean;
+    readonly noAnnotations: boolean;
     /**
      * #getter
      */
@@ -582,26 +526,10 @@ declare const model: import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly mouseOverRowName: string | undefined;
-    /**
-     * #method
-     */
-    getMouseOverResidue(rowName: string): string;
     /**
      * #getter
      */
     readonly root: HierarchyNode<NodeWithIds>;
-    /**
-     * #getter
-     */
-    readonly structures: Record<string, Structure[]>;
-    /**
-     * #getter
-     */
-    readonly inverseStructures: {
-        [k: string]: {
-            id: string;
-        };
-    };
     /**
      * #getter
      * widget width minus the tree area gives the space for the MSA
@@ -672,7 +600,7 @@ declare const model: import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly done: string | false | undefined;
+    readonly isLoading: boolean;
     /**
      * #getter
      */
@@ -681,10 +609,15 @@ declare const model: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    addUniprotTrack(node: {
-        name: string;
-        accession: string;
-    }): void;
+    zoomIn(): void;
+    /**
+     * #action
+     */
+    zoomOut(): void;
+    /**
+     * #action
+     */
+    setLoadedInterProAnnotations(data: Record<string, InterProScanResults>): void;
     /**
      * #action
      */
@@ -700,11 +633,18 @@ declare const model: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setMouseoveredColumn(n: number, chain: string, file: string): void;
+    toggleTrack(id: string): void;
     /**
      * #action
      */
-    toggleTrack(id: string): void;
+    addInterProScanJobId(arg: string): void;
+    /**
+     * #action
+     */
+    setStatus(status?: {
+        msg: string;
+        url?: string;
+    }): void;
 } & {
     /**
      * #getter
@@ -725,51 +665,85 @@ declare const model: import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly adapterTrackModels: BasicTrack[];
-    /**
-     * #getter
-     */
-    readonly boxTrackModels: BasicTrack[];
+    readonly adapterTrackModels: ITextTrack[];
     /**
      * #getter
      */
-    readonly tracks: BasicTrack[];
+    readonly tracks: ITextTrack[];
     /**
      * #getter
      */
-    readonly turnedOnTracks: BasicTrack[];
+    readonly turnedOnTracks: ITextTrack[];
     /**
      * #method
-     * returns coordinate in the current relative coordinate scheme
+     * return a row-specific sequence coordinate, skipping gaps, given a global
+     * coordinate
      */
-    pxToBp(coord: number): number;
+    globalCoordToRowSpecificSeqCoord(rowName: string, position: number): number;
     /**
      * #method
+     * return a global coordinate given a row-specific sequence coordinate
+     * which does not not include gaps
      */
-    rowSpecificBpToPx(rowName: string, position: number): number;
+    seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
+} & {
     /**
-     * #method
+     * #getter
+     * total height of track area (px)
      */
-    globalBpToPx(position: number): number;
+    readonly totalTrackAreaHeight: number;
     /**
-     * #method
+     * #getter
      */
-    relativePxToBp(rowName: string, position: number): number;
+    readonly tidyTypes: Map<string, Accession>;
+    readonly tidyAnnotations: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }[];
     /**
-     * #method
+     * #getter
      */
-    relativePxToBp2(rowName: string, position: number): number;
+    readonly tidyFilteredAnnotations: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }[];
     /**
-     * #method
+     * #getter
      */
-    getPos(pos: number): number;
+    readonly tidyFilteredGatheredAnnotations: Record<string, {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }[] | undefined>;
+} & {
+    readonly fillPalette: Record<string, string>;
+    readonly strokePalette: {
+        [k: string]: string;
+    };
 } & {
     /**
-     * #getter
-     * total height of track area (px)
+     * #action
      */
-    readonly totalTrackAreaHeight: number;
-} & {
+    loadInterProScanResults(jobId: string): Promise<void>;
+    /**
+     * #action
+     */
+    queryInterProScan(programs: string[]): Promise<void>;
+    /**
+     * #action
+     */
+    reset(): void;
     /**
      * #action
      */
@@ -783,43 +757,51 @@ declare const model: import("mobx-state-tree").IModelType<{
      * internal, used for drawing to canvas
      */
     incrementRef(): void;
+    /**
+     * #action
+     */
+    initFilter(arg: string): void;
+    /**
+     * #action
+     */
+    setFilter(arg: string, flag: boolean): void;
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, {
-    id: string;
-    selectedStructures: import("mobx-state-tree").ModelSnapshotType<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        structure: import("mobx-state-tree").IModelType<{
-            pdb: import("mobx-state-tree").ISimpleType<string>;
-            startPos: import("mobx-state-tree").ISimpleType<number>;
-            endPos: import("mobx-state-tree").ISimpleType<number>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }>[];
-    type: "MsaView";
     height: number;
-    treeWidthMatchesArea: boolean;
-    rowHeight: number;
-    scrollY: number;
-    scrollX: number;
+    drawLabels: boolean;
     labelsAlignRight: boolean;
-    colWidth: number;
+    treeAreaWidth: number;
+    treeWidth: number;
+    treeWidthMatchesArea: boolean;
     showBranchLen: boolean;
-    bgColor: boolean;
     drawTree: boolean;
     drawNodeBubbles: boolean;
-    highResScaleFactor: number;
+    bgColor: boolean;
     colorSchemeName: string;
+    id: string;
+    featureMode: boolean;
+    subFeatureRows: boolean;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
     currentAlignment: number;
-    treeAreaWidth: number;
-    treeWidth: number;
+    type: "MsaView";
     treeFilehandle: {
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
+        /**
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
+         */
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
+        }> | undefined; /**
+         * #volatile
+         */
     } | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -832,10 +814,17 @@ declare const model: import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
+        /**
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
+         */
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
+        }> | undefined; /**
+         * #volatile
+         */
     } | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -848,10 +837,17 @@ declare const model: import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
+        /**
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
+         */
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
-        }> | undefined;
+        }> | undefined; /**
+         * #volatile
+         */
     } | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -863,22 +859,14 @@ declare const model: import("mobx-state-tree").IModelType<{
     collapsed: string[];
     collapsed2: string[];
     showOnly: string | undefined;
-    boxTracks: import("mobx-state-tree").ModelSnapshotType<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        accession: import("mobx-state-tree").ISimpleType<string>;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        associatedRowName: import("mobx-state-tree").ISimpleType<string>;
-        height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    }>[];
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    displayName: string | undefined;
-    minimized: boolean;
+    featureFilters: import("mobx").IKeyValueMap<boolean>;
     data: {
         treeMetadata?: string | undefined;
         msa?: string | undefined;
         tree?: string | undefined;
     };
 }>;
-export default model;
-export type MsaViewStateModel = typeof model;
+export default stateModelFactory;
+export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type MsaViewModel = Instance<MsaViewStateModel>;