@jbrowse/plugin-hic 2.16.0 → 2.17.0

package/dist/HicAdapter/HicAdapter.d.ts

@@ -1,28 +1,23 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, FileLocation } from '@jbrowse/core/util/types';
-import type { GenericFilehandle } from 'generic-filehandle';
+import { Region } from '@jbrowse/core/util/types';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 interface HicOptions extends BaseOptions {
     resolution?: number;
     bpPerPx?: number;
+    normalization?: string;
 }
-declare class GenericFilehandleWrapper {
-    private filehandle;
-    constructor(filehandle: GenericFilehandle);
-    read(position: number, length: number): Promise<ArrayBuffer>;
-}
-export declare function openFilehandleWrapper(location: FileLocation, pluginManager?: PluginManager): GenericFilehandleWrapper;
 export default class HicAdapter extends BaseFeatureDataAdapter {
     private hic;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     private setup;
     getHeader(opts?: BaseOptions): Promise<{
+        norms: any;
         resolutions: number[];
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getResolution(bpPerPx: number, opts?: BaseOptions): Promise<number>;
+    getResolution(res: number, opts?: BaseOptions): Promise<number>;
     getFeatures(region: Region, opts?: HicOptions): any;
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;

package/dist/HicAdapter/HicAdapter.js

@@ -3,57 +3,40 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.openFilehandleWrapper = openFilehandleWrapper;
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const io_1 = require("@jbrowse/core/util/io");
 const hic_straw_1 = __importDefault(require("hic-straw"));
-const buffer_1 = require("buffer");
-// wraps generic-filehandle so the read function only takes a position and
-// length in some ways, generic-filehandle wishes it was just this but it has
-// to adapt to the node.js fs promises API
-class GenericFilehandleWrapper {
-    constructor(filehandle) {
-        this.filehandle = filehandle;
-    }
-    async read(position, length) {
-        const { buffer } = await this.filehandle.read(buffer_1.Buffer.alloc(length), 0, length, position);
-        return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + buffer.byteLength);
-    }
-}
-function openFilehandleWrapper(location, pluginManager) {
-    return new GenericFilehandleWrapper((0, io_1.openLocation)(location, pluginManager));
-}
+const util_1 = require("@jbrowse/core/util");
+// locals
+const HicFilehandle_1 = require("./HicFilehandle");
 class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const hicLocation = this.getConf('hicLocation');
         this.hic = new hic_straw_1.default({
-            file: openFilehandleWrapper(hicLocation, this.pluginManager),
+            file: (0, HicFilehandle_1.openHicFilehandle)(this.getConf('hicLocation'), this.pluginManager),
         });
     }
     async setup(opts) {
         const { statusCallback = () => { } } = opts || {};
-        statusCallback('Downloading .hic header');
-        const result = await this.hic.getMetaData();
-        statusCallback('');
-        return result;
+        return (0, util_1.updateStatus)('Downloading .hic header', statusCallback, () => this.hic.getMetaData());
     }
     async getHeader(opts) {
-        const ret = await this.setup(opts);
-        const { chromosomes, ...rest } = ret;
-        return rest;
+        const { chromosomes, ...rest } = await this.setup(opts);
+        // @ts-expect-error
+        const norms = await this.hic.getNormalizationOptions();
+        return { ...rest, norms };
     }
     async getRefNames(opts) {
         const metadata = await this.setup(opts);
         return metadata.chromosomes.map(chr => chr.name);
     }
-    async getResolution(bpPerPx, opts) {
+    async getResolution(res, opts) {
         const { resolutions } = await this.setup(opts);
+        const resolutionMultiplier = this.getConf('resolutionMultiplier');
         let chosenResolution = resolutions.at(-1);
         for (let i = resolutions.length - 1; i >= 0; i -= 1) {
             const r = resolutions[i];
-            if (r <= 2 * bpPerPx) {
+            if (r <= 2 * res * resolutionMultiplier) {
                 chosenResolution = r;
             }
         }
@@ -62,20 +45,22 @@ class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { refName: chr, start, end } = region;
-            const { resolution, bpPerPx = 1, statusCallback = () => { } } = opts;
+            const { resolution, normalization = 'KR', bpPerPx = 1, statusCallback = () => { }, } = opts;
             const res = await this.getResolution(bpPerPx / (resolution || 1000), opts);
-            statusCallback('Downloading .hic data');
-            const records = await this.hic.getContactRecords('KR', { start, chr, end }, { start, chr, end }, 'BP', res);
-            for (const record of records) {
-                observer.next(record);
-            }
-            statusCallback('');
+            await (0, util_1.updateStatus)('Downloading .hic data', statusCallback, async () => {
+                const records = await this.hic.getContactRecords(normalization, { start, chr, end }, { start, chr, end }, 'BP', res);
+                for (const record of records) {
+                    observer.next(record);
+                }
+            });
             observer.complete();
         }, opts.signal);
     }
     // don't do feature stats estimation, similar to bigwigadapter
     async getMultiRegionFeatureDensityStats(_regions) {
-        return { featureDensity: 0 };
+        return {
+            featureDensity: 0,
+        };
     }
     freeResources( /* { region } */) { }
 }

package/dist/HicAdapter/HicFilehandle.d.ts

@@ -0,0 +1,10 @@
+import { FileLocation } from '@jbrowse/core/util';
+import type { GenericFilehandle } from 'generic-filehandle';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare class HicFilehandle {
+    private filehandle;
+    constructor(filehandle: GenericFilehandle);
+    read(position: number, length: number): Promise<ArrayBuffer>;
+}
+export declare function openHicFilehandle(location: FileLocation, pluginManager?: PluginManager): HicFilehandle;
+export {};

package/dist/HicAdapter/HicFilehandle.js

@@ -0,0 +1,22 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.openHicFilehandle = openHicFilehandle;
+const io_1 = require("@jbrowse/core/util/io");
+const buffer_1 = require("buffer");
+// wraps generic-filehandle so the read function only takes a position and
+// length
+//
+// in some ways, generic-filehandle wishes it was just this but it has
+// to adapt to the node.js fs promises API
+class HicFilehandle {
+    constructor(filehandle) {
+        this.filehandle = filehandle;
+    }
+    async read(position, length) {
+        const { buffer } = await this.filehandle.read(buffer_1.Buffer.alloc(length), 0, length, position);
+        return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + buffer.byteLength);
+    }
+}
+function openHicFilehandle(location, pluginManager) {
+    return new HicFilehandle((0, io_1.openLocation)(location, pluginManager));
+}

package/dist/HicAdapter/configSchema.d.ts

@@ -9,5 +9,13 @@ declare const HicAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    /**
+     * #slot
+     */
+    resolutionMultiplier: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HicAdapter;

package/dist/HicAdapter/configSchema.js

@@ -17,5 +17,13 @@ const HicAdapter = (0, configuration_1.ConfigurationSchema)('HicAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
+    resolutionMultiplier: {
+        type: 'number',
+        defaultValue: 1,
+        description: 'Initial resolution multiplier',
+    },
 }, { explicitlyTyped: true });
 exports.default = HicAdapter;

package/dist/HicRenderer/HicRenderer.d.ts

@@ -48,4 +48,4 @@ export default class HicRenderer extends ServerSideRendererType {
     }>;
     getFeatures(args: RenderArgsDeserialized): Promise<any>;
 }
-export { type RenderArgsSerialized, type RenderResults, } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+export type { RenderArgsSerialized, RenderResults, } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';

package/dist/LinearHicDisplay/model.d.ts

@@ -1,12 +1,6 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import(
-    /**
-     * #stateModel LinearHicDisplay
-     * #category display
-     * extends `BaseLinearDisplay`
-     */
-    "mobx-state-tree").ISimpleType<string>, [undefined]>;
+    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>>;
 } & {
@@ -18,12 +12,16 @@ 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>;
+            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").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree" /**
+             * #property
+             */).ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -33,9 +31,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: React.ReactElement /**
-         * #getter
-         */ | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -44,13 +40,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error? /**
-                 * #method
-                 */: unknown;
+                error?: unknown;
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status?: string;
+                status
+                /**
+                 * #getter
+                 */
+                ? /**
+                 * #getter
+                 */: string;
                 reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
@@ -106,6 +106,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     useLogScale: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorScheme: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    activeNormalization: import("mobx-state-tree").IType<string | undefined, string, string>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -120,17 +121,19 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #getter
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        } & import("mobx-state-tree" /**
+         * #property
+         */).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>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree" /**
+         * #method
+         */)._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -233,6 +236,11 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
     afterAttach(): void;
+} & {
+    /**
+     * #volatile
+     */
+    availableNormalizations: string[] | undefined;
 } & {
     /**
      * #getter
@@ -259,6 +267,14 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #action
      */
     setColorScheme(f?: string): void;
+    /**
+     * #action
+     */
+    setActiveNormalization(f: string): void;
+    /**
+     * #action
+     */
+    setAvailableNormalizations(f: string[]): void;
 } & {
     /**
      * #getter
@@ -278,7 +294,20 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         }[];
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     })[];
+} & {
+    afterAttach(): void;
 }, {
     type: string;
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -309,9 +338,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: React.ReactElement /**
-         * #getter
-         */ | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -320,13 +347,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error? /**
-                 * #method
-                 */: unknown;
+                error?: unknown;
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status?: string;
+                status
+                /**
+                 * #getter
+                 */
+                ? /**
+                 * #getter
+                 */: string;
                 reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;

package/dist/LinearHicDisplay/model.js

@@ -4,6 +4,8 @@ exports.default = stateModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
 /**
  * #stateModel LinearHicDisplay
  * #category display
@@ -33,6 +35,16 @@ function stateModelFactory(configSchema) {
          * #property
          */
         colorScheme: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        /**
+         * #property
+         */
+        activeNormalization: 'KR',
+    }))
+        .volatile(() => ({
+        /**
+         * #volatile
+         */
+        availableNormalizations: undefined,
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
@@ -63,6 +75,7 @@ function stateModelFactory(configSchema) {
                 return {
                     ...superRenderProps(),
                     config,
+                    normalization: self.activeNormalization,
                     rpcDriverName: self.rpcDriverName,
                     displayModel: self,
                     resolution: self.resolution,
@@ -91,6 +104,18 @@ function stateModelFactory(configSchema) {
         setColorScheme(f) {
             self.colorScheme = f;
         },
+        /**
+         * #action
+         */
+        setActiveNormalization(f) {
+            self.activeNormalization = f;
+        },
+        /**
+         * #action
+         */
+        setAvailableNormalizations(f) {
+            self.availableNormalizations = f;
+        },
     }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
@@ -156,8 +181,44 @@ function stateModelFactory(configSchema) {
                             },
                         ],
                     },
+                    ...(self.availableNormalizations
+                        ? [
+                            {
+                                label: 'Normalization scheme',
+                                subMenu: self.availableNormalizations.map(norm => ({
+                                    label: norm,
+                                    type: 'checkbox',
+                                    checked: norm === self.activeNormalization,
+                                    onClick: () => {
+                                        self.setActiveNormalization(norm);
+                                    },
+                                })),
+                            },
+                        ]
+                        : []),
                 ];
             },
         };
-    });
+    })
+        .actions(self => ({
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+                try {
+                    const { rpcManager } = (0, util_1.getSession)(self);
+                    const track = (0, util_1.getContainingTrack)(self);
+                    const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
+                    const { norms } = (await rpcManager.call((0, configuration_1.getConf)(track, 'trackId'), 'CoreGetInfo', {
+                        adapterConfig,
+                    }));
+                    if (norms) {
+                        self.setAvailableNormalizations(norms);
+                    }
+                }
+                catch (e) {
+                    console.error(e);
+                    (0, util_1.getSession)(self).notifyError(`${e}`, e);
+                }
+            }));
+        },
+    }));
 }

package/esm/HicAdapter/HicAdapter.d.ts

@@ -1,28 +1,23 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, FileLocation } from '@jbrowse/core/util/types';
-import type { GenericFilehandle } from 'generic-filehandle';
+import { Region } from '@jbrowse/core/util/types';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 interface HicOptions extends BaseOptions {
     resolution?: number;
     bpPerPx?: number;
+    normalization?: string;
 }
-declare class GenericFilehandleWrapper {
-    private filehandle;
-    constructor(filehandle: GenericFilehandle);
-    read(position: number, length: number): Promise<ArrayBuffer>;
-}
-export declare function openFilehandleWrapper(location: FileLocation, pluginManager?: PluginManager): GenericFilehandleWrapper;
 export default class HicAdapter extends BaseFeatureDataAdapter {
     private hic;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     private setup;
     getHeader(opts?: BaseOptions): Promise<{
+        norms: any;
         resolutions: number[];
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getResolution(bpPerPx: number, opts?: BaseOptions): Promise<number>;
+    getResolution(res: number, opts?: BaseOptions): Promise<number>;
     getFeatures(region: Region, opts?: HicOptions): any;
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;

package/esm/HicAdapter/HicAdapter.js

@@ -1,53 +1,37 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { openLocation } from '@jbrowse/core/util/io';
 import HicStraw from 'hic-straw';
-import { Buffer } from 'buffer';
-// wraps generic-filehandle so the read function only takes a position and
-// length in some ways, generic-filehandle wishes it was just this but it has
-// to adapt to the node.js fs promises API
-class GenericFilehandleWrapper {
-    constructor(filehandle) {
-        this.filehandle = filehandle;
-    }
-    async read(position, length) {
-        const { buffer } = await this.filehandle.read(Buffer.alloc(length), 0, length, position);
-        return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + buffer.byteLength);
-    }
-}
-export function openFilehandleWrapper(location, pluginManager) {
-    return new GenericFilehandleWrapper(openLocation(location, pluginManager));
-}
+import { updateStatus } from '@jbrowse/core/util';
+// locals
+import { openHicFilehandle } from './HicFilehandle';
 export default class HicAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const hicLocation = this.getConf('hicLocation');
         this.hic = new HicStraw({
-            file: openFilehandleWrapper(hicLocation, this.pluginManager),
+            file: openHicFilehandle(this.getConf('hicLocation'), this.pluginManager),
         });
     }
     async setup(opts) {
         const { statusCallback = () => { } } = opts || {};
-        statusCallback('Downloading .hic header');
-        const result = await this.hic.getMetaData();
-        statusCallback('');
-        return result;
+        return updateStatus('Downloading .hic header', statusCallback, () => this.hic.getMetaData());
     }
     async getHeader(opts) {
-        const ret = await this.setup(opts);
-        const { chromosomes, ...rest } = ret;
-        return rest;
+        const { chromosomes, ...rest } = await this.setup(opts);
+        // @ts-expect-error
+        const norms = await this.hic.getNormalizationOptions();
+        return { ...rest, norms };
     }
     async getRefNames(opts) {
         const metadata = await this.setup(opts);
         return metadata.chromosomes.map(chr => chr.name);
     }
-    async getResolution(bpPerPx, opts) {
+    async getResolution(res, opts) {
         const { resolutions } = await this.setup(opts);
+        const resolutionMultiplier = this.getConf('resolutionMultiplier');
         let chosenResolution = resolutions.at(-1);
         for (let i = resolutions.length - 1; i >= 0; i -= 1) {
             const r = resolutions[i];
-            if (r <= 2 * bpPerPx) {
+            if (r <= 2 * res * resolutionMultiplier) {
                 chosenResolution = r;
             }
         }
@@ -56,20 +40,22 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { refName: chr, start, end } = region;
-            const { resolution, bpPerPx = 1, statusCallback = () => { } } = opts;
+            const { resolution, normalization = 'KR', bpPerPx = 1, statusCallback = () => { }, } = opts;
             const res = await this.getResolution(bpPerPx / (resolution || 1000), opts);
-            statusCallback('Downloading .hic data');
-            const records = await this.hic.getContactRecords('KR', { start, chr, end }, { start, chr, end }, 'BP', res);
-            for (const record of records) {
-                observer.next(record);
-            }
-            statusCallback('');
+            await updateStatus('Downloading .hic data', statusCallback, async () => {
+                const records = await this.hic.getContactRecords(normalization, { start, chr, end }, { start, chr, end }, 'BP', res);
+                for (const record of records) {
+                    observer.next(record);
+                }
+            });
             observer.complete();
         }, opts.signal);
     }
     // don't do feature stats estimation, similar to bigwigadapter
     async getMultiRegionFeatureDensityStats(_regions) {
-        return { featureDensity: 0 };
+        return {
+            featureDensity: 0,
+        };
     }
     freeResources( /* { region } */) { }
 }

package/esm/HicAdapter/HicFilehandle.d.ts

@@ -0,0 +1,10 @@
+import { FileLocation } from '@jbrowse/core/util';
+import type { GenericFilehandle } from 'generic-filehandle';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare class HicFilehandle {
+    private filehandle;
+    constructor(filehandle: GenericFilehandle);
+    read(position: number, length: number): Promise<ArrayBuffer>;
+}
+export declare function openHicFilehandle(location: FileLocation, pluginManager?: PluginManager): HicFilehandle;
+export {};

package/esm/HicAdapter/HicFilehandle.js

@@ -0,0 +1,19 @@
+import { openLocation } from '@jbrowse/core/util/io';
+import { Buffer } from 'buffer';
+// wraps generic-filehandle so the read function only takes a position and
+// length
+//
+// in some ways, generic-filehandle wishes it was just this but it has
+// to adapt to the node.js fs promises API
+class HicFilehandle {
+    constructor(filehandle) {
+        this.filehandle = filehandle;
+    }
+    async read(position, length) {
+        const { buffer } = await this.filehandle.read(Buffer.alloc(length), 0, length, position);
+        return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + buffer.byteLength);
+    }
+}
+export function openHicFilehandle(location, pluginManager) {
+    return new HicFilehandle(openLocation(location, pluginManager));
+}

package/esm/HicAdapter/configSchema.d.ts

@@ -9,5 +9,13 @@ declare const HicAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    /**
+     * #slot
+     */
+    resolutionMultiplier: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HicAdapter;

package/esm/HicAdapter/configSchema.js

@@ -15,5 +15,13 @@ const HicAdapter = ConfigurationSchema('HicAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
+    resolutionMultiplier: {
+        type: 'number',
+        defaultValue: 1,
+        description: 'Initial resolution multiplier',
+    },
 }, { explicitlyTyped: true });
 export default HicAdapter;

package/esm/HicRenderer/HicRenderer.d.ts

@@ -48,4 +48,4 @@ export default class HicRenderer extends ServerSideRendererType {
     }>;
     getFeatures(args: RenderArgsDeserialized): Promise<any>;
 }
-export { type RenderArgsSerialized, type RenderResults, } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+export type { RenderArgsSerialized, RenderResults, } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';

package/esm/LinearHicDisplay/model.d.ts

@@ -1,12 +1,6 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import(
-    /**
-     * #stateModel LinearHicDisplay
-     * #category display
-     * extends `BaseLinearDisplay`
-     */
-    "mobx-state-tree").ISimpleType<string>, [undefined]>;
+    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>>;
 } & {
@@ -18,12 +12,16 @@ 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>;
+            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").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree" /**
+             * #property
+             */).ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -33,9 +31,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: React.ReactElement /**
-         * #getter
-         */ | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -44,13 +40,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error? /**
-                 * #method
-                 */: unknown;
+                error?: unknown;
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status?: string;
+                status
+                /**
+                 * #getter
+                 */
+                ? /**
+                 * #getter
+                 */: string;
                 reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
@@ -106,6 +106,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     useLogScale: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorScheme: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    activeNormalization: import("mobx-state-tree").IType<string | undefined, string, string>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -120,17 +121,19 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #getter
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        } & import("mobx-state-tree" /**
+         * #property
+         */).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>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree" /**
+         * #method
+         */)._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -233,6 +236,11 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
     afterAttach(): void;
+} & {
+    /**
+     * #volatile
+     */
+    availableNormalizations: string[] | undefined;
 } & {
     /**
      * #getter
@@ -259,6 +267,14 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #action
      */
     setColorScheme(f?: string): void;
+    /**
+     * #action
+     */
+    setActiveNormalization(f: string): void;
+    /**
+     * #action
+     */
+    setAvailableNormalizations(f: string[]): void;
 } & {
     /**
      * #getter
@@ -278,7 +294,20 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         }[];
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     })[];
+} & {
+    afterAttach(): void;
 }, {
     type: string;
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -309,9 +338,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: React.ReactElement /**
-         * #getter
-         */ | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -320,13 +347,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: {
-                error? /**
-                 * #method
-                 */: unknown;
+                error?: unknown;
                 reload: () => void;
                 message: React.ReactNode;
                 filled?: boolean;
-                status?: string;
+                status
+                /**
+                 * #getter
+                 */
+                ? /**
+                 * #getter
+                 */: string;
                 reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;

package/esm/LinearHicDisplay/model.js

@@ -1,6 +1,8 @@
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
-import { types, getEnv } from 'mobx-state-tree';
+import { types, getEnv, addDisposer } from 'mobx-state-tree';
+import { autorun } from 'mobx';
+import { getContainingTrack, getSession } from '@jbrowse/core/util';
 /**
  * #stateModel LinearHicDisplay
  * #category display
@@ -30,6 +32,16 @@ export default function stateModelFactory(configSchema) {
          * #property
          */
         colorScheme: types.maybe(types.string),
+        /**
+         * #property
+         */
+        activeNormalization: 'KR',
+    }))
+        .volatile(() => ({
+        /**
+         * #volatile
+         */
+        availableNormalizations: undefined,
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
@@ -60,6 +72,7 @@ export default function stateModelFactory(configSchema) {
                 return {
                     ...superRenderProps(),
                     config,
+                    normalization: self.activeNormalization,
                     rpcDriverName: self.rpcDriverName,
                     displayModel: self,
                     resolution: self.resolution,
@@ -88,6 +101,18 @@ export default function stateModelFactory(configSchema) {
         setColorScheme(f) {
             self.colorScheme = f;
         },
+        /**
+         * #action
+         */
+        setActiveNormalization(f) {
+            self.activeNormalization = f;
+        },
+        /**
+         * #action
+         */
+        setAvailableNormalizations(f) {
+            self.availableNormalizations = f;
+        },
     }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
@@ -153,8 +178,44 @@ export default function stateModelFactory(configSchema) {
                             },
                         ],
                     },
+                    ...(self.availableNormalizations
+                        ? [
+                            {
+                                label: 'Normalization scheme',
+                                subMenu: self.availableNormalizations.map(norm => ({
+                                    label: norm,
+                                    type: 'checkbox',
+                                    checked: norm === self.activeNormalization,
+                                    onClick: () => {
+                                        self.setActiveNormalization(norm);
+                                    },
+                                })),
+                            },
+                        ]
+                        : []),
                 ];
             },
         };
-    });
+    })
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, autorun(async () => {
+                try {
+                    const { rpcManager } = getSession(self);
+                    const track = getContainingTrack(self);
+                    const adapterConfig = getConf(track, 'adapter');
+                    const { norms } = (await rpcManager.call(getConf(track, 'trackId'), 'CoreGetInfo', {
+                        adapterConfig,
+                    }));
+                    if (norms) {
+                        self.setAvailableNormalizations(norms);
+                    }
+                }
+                catch (e) {
+                    console.error(e);
+                    getSession(self).notifyError(`${e}`, e);
+                }
+            }));
+        },
+    }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }