@jbrowse/plugin-gccontent 2.17.0 → 3.0.0

package/esm/GCContentAdapter/configSchema.d.ts

@@ -1,22 +1,13 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const GCContentAdapterF: (_pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: string;
         defaultValue: null;
     };
-    /**
-     * #slot
-     */
     windowSize: {
         type: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     windowDelta: {
         type: string;
         defaultValue: number;

package/esm/GCContentAdapter/configSchema.js

@@ -1,28 +1,15 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config GCContentAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const GCContentAdapterF = (_pluginManager) => {
     return ConfigurationSchema('GCContentAdapter', {
-        /**
-         * #slot
-         */
         sequenceAdapter: {
             type: 'frozen',
             defaultValue: null,
         },
-        /**
-         * #slot
-         */
         windowSize: {
             type: 'number',
             defaultValue: 100,
         },
-        /**
-         * #slot
-         */
         windowDelta: {
             type: 'number',
             defaultValue: 100,

package/esm/GCContentAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function GCContentAdapterF(pluginManager: PluginManager): void;

package/esm/GCContentTrack/configSchema.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;

package/esm/GCContentTrack/configSchema.js

@@ -1,14 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-/**
- * #config GCContentTrack
- * used for having a gc content track outside of the "reference sequence display"
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (pluginManager) => ConfigurationSchema('GCContentTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: createBaseTrackConfig(pluginManager),
 });
 export default configSchema;

package/esm/GCContentTrack/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function GCContentTrackF(pm: PluginManager): void;

package/esm/LinearGCContentDisplay/components/EditGCContentParams.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 declare const EditGCContentParamsDialog: ({ model, handleClose, }: {
     model: {
         windowSizeSetting: number;
@@ -9,5 +8,5 @@ declare const EditGCContentParamsDialog: ({ model, handleClose, }: {
         }) => void;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default EditGCContentParamsDialog;

package/esm/LinearGCContentDisplay/components/EditGCContentParams.js

@@ -1,30 +1,23 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
 const EditGCContentParamsDialog = observer(function ({ model, handleClose, }) {
     const [windowSize, setWindowSize] = useState(`${model.windowSizeSetting}`);
     const [windowDelta, setWindowDelta] = useState(`${model.windowDeltaSetting}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Edit GC content params" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "GC content is calculated in a particular sliding window of size N, and then the sliding window moves (steps) some number of bases M forward. Note that small step sizes can result in high CPU over large areas, and it is not recommended to make the step size larger than the window size as then the sliding window will miss contents."),
-            windowDelta > windowSize ? (React.createElement(ErrorMessage, { error: "It is not recommended to make the step size larger than the window size" })) : null,
-            React.createElement(TextField, { label: "Size of sliding window (bp)", value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                } }),
-            React.createElement(TextField, { label: "Step size of sliding window (bp)", value: windowDelta, onChange: event => {
-                    setWindowDelta(event.target.value);
-                } }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", onClick: () => {
-                        model.setGCContentParams({
-                            windowSize: +windowSize,
-                            windowDelta: +windowDelta,
-                        });
-                        handleClose();
-                    } }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return (_jsx(Dialog, { open: true, onClose: handleClose, title: "Edit GC content params", children: _jsxs(DialogContent, { children: [_jsx(Typography, { children: "GC content is calculated in a particular sliding window of size N, and then the sliding window moves (steps) some number of bases M forward. Note that small step sizes can result in high CPU over large areas, and it is not recommended to make the step size larger than the window size as then the sliding window will miss contents." }), +windowDelta > +windowSize ? (_jsx(ErrorMessage, { error: "It is not recommended to make the step size larger than the window size" })) : null, _jsx(TextField, { label: "Size of sliding window (bp)", value: windowSize, onChange: event => {
+                        setWindowSize(event.target.value);
+                    } }), _jsx(TextField, { label: "Step size of sliding window (bp)", value: windowDelta, onChange: event => {
+                        setWindowDelta(event.target.value);
+                    } }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                                model.setGCContentParams({
+                                    windowSize: +windowSize,
+                                    windowDelta: +windowDelta,
+                                });
+                                handleClose();
+                            }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 export default EditGCContentParamsDialog;

package/esm/LinearGCContentDisplay/config1.d.ts

@@ -1,9 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearGCContentDisplay
- * #category display
- * extends LinearWiggleDisplay
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearGCContentDisplay(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     windowSize: {
         type: string;

package/esm/LinearGCContentDisplay/config1.js

@@ -1,9 +1,4 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config LinearGCContentDisplay
- * #category display
- * extends LinearWiggleDisplay
- */
 export default function LinearGCContentDisplay(pluginManager) {
     return ConfigurationSchema('LinearGCContentDisplay', {
         windowSize: {
@@ -15,9 +10,6 @@ export default function LinearGCContentDisplay(pluginManager) {
             defaultValue: 100,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')
             .configSchema,
         explicitlyTyped: true,

package/esm/LinearGCContentDisplay/config2.d.ts

@@ -1,9 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearGCContentTrackDisplay
- * #category display
- * extends LinearWiggleDisplay, used specifically for GCContentTrack
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearGCContentTrackDisplayF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     windowSize: {
         type: string;

package/esm/LinearGCContentDisplay/config2.js

@@ -1,9 +1,4 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config LinearGCContentTrackDisplay
- * #category display
- * extends LinearWiggleDisplay, used specifically for GCContentTrack
- */
 export default function LinearGCContentTrackDisplayF(pluginManager) {
     return ConfigurationSchema('LinearGCContentTrackDisplay', {
         windowSize: {
@@ -15,9 +10,6 @@ export default function LinearGCContentTrackDisplayF(pluginManager) {
             defaultValue: 100,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')
             .configSchema,
         explicitlyTyped: true,

package/esm/LinearGCContentDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearGCContentDisplayF(pluginManager: PluginManager): void;

package/esm/LinearGCContentDisplay/shared.d.ts

@@ -1,11 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel SharedGCContentModel
- * #category display
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function SharedModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -18,23 +12,12 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -52,21 +35,15 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -120,13 +97,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
-    /**
-     * #property
-     */
     windowSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
     windowDelta: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }, {
     rendererTypeName: string;
@@ -217,14 +188,15 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -251,7 +223,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     message: undefined | string;
@@ -260,7 +232,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
         currStatsBpPerPx: number;
@@ -270,7 +242,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setStatsLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -367,7 +339,17 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     readonly quantitativeStatsReady: boolean;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        type: string;
+        label?: undefined;
+        icon?: undefined;
+        subMenu?: undefined;
+        onClick?: undefined;
+        checked?: undefined;
+    } | {
         label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         subMenu: ({
             label: string;
             subMenu: {
@@ -390,8 +372,8 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
             subMenu?: undefined;
         })[];
         type?: undefined;
-        checked?: undefined;
         onClick?: undefined;
+        checked?: undefined;
     } | {
         label: string;
         subMenu: {
@@ -401,10 +383,23 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
             onClick: () => void;
         }[];
         type?: undefined;
-        checked?: undefined;
+        icon?: undefined;
         onClick?: undefined;
+        checked?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        subMenu?: undefined;
+        checked?: undefined;
     } | {
         type: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         label: string;
         checked: boolean;
         onClick: () => void;
@@ -412,7 +407,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     })[];
 } & {
     afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 } & {
     setGCContentParams({ windowSize, windowDelta, }: {
         windowSize: number;
@@ -423,10 +418,5 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     readonly windowDeltaSetting: any;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    /**
-     * #method
-     * retrieves the sequence adapter from parent track, and puts it as a
-     * subadapter on a GCContentAdapter
-     */
-    renderProps(): any;
+    adapterProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LinearGCContentDisplay/shared.js

@@ -1,25 +1,13 @@
-import { getConf, } from '@jbrowse/core/configuration';
+import { lazy } from 'react';
+import { getConf } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
 import { types } from 'mobx-state-tree';
-import { lazy } from 'react';
 const EditGCContentParamsDialog = lazy(() => import('./components/EditGCContentParams'));
-/**
- * #stateModel SharedGCContentModel
- * #category display
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
 export default function SharedModelF(pluginManager, configSchema) {
     return types
         .compose('SharedGCContentModel', linearWiggleDisplayModelFactory(pluginManager, configSchema), types.model({
-        /**
-         * #property
-         */
         windowSize: types.maybe(types.number),
-        /**
-         * #property
-         */
         windowDelta: types.maybe(types.number),
     }))
         .actions(self => ({
@@ -39,7 +27,7 @@ export default function SharedModelF(pluginManager, configSchema) {
         },
     }))
         .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        const { trackMenuItems: superTrackMenuItems, adapterProps: superAdapterProps, } = self;
         return {
             trackMenuItems() {
                 return [
@@ -55,15 +43,10 @@ export default function SharedModelF(pluginManager, configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             * retrieves the sequence adapter from parent track, and puts it as a
-             * subadapter on a GCContentAdapter
-             */
-            renderProps() {
+            adapterProps() {
                 const sequenceAdapter = getConf(self.parentTrack, 'adapter');
                 return {
-                    ...superRenderProps(),
+                    ...superAdapterProps(),
                     adapterConfig: {
                         type: 'GCContentAdapter',
                         sequenceAdapter,

package/esm/LinearGCContentDisplay/stateModel1.d.ts

@@ -1,10 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `SharedGCContentModel`
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -17,21 +12,12 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -49,21 +35,15 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -210,14 +190,15 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -244,7 +225,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     message: undefined | string;
@@ -253,7 +234,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
         currStatsBpPerPx: number;
@@ -263,7 +244,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setStatsLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -360,7 +341,17 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly quantitativeStatsReady: boolean;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        type: string;
+        label?: undefined;
+        icon?: undefined;
+        subMenu?: undefined;
+        onClick?: undefined;
+        checked?: undefined;
+    } | {
         label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         subMenu: ({
             label: string;
             subMenu: {
@@ -383,8 +374,8 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
             subMenu?: undefined;
         })[];
         type?: undefined;
-        checked?: undefined;
         onClick?: undefined;
+        checked?: undefined;
     } | {
         label: string;
         subMenu: {
@@ -394,10 +385,23 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
             onClick: () => void;
         }[];
         type?: undefined;
-        checked?: undefined;
+        icon?: undefined;
         onClick?: undefined;
+        checked?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        subMenu?: undefined;
+        checked?: undefined;
     } | {
         type: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         label: string;
         checked: boolean;
         onClick: () => void;
@@ -405,7 +409,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     })[];
 } & {
     afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 } & {
     setGCContentParams({ windowSize, windowDelta, }: {
         windowSize: number;
@@ -416,5 +420,5 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly windowDeltaSetting: any;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
+    adapterProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;