@jbrowse/plugin-wiggle 2.16.1 → 2.18.0

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 interface WiggleOptions extends BaseOptions {
     resolution?: number;
 }
@@ -21,7 +22,7 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    getSources(): Promise<{
+    getSources(_regions: Region[]): Promise<{
         name: string;
         __name: unknown;
     }[]>;

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -1,6 +1,6 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, max, min } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, min, max } from '@jbrowse/core/util';
 import { merge } from 'rxjs';
 import { map } from 'rxjs/operators';
 function getFilename(uri) {
@@ -34,7 +34,6 @@ class MultiWiggleAdapter extends BaseFeatureDataAdapter {
             };
         }));
     }
-    // note: can't really have dis-agreeing refNames
     async getRefNames(opts) {
         const adapters = await this.getAdapters();
         const allNames = await Promise.all(adapters.map(a => a.dataAdapter.getRefNames(opts)));
@@ -42,34 +41,32 @@ class MultiWiggleAdapter extends BaseFeatureDataAdapter {
     }
     async getGlobalStats(opts) {
         const adapters = await this.getAdapters();
-        const stats = (await Promise.all(
-        // @ts-expect-error
-        adapters.map(adp => { var _a, _b; return (_b = (_a = adp.dataAdapter).getGlobalStats) === null || _b === void 0 ? void 0 : _b.call(_a, opts); }))).filter(f => !!f);
+        const stats = (await Promise.all(adapters.map(adp => { var _a, _b; return (_b = (_a = adp.dataAdapter).getGlobalStats) === null || _b === void 0 ? void 0 : _b.call(_a, opts); }))).filter(f => !!f);
         const scoreMin = min(stats.map(s => s.scoreMin));
         const scoreMax = max(stats.map(s => s.scoreMax));
-        return { scoreMin, scoreMax };
+        return {
+            scoreMin,
+            scoreMax,
+        };
     }
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             const adapters = await this.getAdapters();
-            merge(...adapters.map(adp => adp.dataAdapter.getFeatures(region, opts).pipe(map(p => 
-            // add source field if it does not exist
-            p.get('source')
+            merge(...adapters.map(adp => adp.dataAdapter.getFeatures(region, opts).pipe(map(p => p.get('source')
                 ? p
                 : new SimpleFeature({
                     ...p.toJSON(),
                     uniqueId: `${adp.source}-${p.id()}`,
                     source: adp.source,
                 }))))).subscribe(observer);
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    // always render bigwig instead of calculating a feature density for it
     async getMultiRegionFeatureDensityStats(_regions) {
-        return { featureDensity: 0 };
+        return {
+            featureDensity: 0,
+        };
     }
-    // in another adapter type, this could be dynamic depending on region or
-    // something, but it is static for this particular multi-wiggle adapter type
-    async getSources() {
+    async getSources(_regions) {
         const adapters = await this.getAdapters();
         return adapters.map(({ dataAdapter, source, name, ...rest }) => ({
             name: source,

package/esm/MultiWiggleAdapter/configSchema.d.ts

@@ -1,15 +1,9 @@
 declare const MultiWiggleAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     subadapters: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     bigWigs: {
         type: string;
         description: string;

package/esm/MultiWiggleAdapter/configSchema.js

@@ -1,20 +1,11 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MultiWiggleAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MultiWiggleAdapter = ConfigurationSchema('MultiWiggleAdapter', {
-    /**
-     * #slot
-     */
     subadapters: {
         type: 'frozen',
         defaultValue: [],
         description: 'array of subadapter JSON objects',
     },
-    /**
-     * #slot
-     */
     bigWigs: {
         type: 'frozen',
         description: 'array of bigwig filenames, alternative to the subadapters slot',

package/esm/MultiWiggleAdapter/index.d.ts

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

package/esm/MultiWiggleAdapter/index.js

@@ -1,5 +1,5 @@
-import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
 export default function MultiWiggleAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'MultiWiggleAdapter',

package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '@jbrowse/plugin-data-management';
+import type { AddTrackModel } from '@jbrowse/plugin-data-management';
 export default function MultiWiggleWidget({ model }: {
     model: AddTrackModel;
 }): React.JSX.Element;

package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
-import { Button, Paper, TextField } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import { getSession, isElectron, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
 import { storeBlobLocation } from '@jbrowse/core/util/tracks';
+import { Button, Paper, TextField } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     paper: {
         margin: theme.spacing(),
@@ -14,7 +14,6 @@ const useStyles = makeStyles()(theme => ({
         display: 'block',
     },
 }));
-// on electron, use path to LocalFileLocation, on web, use the BlobLocation
 function makeFileLocation(file) {
     const { webUtils } = window.require('electron');
     return isElectron
@@ -56,7 +55,6 @@ export default function MultiWiggleWidget({ model }) {
                         `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
                         session.adminMode ? '' : '-sessionTrack',
                     ].join('');
-                    // allow list of bigwigs in JSON format or line-by-line
                     let bigWigs;
                     try {
                         bigWigs = JSON.parse(val);

package/esm/MultiWiggleAddTrackWorkflow/index.d.ts

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

package/esm/MultiWiggleAddTrackWorkflow/index.js

@@ -1,7 +1,6 @@
+import { lazy } from 'react';
 import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes';
 import { types } from 'mobx-state-tree';
-// locals
-import { lazy } from 'react';
 export default function MultiWiggleAddTrackWorkflowF(pm) {
     pm.addAddTrackWorkflowType(() => new AddTrackWorkflowType({
         name: 'Multi-wiggle track',

package/esm/MultiWiggleRendering.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { Source } from './util';
+import type { Source } from './util';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 declare const MultiWiggleRendering: (props: {
     regions: Region[];
     features: Map<string, Feature>;

package/esm/MultiWiggleRendering.js

@@ -1,7 +1,7 @@
-import { observer } from 'mobx-react';
 import React, { useRef } from 'react';
-import { SimpleFeature } from '@jbrowse/core/util';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
 const MultiWiggleRendering = observer(function (props) {
     const { regions, features, bpPerPx, width, height, sources, onMouseLeave = () => { }, onMouseMove = () => { }, onFeatureClick = () => { }, displayModel, } = props;
     const region = regions[0];

package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts

@@ -1,5 +1,6 @@
-import { Feature } from '@jbrowse/core/util';
-import WiggleBaseRenderer, { MultiRenderArgsDeserialized as MultiArgs } from '../WiggleBaseRenderer';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import type { MultiRenderArgsDeserialized as MultiArgs } from '../WiggleBaseRenderer';
+import type { Feature } from '@jbrowse/core/util';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: MultiArgs): Promise<{
         reducedFeatures: Feature[];

package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js

@@ -1,9 +1,8 @@
 import { groupBy } from '@jbrowse/core/util';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
 import { drawXY } from '../drawXY';
 import { YSCALEBAR_LABEL_OFFSET } from '../util';
-import WiggleBaseRenderer from '../WiggleBaseRenderer';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
-    // @ts-expect-error
     async draw(ctx, props) {
         const { sources, features } = props;
         const groups = groupBy(features.values(), f => f.get('source'));

package/esm/MultiXYPlotRenderer/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     filled: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     displayCrossHatches: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     summaryScoreMode: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     minSize: {
         type: string;
         defaultValue: number;

package/esm/MultiXYPlotRenderer/configSchema.js

@@ -1,46 +1,28 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
 import baseWiggleRendererConfigSchema from '../configSchema';
-/**
- * #config MultiXYPlotRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('MultiXYPlotRenderer', {
-    /**
-     * #slot
-     */
     filled: {
         type: 'boolean',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     displayCrossHatches: {
         type: 'boolean',
         description: 'choose to draw cross hatches (sideways lines)',
         defaultValue: false,
     },
-    /**
-     * #slot
-     */
     summaryScoreMode: {
         type: 'stringEnum',
         model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
         description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
         defaultValue: 'avg',
     },
-    /**
-     * #slot
-     */
     minSize: {
         type: 'number',
-        defaultValue: 0,
+        defaultValue: 0.7,
     },
 }, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: baseWiggleRendererConfigSchema,
     explicitlyTyped: true,
 });

package/esm/MultiXYPlotRenderer/index.d.ts

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

package/esm/QuantitativeTrack/configSchema.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare function configSchemaFactory(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/QuantitativeTrack/configSchema.js

@@ -1,14 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes/models';
-/**
- * #config QuantitativeTrack
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 function configSchemaFactory(pluginManager) {
     return ConfigurationSchema('QuantitativeTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: createBaseTrackConfig(pluginManager),
     });
 }

package/esm/QuantitativeTrack/index.d.ts

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

package/esm/QuantitativeTrack/index.js

@@ -1,5 +1,5 @@
-import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import configSchemaF from './configSchema';
 export default function QuantitativeTrackF(pluginManager) {
     pluginManager.addTrackType(() => {

package/esm/Tooltip.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 export type TooltipContentsComponent = React.ForwardRefExoticComponent<{
     feature: Feature;

package/esm/Tooltip.js

@@ -1,8 +1,7 @@
 import React, { Suspense } from 'react';
+import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
-// locals
 import { YSCALEBAR_LABEL_OFFSET } from './util';
 const useStyles = makeStyles()({
     hoverVertical: {

package/esm/WiggleBaseRenderer.d.ts

@@ -1,7 +1,8 @@
-import FeatureRendererType, { RenderArgs as FeatureRenderArgs, RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { Feature } from '@jbrowse/core/util';
-import { ThemeOptions } from '@mui/material';
-import { ScaleOpts, Source } from './util';
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { ScaleOpts, Source } from './util';
+import type { RenderArgs as FeatureRenderArgs, RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ThemeOptions } from '@mui/material';
 export interface RenderArgs extends FeatureRenderArgs {
     scaleOpts: ScaleOpts;
 }
@@ -48,10 +49,6 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         reactElement?: import("react").ReactElement;
         html?: string;
     }>;
-    /**
-     * draw features to context given props, to be used by derived renderer
-     * classes
-     */
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;
 }
-export { type RenderArgsSerialized, type RenderResults, type ResultsDeserialized, type ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/esm/WiggleBaseRenderer.js

@@ -10,7 +10,6 @@ export default class WiggleBaseRenderer extends FeatureRendererType {
         const { height, regions, bpPerPx } = renderProps;
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
-        // @ts-expect-error
         const { reducedFeatures, ...rest } = await renderToAbstractCanvas(width, height, renderProps, ctx => this.draw(ctx, {
             ...renderProps,
             features,

package/esm/WiggleRPC/MultiWiggleGetSources.d.ts

@@ -1,18 +1,11 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export declare class MultiWiggleGetSources extends RpcMethodType {
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiWiggleGetSources extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriverClassName: string): Promise<Record<string, unknown>>;
     execute(args: {
         adapterConfig: AnyConfigurationModel;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/WiggleRPC/MultiWiggleGetSources.js

@@ -1,42 +1,15 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { renameRegionsIfNeeded } from '@jbrowse/core/util';
-export class MultiWiggleGetSources extends RpcMethodType {
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+export class MultiWiggleGetSources extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
         this.name = 'MultiWiggleGetSources';
     }
-    async deserializeArguments(args, rpcDriverClassName) {
-        const l = await super.deserializeArguments(args, rpcDriverClassName);
-        return {
-            ...l,
-            filters: args.filters
-                ? new SerializableFilterChain({
-                    filters: args.filters,
-                })
-                : undefined,
-        };
-    }
-    async serializeArguments(args, rpcDriverClassName) {
-        var _a, _b, _c;
-        const pm = this.pluginManager;
-        const assemblyManager = (_b = (_a = pm.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
-        if (!assemblyManager) {
-            return args;
-        }
-        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-            ...args,
-            filters: (_c = args.filters) === null || _c === void 0 ? void 0 : _c.toJSON().filters,
-        });
-        return super.serializeArguments(renamedArgs, rpcDriverClassName);
-    }
     async execute(args, rpcDriverClassName) {
         const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { regions, adapterConfig, sessionId } = deserializedArgs;
         const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
-        // @ts-expect-error
         return dataAdapter.getSources(regions, deserializedArgs);
     }
 }

package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts

@@ -1,13 +1,11 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-import { QuantitativeStats } from '@jbrowse/core/util/stats';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export declare class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { QuantitativeStats } from '@jbrowse/core/util/stats';
+export declare class WiggleGetGlobalQuantitativeStats extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
     execute(args: {
         adapterConfig: AnyConfigurationModel;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         headers?: Record<string, string>;
         sessionId: string;
     }, rpcDriverClassName: string): Promise<QuantitativeStats>;

package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js

@@ -1,28 +1,15 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+export class WiggleGetGlobalQuantitativeStats extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
         this.name = 'WiggleGetGlobalQuantitativeStats';
     }
-    async deserializeArguments(args, rpcDriverClassName) {
-        const l = await super.deserializeArguments(args, rpcDriverClassName);
-        return {
-            ...l,
-            filters: args.filters
-                ? new SerializableFilterChain({
-                    filters: args.filters,
-                })
-                : undefined,
-        };
-    }
     async execute(args, rpcDriverClassName) {
         const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { adapterConfig, sessionId } = deserializedArgs;
         const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
-        // @ts-expect-error
         return dataAdapter.getGlobalStats(deserializedArgs);
     }
 }

package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts

@@ -1,17 +1,10 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-import { Region } from '@jbrowse/core/util';
-export declare class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { Region } from '@jbrowse/core/util';
+export declare class WiggleGetMultiRegionQuantitativeStats extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriverClassName: string): Promise<Record<string, unknown>>;
     execute(args: {
         adapterConfig: Record<string, unknown>;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js

@@ -1,42 +1,15 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { renameRegionsIfNeeded } from '@jbrowse/core/util';
-export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
         this.name = 'WiggleGetMultiRegionQuantitativeStats';
     }
-    async deserializeArguments(args, rpcDriverClassName) {
-        const l = await super.deserializeArguments(args, rpcDriverClassName);
-        return {
-            ...l,
-            filters: args.filters
-                ? new SerializableFilterChain({
-                    filters: args.filters,
-                })
-                : undefined,
-        };
-    }
-    async serializeArguments(args, rpcDriverClassName) {
-        var _a, _b, _c;
-        const pm = this.pluginManager;
-        const assemblyManager = (_b = (_a = pm.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
-        if (!assemblyManager) {
-            return args;
-        }
-        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-            ...args,
-            filters: (_c = args.filters) === null || _c === void 0 ? void 0 : _c.toJSON().filters,
-        });
-        return super.serializeArguments(renamedArgs, rpcDriverClassName);
-    }
     async execute(args, rpcDriverClassName) {
         const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { regions, adapterConfig, sessionId } = deserializedArgs;
         const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
-        // @ts-expect-error
         return dataAdapter.getMultiRegionQuantitativeStats(regions, deserializedArgs);
     }
 }

package/esm/WiggleRendering.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 declare const WiggleRendering: (props: {
     regions: Region[];
     features: Map<string, Feature>;

package/esm/WiggleRendering.js

@@ -1,12 +1,11 @@
-import { observer } from 'mobx-react';
 import React, { useRef } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
 const WiggleRendering = observer(function (props) {
     const { regions, features, bpPerPx, width, height, onMouseLeave, onMouseMove, onFeatureClick, } = props;
     const region = regions[0];
     const ref = useRef(null);
     function getFeatureUnderMouse(eventClientX) {
-        // calculates feature under mouse
         let offset = 0;
         if (ref.current) {
             offset = ref.current.getBoundingClientRect().left;
@@ -16,7 +15,6 @@ const WiggleRendering = observer(function (props) {
         const clientBp = region.start + bpPerPx * px;
         let featureUnderMouse;
         for (const feature of features.values()) {
-            // bpPerPx added to the end to accommodate "reduced features" (one feature per px)
             if (clientBp <= feature.get('end') + bpPerPx &&
                 clientBp >= feature.get('start')) {
                 featureUnderMouse = feature;