@jbrowse/plugin-hic 2.17.0 → 3.0.0

package/esm/HicRenderer/configSchema.d.ts

@@ -1,24 +1,15 @@
 declare const HicRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     baseColor: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     color: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     maxHeight: {
         type: string;
         description: string;

package/esm/HicRenderer/configSchema.js

@@ -1,30 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config HicRenderer
- * #category renderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const HicRenderer = ConfigurationSchema('HicRenderer', {
-    /**
-     * #slot
-     */
     baseColor: {
         type: 'color',
         description: 'base color to be used in the hic alignment',
         defaultValue: '#f00',
     },
-    /**
-     * #slot
-     */
     color: {
         type: 'color',
         description: 'the color of each feature in a hic alignment',
         defaultValue: 'jexl:interpolate(count,scale)',
         contextVariable: ['count', 'maxScore', 'baseColor', 'scale'],
     },
-    /**
-     * #slot
-     */
     maxHeight: {
         type: 'integer',
         description: 'the maximum height to be used in a hic rendering',

package/esm/HicRenderer/index.d.ts

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

package/esm/HicRenderer/index.js

@@ -1,6 +1,6 @@
+import HicRenderer from './HicRenderer';
 import ReactComponent from './components/HicRendering';
 import configSchema from './configSchema';
-import HicRenderer from './HicRenderer';
 export default function HicRendererF(pluginManager) {
     pluginManager.addRendererType(() => new HicRenderer({
         name: 'HicRenderer',

package/esm/HicRenderer/makeImageData.d.ts

@@ -1,7 +1,7 @@
-import { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
-import { Region } from '@jbrowse/core/util/types';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { RenderArgsDeserializedWithFeatures } from './HicRenderer';
+import type { RenderArgsDeserializedWithFeatures } from './HicRenderer';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { Region } from '@jbrowse/core/util/types';
 export interface RenderArgs extends ServerSideRenderArgs {
     regions: Region[];
 }

package/esm/HicRenderer/makeImageData.js

@@ -1,12 +1,14 @@
-import { abortBreakPoint } from '@jbrowse/core/util';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { colord } from '@jbrowse/core/util/colord';
-import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-scale';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
+import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-scale';
 import interpolateViridis from './viridis';
 export async function makeImageData(ctx, props) {
-    const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, } = props;
+    const { features, config, bpPerPx, stopToken, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, } = props;
+    const { statusCallback = () => { } } = props;
+    statusCallback('Drawing Hi-C matrix');
     const region = regions[0];
     const { dataAdapter } = await getAdapter(pluginManager, sessionId, adapterConfig);
     const res = await dataAdapter.getResolution(bpPerPx / resolution);
@@ -18,13 +20,13 @@ export async function makeImageData(ctx, props) {
         let maxScore = 0;
         let minBin = 0;
         let maxBin = 0;
-        await abortBreakPoint(signal);
+        checkStopToken(stopToken);
         for (const { bin1, bin2, counts } of features) {
             maxScore = Math.max(counts, maxScore);
             minBin = Math.min(Math.min(bin1, bin2), minBin);
             maxBin = Math.max(Math.max(bin1, bin2), maxBin);
         }
-        await abortBreakPoint(signal);
+        checkStopToken(stopToken);
         const colorSchemes = {
             juicebox: ['rgba(0,0,0,0)', 'red'],
             fall: interpolateRgbBasis([
@@ -43,7 +45,6 @@ export async function makeImageData(ctx, props) {
             viridis: interpolateViridis,
         };
         const m = useLogScale ? maxScore : maxScore / 20;
-        // @ts-expect-error
         const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
         const scale = useLogScale
             ? scaleSequentialLog(x1).domain([1, m])
@@ -54,7 +55,7 @@ export async function makeImageData(ctx, props) {
             ctx.translate(-width, 0);
         }
         ctx.rotate(-Math.PI / 4);
-        let start = Date.now();
+        let start = performance.now();
         for (const { bin1, bin2, counts } of features) {
             ctx.fillStyle = readConfObject(config, 'color', {
                 count: counts,
@@ -64,9 +65,9 @@ export async function makeImageData(ctx, props) {
                 useLogScale,
             });
             ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
-            if (+Date.now() - start > 400) {
-                await abortBreakPoint(signal);
-                start = +Date.now();
+            if (performance.now() - start > 400) {
+                checkStopToken(stopToken);
+                start = performance.now();
             }
         }
         ctx.restore();

package/esm/HicRenderer/viridis.js

@@ -1,20 +1,3 @@
-// @ts-nocheck
-// vendored from
-// https://github.com/d3/d3-scale-chromatic/blob/main/src/sequential-multi/viridis.js,
-// license reproduced below
-//
-// Copyright 2010-2024 Mike Bostock
-// Permission to use, copy, modify, and/or distribute this software for any purpose
-// with or without fee is hereby granted, provided that the above copyright notice
-// and this permission notice appear in all copies.
-//
-// THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-// REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-// FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-// INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-// OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
-// TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-// THIS SOFTWARE.
 function colors(specifier) {
     const n = (specifier.length / 6) | 0;
     const colors = new Array(n);

package/esm/HicTrack/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/HicTrack/configSchema.js

@@ -1,14 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-/**
- * #config HicTrack
- * #category track
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (pluginManager) => ConfigurationSchema('HicTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: createBaseTrackConfig(pluginManager),
 });
 export default configSchema;

package/esm/HicTrack/index.d.ts

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

package/esm/LinearHicDisplay/configSchema.d.ts

@@ -1,9 +1,6 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 declare const HicTrackConfigFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     renderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {

package/esm/LinearHicDisplay/configSchema.js

@@ -1,20 +1,10 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
-/**
- * #config LinearHicDisplay
- * #category display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const HicTrackConfigFactory = (pluginManager) => {
     return ConfigurationSchema('LinearHicDisplay', {
-        /**
-         * #slot
-         */
         renderer: pluginManager.getRendererType('HicRenderer').configSchema,
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/esm/LinearHicDisplay/index.d.ts

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

package/esm/LinearHicDisplay/model.d.ts

@@ -1,4 +1,4 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelFactory(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>;
@@ -11,25 +11,12 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     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" /**
-             * #property
-             */).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" /**
-             * #property
-             */).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;
@@ -44,30 +31,18 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status
-                /**
-                 * #getter
-                 */
-                ? /**
-                 * #getter
-                 */: string;
+                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;
@@ -121,9 +96,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree" /**
-         * #property
-         */).IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & import("mobx-state-tree").IStateTreeNode<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>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -131,9 +104,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree" /**
-         * #method
-         */)._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -200,14 +171,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     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;
@@ -234,51 +206,21 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     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;
 } & {
-    /**
-     * #volatile
-     */
     availableNormalizations: string[] | undefined;
 } & {
-    /**
-     * #getter
-     */
     readonly blockType: string;
-    /**
-     * #getter
-     */
     readonly rendererTypeName: string;
-    /**
-     * #method
-     */
     renderProps(): any;
 } & {
-    /**
-     * #action
-     */
     setResolution(n: number): void;
-    /**
-     * #action
-     */
     setUseLogScale(f: boolean): void;
-    /**
-     * #action
-     */
     setColorScheme(f?: string): void;
-    /**
-     * #action
-     */
     setActiveNormalization(f: string): void;
-    /**
-     * #action
-     */
     setAvailableNormalizations(f: string[]): void;
 } & {
-    /**
-     * #getter
-     */
     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;
         type: string;
@@ -322,21 +264,12 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     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;
@@ -351,30 +284,18 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status
-                /**
-                 * #getter
-                 */
-                ? /**
-                 * #getter
-                 */: string;
+                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;
@@ -411,8 +332,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     type: string;
     id: string;
     configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    heightPreConfig: number | undefined;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/esm/LinearHicDisplay/model.js

@@ -1,70 +1,34 @@
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import { getContainingTrack, getSession } from '@jbrowse/core/util';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
-import { types, getEnv, addDisposer } from 'mobx-state-tree';
 import { autorun } from 'mobx';
-import { getContainingTrack, getSession } from '@jbrowse/core/util';
-/**
- * #stateModel LinearHicDisplay
- * #category display
- * extends `BaseLinearDisplay`
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import { addDisposer, getEnv, types } from 'mobx-state-tree';
+function x() { }
 export default function stateModelFactory(configSchema) {
     return types
         .compose('LinearHicDisplay', BaseLinearDisplay, types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearHicDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
         resolution: types.optional(types.number, 1),
-        /**
-         * #property
-         */
         useLogScale: false,
-        /**
-         * #property
-         */
         colorScheme: types.maybe(types.string),
-        /**
-         * #property
-         */
         activeNormalization: 'KR',
     }))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         availableNormalizations: undefined,
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
         return {
-            /**
-             * #getter
-             */
             get blockType() {
                 return 'dynamicBlocks';
             },
-            /**
-             * #getter
-             */
             get rendererTypeName() {
                 return 'HicRenderer';
             },
-            /**
-             * #method
-             */
             renderProps() {
                 const config = self.rendererType.configSchema.create({
                     ...getConf(self, 'renderer'),
-                    // add specific jexl color callback when using pre-defined color schemes
                     ...(self.colorScheme
                         ? { color: 'jexl:interpolate(count,scale)' }
                         : {}),
@@ -83,33 +47,18 @@ export default function stateModelFactory(configSchema) {
         };
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         setResolution(n) {
             self.resolution = n;
         },
-        /**
-         * #action
-         */
         setUseLogScale(f) {
             self.useLogScale = f;
         },
-        /**
-         * #action
-         */
         setColorScheme(f) {
             self.colorScheme = f;
         },
-        /**
-         * #action
-         */
         setActiveNormalization(f) {
             self.activeNormalization = f;
         },
-        /**
-         * #action
-         */
         setAvailableNormalizations(f) {
             self.availableNormalizations = f;
         },
@@ -117,9 +66,6 @@ export default function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
-            /**
-             * #getter
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),

package/esm/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 HicPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,11 +1,10 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { colord } from '@jbrowse/core/util/colord';
-import { getFileName, } from '@jbrowse/core/util/tracks';
-// locals
+import GuessAdapterF from './GuessAdapter';
+import HicAdapterF from './HicAdapter';
 import HicRendererF from './HicRenderer';
 import HicTrackF from './HicTrack';
 import LinearHicDisplayF from './LinearHicDisplay';
-import HicAdapterF from './HicAdapter';
 export default class HicPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -16,31 +15,7 @@ export default class HicPlugin extends Plugin {
         HicRendererF(pluginManager);
         HicTrackF(pluginManager);
         LinearHicDisplayF(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.hic/i;
-                const adapterName = 'HicAdapter';
-                const fileName = getFileName(file);
-                const obj = {
-                    type: adapterName,
-                    hicLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                else {
-                    return adapterGuesser(file, index, adapterHint);
-                }
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => adapterName === 'HicAdapter'
-                ? 'HicTrack'
-                : trackTypeGuesser(adapterName);
-        });
+        GuessAdapterF(pluginManager);
     }
     configure(pluginManager) {
         const { jexl } = pluginManager;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }