@jbrowse/plugin-wiggle 2.11.2 → 2.12.1

package/dist/shared/SetMinMaxDialog.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SetMinMaxDialog;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
@@ -49,4 +50,3 @@ function SetMinMaxDialog(props) {
                     handleClose();
                 } }, "Submit"))));
 }
-exports.default = SetMinMaxDialog;

package/dist/shared/configShared.d.ts

@@ -71,9 +71,7 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
-        description: string; /**
-         * #slot
-         */
+        description: string;
     };
     height: {
         type: string;

package/dist/shared/configShared.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = sharedWiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -82,4 +83,3 @@ function sharedWiggleConfigFactory() {
         explicitlyTyped: true,
     });
 }
-exports.default = sharedWiggleConfigFactory;

package/dist/shared/modelShared.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 /**
@@ -22,7 +21,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree" /**
+             * #property
+             */).ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -32,7 +33,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -44,9 +45,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement? /**
+                 * #property
+                 */: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -57,7 +60,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -76,9 +79,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         fetchSizeLimit: {
             type: string;
             defaultValue: number;
-            description: string; /**
-             * #property
-             */
+            description: string;
         };
         height: {
             type: string;
@@ -171,21 +172,19 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree" /**
+         * #property
+         */).IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: unknown; /**
-             * #property
-             */
+            error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined; /**
-         * #property
-         */
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -203,21 +202,19 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #action
-             */
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -230,10 +227,8 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined; /**
-     * #property
-     */
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -245,23 +240,20 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null; /**
-     * #getter
-     * subclasses can define these, as snpcoverage track does
-     */
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -269,15 +261,12 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    /**
-     * #action
-     */
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
@@ -285,8 +274,8 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -295,17 +284,14 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
-    /**
-     * #method
-     */
     afterAttach(): void;
 } & {
-    message: string | undefined;
+    message: undefined | string;
     stats: {
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: AbortController | undefined;
+    statsFetchInProgress: undefined | AbortController;
 } & {
     /**
      * #action
@@ -418,7 +404,15 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree" /**
+         * #property
+         */).IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     /**
      * #getter
@@ -527,7 +521,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -539,9 +533,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement? /**
+                 * #property
+                 */: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -552,7 +548,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -571,9 +567,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         fetchSizeLimit: {
             type: string;
             defaultValue: number;
-            description: string; /**
-             * #property
-             */
+            description: string;
         };
         height: {
             type: string;

package/dist/shared/modelShared.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SharedWiggleMixin;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
@@ -476,4 +477,3 @@ function SharedWiggleMixin(configSchema) {
         };
     });
 }
-exports.default = SharedWiggleMixin;

package/dist/util.d.ts

@@ -9,6 +9,7 @@ export interface ScaleOpts {
     inverted?: boolean;
 }
 export interface Source {
+    baseUri?: string;
     name: string;
     color?: string;
     group?: string;

package/dist/util.js

@@ -1,6 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fillRectCtx = exports.round = exports.toP = exports.quantitativeStatsAutorun = exports.getQuantitativeStats = exports.getNiceDomain = exports.getOrigin = exports.getScale = exports.YSCALEBAR_LABEL_OFFSET = void 0;
+exports.YSCALEBAR_LABEL_OFFSET = void 0;
+exports.getScale = getScale;
+exports.getOrigin = getOrigin;
+exports.getNiceDomain = getNiceDomain;
+exports.getQuantitativeStats = getQuantitativeStats;
+exports.quantitativeStatsAutorun = quantitativeStatsAutorun;
+exports.toP = toP;
+exports.round = round;
+exports.fillRectCtx = fillRectCtx;
 const d3_scale_1 = require("d3-scale");
 const mobx_1 = require("mobx");
 const util_1 = require("@jbrowse/core/util");
@@ -47,7 +55,6 @@ function getScale({ domain = [], range = [], scaleType, pivotValue, inverted, })
     scale.range(inverted ? range.slice().reverse() : range);
     return scale;
 }
-exports.getScale = getScale;
 /**
  * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
  *
@@ -71,7 +78,6 @@ function getOrigin(scaleType /* , pivot, stats */) {
     }
     return 0;
 }
-exports.getOrigin = getOrigin;
 /**
  * produces a "nice" domain that actually rounds down to 0 for the min
  * or 0 to the max depending on if all values are positive or negative
@@ -131,7 +137,6 @@ function getNiceDomain({ scaleType, domain, bounds, }) {
     scale.nice();
     return scale.domain();
 }
-exports.getNiceDomain = getNiceDomain;
 async function getQuantitativeStats(self, opts) {
     const { rpcManager } = (0, util_1.getSession)(self);
     const nd = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
@@ -192,7 +197,6 @@ async function getQuantitativeStats(self, opts) {
     }
     throw new Error(`invalid autoscaleType '${autoscaleType}'`);
 }
-exports.getQuantitativeStats = getQuantitativeStats;
 function quantitativeStatsAutorun(self) {
     (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
         try {
@@ -222,15 +226,12 @@ function quantitativeStatsAutorun(self) {
         }
     }, { delay: 1000 }));
 }
-exports.quantitativeStatsAutorun = quantitativeStatsAutorun;
 function toP(s = 0) {
     return +(+s).toPrecision(6);
 }
-exports.toP = toP;
 function round(value) {
     return Math.round(value * 1e5) / 1e5;
 }
-exports.round = round;
 // avoid drawing negative width features for SVG exports
 function fillRectCtx(x, y, width, height, ctx, color) {
     if (width < 0) {
@@ -246,4 +247,3 @@ function fillRectCtx(x, y, width, height, ctx, color) {
     }
     ctx.fillRect(x, y, width, height);
 }
-exports.fillRectCtx = fillRectCtx;

package/esm/BigWigAdapter/BigWigAdapter.d.ts

@@ -11,7 +11,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     private setupPre;
     setup(opts?: BaseOptions): Promise<{
         bigwig: BigWig;
-        header: import("@gmod/bbi").Header;
+        header: Awaited<ReturnType<BigWig["getHeader"]>>;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refIdToName(refId: number): Promise<string>;

package/esm/LinePlotRenderer/configSchema.d.ts

@@ -11,9 +11,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
     color: {
         type: string;
         description: string;
-        defaultValue: string; /**
-         * #baseConfiguration
-         */
+        defaultValue: string;
     };
     posColor: {
         type: string;

package/esm/LinearWiggleDisplay/models/configSchema.d.ts

@@ -69,9 +69,7 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         type: string;
         defaultValue: number;
         description: string;
-    }; /**
-     * #slot
-     */
+    };
     height: {
         type: string;
         defaultValue: number;

package/esm/LinearWiggleDisplay/models/model.d.ts

@@ -24,7 +24,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            reversed: import("mobx-state-tree" /**
+             * #getter
+             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -36,7 +38,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -45,25 +47,25 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error?: unknown;
+                error? /**
+                 * #getter
+                 */: unknown;
                 reload: () => void;
                 message: React.ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: React.ReactElement;
             };
         }) => React.JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
-         * #method
-         */
+        setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            reactElement: React.ReactElement;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -134,7 +136,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import(
+        /**
+         * #stateModel LinearWiggleDisplay
+         * extends
+         * - [SharedWiggleMixin](../sharedwigglemixin)
+         */
+        "mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
@@ -146,9 +154,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree" /**
+         * #getter
+         */)._NotCustomized>>;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -171,16 +181,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -193,8 +201,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -206,12 +214,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void; /**
-     * #method
-     */
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -220,8 +226,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -229,7 +235,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly renderDelay: number;
     readonly TooltipComponent: React.FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -242,8 +248,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -254,31 +260,31 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     renderSvg(opts: ExportSvgDisplayOptions): Promise<React.JSX.Element>;
     afterAttach(): void;
 } & {
-    message: string | undefined;
+    message: undefined | string;
     stats: {
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: AbortController | undefined;
+    statsFetchInProgress: undefined | AbortController;
 } & {
     updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
-    setColor(color?: string | undefined): void;
-    setPosColor(color?: string | undefined): void;
-    setNegColor(color?: string | undefined): void;
+    setColor(color?: string): void;
+    setPosColor(color?: string): void;
+    setNegColor(color?: string): void;
     setLoading(aborter: AbortController): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
     toggleLogScale(): void;
-    setScaleType(scale?: string | undefined): void;
+    setScaleType(scale?: string): void;
     setSummaryScoreMode(val: string): void;
     setAutoscale(val: string): void;
-    setMaxScore(val?: number | undefined): void;
+    setMaxScore(val?: number): void;
     setRendererType(val: string): void;
-    setMinScore(val?: number | undefined): void;
+    setMinScore(val?: number): void;
     toggleCrossHatches(): void;
     setCrossHatches(cross: boolean): void;
 } & {
@@ -293,7 +299,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     readonly autoscaleType: any;
 } & {
@@ -343,7 +355,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly TooltipComponent: React.FC<{}>;
+    readonly TooltipComponent: React.FC;
     /**
      * #getter
      */