@jbrowse/plugin-gccontent 2.17.0 → 3.0.0

package/dist/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,15 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class GCContentAdapter extends BaseFeatureDataAdapter {
     private gcMode;
     static capabilities: string[];
     configure(): Promise<BaseFeatureDataAdapter>;
-    getRefNames(): Promise<string[]>;
-    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -1,9 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const rxjs_1 = require("rxjs");
-const rxjs_2 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const rxjs_2 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 class GCContentAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -18,71 +19,76 @@ class GCContentAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return adapter.dataAdapter;
     }
-    async getRefNames() {
+    async getRefNames(opts) {
         const adapter = await this.configure();
-        return adapter.getRefNames();
+        return adapter.getRefNames(opts);
     }
     getFeatures(query, opts) {
-        return (0, rxjs_2.ObservableCreate)(async (observer) => {
+        const { statusCallback = () => { }, stopToken } = opts || {};
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
             var _a;
             const sequenceAdapter = await this.configure();
             const windowSize = this.getConf('windowSize');
             const windowDelta = this.getConf('windowDelta');
-            const hw = windowSize === 1 ? 1 : windowSize / 2; // Half the window size
-            const f = windowSize === 1;
-            let { start: queryStart, end: queryEnd } = query;
-            queryStart = Math.max(0, queryStart - hw);
-            queryEnd += hw;
-            if (queryEnd < 0 || queryStart > queryEnd) {
+            const halfWindowSize = windowSize === 1 ? 1 : Math.ceil(windowSize / 2);
+            const isWindowSizeOneBp = windowSize === 1;
+            const qs = Math.max(0, Math.floor((query.start - halfWindowSize) / windowSize) * windowSize);
+            const qe = Math.ceil((query.end + halfWindowSize) / windowSize) * windowSize;
+            if (qe < 0 || qs > qe) {
                 observer.complete();
                 return;
             }
-            const ret = sequenceAdapter.getFeatures({
+            const feats = await (0, rxjs_2.firstValueFrom)(sequenceAdapter
+                .getFeatures({
                 ...query,
-                start: queryStart,
-                end: queryEnd,
-            }, opts);
-            const feats = await (0, rxjs_1.firstValueFrom)(ret.pipe((0, operators_1.toArray)()));
+                start: qs,
+                end: qe,
+            }, opts)
+                .pipe((0, operators_1.toArray)()));
             const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
-            for (let i = hw; i < residues.length - hw; i += windowDelta) {
-                const r = f ? residues[i] : residues.slice(i - hw, i + hw);
-                let nc = 0;
-                let ng = 0;
-                let len = 0;
-                for (const letter of r) {
-                    if (letter === 'c' || letter === 'C') {
-                        nc++;
+            let start = performance.now();
+            await (0, util_1.updateStatus)('Calculating GC', statusCallback, () => {
+                for (let i = halfWindowSize; i < residues.length - halfWindowSize; i += windowDelta) {
+                    if (performance.now() - start > 400) {
+                        (0, stopToken_1.checkStopToken)(stopToken);
+                        start = performance.now();
                     }
-                    else if (letter === 'g' || letter === 'G') {
-                        ng++;
-                    }
-                    if (letter !== 'N') {
-                        len++;
+                    const r = isWindowSizeOneBp
+                        ? residues[i]
+                        : residues.slice(i - halfWindowSize, i + halfWindowSize);
+                    let nc = 0;
+                    let ng = 0;
+                    let len = 0;
+                    for (const letter of r) {
+                        if (letter === 'c' || letter === 'C') {
+                            nc++;
+                        }
+                        else if (letter === 'g' || letter === 'G') {
+                            ng++;
+                        }
+                        if (letter !== 'N') {
+                            len++;
+                        }
                     }
+                    const pos = qs;
+                    const score = this.gcMode === 'content'
+                        ? (ng + nc) / (len || 1)
+                        : this.gcMode === 'skew'
+                            ? (ng - nc) / (ng + nc || 1)
+                            : 0;
+                    observer.next(new util_1.SimpleFeature({
+                        uniqueId: `${this.id}_${pos + i}`,
+                        refName: query.refName,
+                        start: pos + i,
+                        end: pos + i + windowDelta,
+                        score,
+                    }));
                 }
-                const pos = queryStart;
-                const score = this.gcMode === 'content'
-                    ? (ng + nc) / (len || 1)
-                    : this.gcMode === 'skew'
-                        ? (ng - nc) / (ng + nc || 1)
-                        : 0;
-                observer.next(new util_1.SimpleFeature({
-                    uniqueId: `${this.id}_${pos + i}`,
-                    refName: query.refName,
-                    start: pos + i,
-                    end: pos + i + windowDelta,
-                    score,
-                }));
-            }
+            });
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 GCContentAdapter.capabilities = ['hasLocalStats'];
 exports.default = GCContentAdapter;

package/dist/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/dist/GCContentAdapter/configSchema.js

@@ -1,30 +1,17 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config GCContentAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const GCContentAdapterF = (_pluginManager) => {
     return (0, configuration_1.ConfigurationSchema)('GCContentAdapter', {
-        /**
-         * #slot
-         */
         sequenceAdapter: {
             type: 'frozen',
             defaultValue: null,
         },
-        /**
-         * #slot
-         */
         windowSize: {
             type: 'number',
             defaultValue: 100,
         },
-        /**
-         * #slot
-         */
         windowDelta: {
             type: 'number',
             defaultValue: 100,

package/dist/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/dist/GCContentAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/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/dist/GCContentTrack/configSchema.js

@@ -2,15 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@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) => (0, configuration_1.ConfigurationSchema)('GCContentTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
 });
 exports.default = configSchema;

package/dist/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/dist/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/dist/LinearGCContentDisplay/components/EditGCContentParams.js

@@ -1,55 +1,25 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const EditGCContentParamsDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const [windowSize, setWindowSize] = (0, react_1.useState)(`${model.windowSizeSetting}`);
     const [windowDelta, setWindowDelta] = (0, react_1.useState)(`${model.windowDeltaSetting}`);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Edit GC content params" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.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_1.default.createElement(ui_1.ErrorMessage, { error: "It is not recommended to make the step size larger than the window size" })) : null,
-            react_1.default.createElement(material_1.TextField, { label: "Size of sliding window (bp)", value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                } }),
-            react_1.default.createElement(material_1.TextField, { label: "Step size of sliding window (bp)", value: windowDelta, onChange: event => {
-                    setWindowDelta(event.target.value);
-                } }),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                        model.setGCContentParams({
-                            windowSize: +windowSize,
-                            windowDelta: +windowDelta,
-                        });
-                        handleClose();
-                    } }, "Submit"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Edit GC content params", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.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 ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: "It is not recommended to make the step size larger than the window size" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Size of sliding window (bp)", value: windowSize, onChange: event => {
+                        setWindowSize(event.target.value);
+                    } }), (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Step size of sliding window (bp)", value: windowDelta, onChange: event => {
+                        setWindowDelta(event.target.value);
+                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                model.setGCContentParams({
+                                    windowSize: +windowSize,
+                                    windowDelta: +windowDelta,
+                                });
+                                handleClose();
+                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
 });
 exports.default = EditGCContentParamsDialog;

package/dist/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/dist/LinearGCContentDisplay/config1.js

@@ -2,11 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearGCContentDisplay;
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config LinearGCContentDisplay
- * #category display
- * extends LinearWiggleDisplay
- */
 function LinearGCContentDisplay(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearGCContentDisplay', {
         windowSize: {
@@ -18,9 +13,6 @@ function LinearGCContentDisplay(pluginManager) {
             defaultValue: 100,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')
             .configSchema,
         explicitlyTyped: true,

package/dist/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/dist/LinearGCContentDisplay/config2.js

@@ -2,11 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearGCContentTrackDisplayF;
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config LinearGCContentTrackDisplay
- * #category display
- * extends LinearWiggleDisplay, used specifically for GCContentTrack
- */
 function LinearGCContentTrackDisplayF(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearGCContentTrackDisplay', {
         windowSize: {
@@ -18,9 +13,6 @@ function LinearGCContentTrackDisplayF(pluginManager) {
             defaultValue: 100,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')
             .configSchema,
         explicitlyTyped: true,

package/dist/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/dist/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>;