@jbrowse/plugin-gccontent 2.16.1 → 2.18.0

package/dist/LinearGCContentDisplay/stateModel1.js

@@ -5,13 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelF;
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const shared_1 = __importDefault(require("./shared"));
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `SharedGCContentModel`
- */
 function stateModelF(pluginManager, configSchema) {
     return mobx_state_tree_1.types.compose('LinearGCContentDisplay', (0, shared_1.default)(pluginManager, configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearGCContentDisplay'),

package/dist/LinearGCContentDisplay/stateModel2.d.ts

@@ -1,15 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearGCContentTrackDisplay
- * #category display
- *
- * used on GCContentTrack, separately from the display type on the
- * ReferenceSequenceTrack
- *
- * extends
- * - [SharedGCContentModel](../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>;
@@ -22,21 +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;
@@ -60,15 +41,9 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
         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;
@@ -215,6 +190,7 @@ 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;
 } & {
@@ -254,19 +230,21 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -308,6 +286,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -346,7 +325,9 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly rendererTypeName: string;
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
+    adapterProps(): any;
     readonly ticks: {
         range: number[];
         values: number[];
@@ -357,6 +338,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     renderProps(): any;
     readonly needsScalebar: boolean;
     readonly fillSetting: 1 | 2 | 0;
+    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 | {
         label: string;
@@ -415,5 +397,5 @@ 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>;

package/dist/LinearGCContentDisplay/stateModel2.js

@@ -5,18 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelF;
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const shared_1 = __importDefault(require("./shared"));
-/**
- * #stateModel LinearGCContentTrackDisplay
- * #category display
- *
- * used on GCContentTrack, separately from the display type on the
- * ReferenceSequenceTrack
- *
- * extends
- * - [SharedGCContentModel](../sharedgccontentmodel)
- */
 function stateModelF(pluginManager, configSchema) {
     return mobx_state_tree_1.types.compose('LinearGCContentTrackDisplay', (0, shared_1.default)(pluginManager, configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearGCContentTrackDisplay'),

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class GCContentPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-// locals
 const GCContentAdapter_1 = __importDefault(require("./GCContentAdapter"));
 const GCContentTrack_1 = __importDefault(require("./GCContentTrack"));
 const LinearGCContentDisplay_1 = __importDefault(require("./LinearGCContentDisplay"));

package/esm/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/esm/GCContentAdapter/GCContentAdapter.js

@@ -1,7 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { firstValueFrom } from 'rxjs';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
 class GCContentAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -16,17 +17,18 @@ class GCContentAdapter extends BaseFeatureDataAdapter {
         }
         return adapter.dataAdapter;
     }
-    async getRefNames() {
+    async getRefNames(opts) {
         const adapter = await this.configure();
-        return adapter.getRefNames();
+        return adapter.getRefNames(opts);
     }
     getFeatures(query, opts) {
+        const { statusCallback = () => { }, stopToken } = opts || {};
         return 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 hw = windowSize === 1 ? 1 : windowSize / 2;
             const f = windowSize === 1;
             let { start: queryStart, end: queryEnd } = query;
             queryStart = Math.max(0, queryStart - hw);
@@ -35,52 +37,55 @@ class GCContentAdapter extends BaseFeatureDataAdapter {
                 observer.complete();
                 return;
             }
-            const ret = sequenceAdapter.getFeatures({
+            const feats = await firstValueFrom(sequenceAdapter
+                .getFeatures({
                 ...query,
                 start: queryStart,
                 end: queryEnd,
-            }, opts);
-            const feats = await firstValueFrom(ret.pipe(toArray()));
+            }, opts)
+                .pipe(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 updateStatus('Calculating GC', statusCallback, () => {
+                for (let i = hw; i < residues.length - hw; i += windowDelta) {
+                    if (performance.now() - start > 400) {
+                        checkStopToken(stopToken);
+                        start = performance.now();
                     }
-                    else if (letter === 'g' || letter === 'G') {
-                        ng++;
-                    }
-                    if (letter !== 'N') {
-                        len++;
+                    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++;
+                        }
+                        else if (letter === 'g' || letter === 'G') {
+                            ng++;
+                        }
+                        if (letter !== 'N') {
+                            len++;
+                        }
                     }
+                    const pos = queryStart;
+                    const score = this.gcMode === 'content'
+                        ? (ng + nc) / (len || 1)
+                        : this.gcMode === 'skew'
+                            ? (ng - nc) / (ng + nc || 1)
+                            : 0;
+                    observer.next(new 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 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'];
 export default GCContentAdapter;

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.js

@@ -1,14 +1,14 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 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,
+            +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);
                 } }),

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;
@@ -58,15 +41,9 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
         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;
@@ -217,6 +188,7 @@ 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;
 } & {
@@ -256,19 +228,21 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -310,6 +284,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -348,7 +323,9 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
 } & {
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly rendererTypeName: string;
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
+    adapterProps(): any;
     readonly ticks: {
         range: number[];
         values: number[];
@@ -359,6 +336,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
     renderProps(): any;
     readonly needsScalebar: boolean;
     readonly fillSetting: 1 | 2 | 0;
+    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 | {
         label: string;
@@ -417,10 +395,5 @@ 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>;