@jbrowse/plugin-hic 2.18.0 → 3.0.0

package/dist/GuessAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GuessAdapterF(pluginManager: PluginManager): void;

package/dist/GuessAdapter/index.js

@@ -0,0 +1,23 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = GuessAdapterF;
+const tracks_1 = require("@jbrowse/core/util/tracks");
+function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = (0, tracks_1.getFileName)(file);
+            return (/\.hic$/i.test(fileName) && !adapterHint) ||
+                adapterHint === 'HicAdapter'
+                ? {
+                    type: 'HicAdapter',
+                    hicLocation: file,
+                }
+                : adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => adapterName === 'HicAdapter'
+            ? 'HicTrack'
+            : trackTypeGuesser(adapterName);
+    });
+}

package/dist/HicAdapter/HicFilehandle.d.ts

@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { FileLocation } from '@jbrowse/core/util';
-import type { GenericFilehandle } from 'generic-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
 declare class HicFilehandle {
     private filehandle;
     constructor(filehandle: GenericFilehandle);

package/dist/HicAdapter/HicFilehandle.js

@@ -1,14 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.openHicFilehandle = openHicFilehandle;
-const buffer_1 = require("buffer");
 const io_1 = require("@jbrowse/core/util/io");
 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);
+        const buffer = await this.filehandle.read(length, position);
         return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + buffer.byteLength);
     }
 }

package/dist/HicAdapter/index.js

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

package/dist/HicRenderer/HicRenderer.d.ts

@@ -33,18 +33,18 @@ export default class HicRenderer extends ServerSideRendererType {
         height: any;
         width: number;
         canvasRecordedData: any;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         height: any;
         width: number;
-        reactElement: React.JSX.Element;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         html?: string;
     } | {
         height: any;
         width: number;
         imageData: any;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     }>;
     getFeatures(args: RenderArgsDeserialized): Promise<any>;

package/dist/HicRenderer/HicRenderer.js

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

package/dist/HicRenderer/components/HicRendering.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { Region } from '@jbrowse/core/util/types';
 declare const HicRendering: (props: {
     blockKey: string;
@@ -6,5 +5,5 @@ declare const HicRendering: (props: {
     height: number;
     regions: Region[];
     bpPerPx: number;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default HicRendering;

package/dist/HicRenderer/components/HicRendering.js

@@ -1,15 +1,11 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
 const HicRendering = (0, mobx_react_1.observer)(function HicRendering(props) {
     const { width, height } = props;
     const canvasWidth = Math.ceil(width);
-    return (react_1.default.createElement("div", { style: { position: 'relative', width: canvasWidth, height } },
-        react_1.default.createElement(ui_1.PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } })));
+    return ((0, jsx_runtime_1.jsx)("div", { style: { position: 'relative', width: canvasWidth, height }, children: (0, jsx_runtime_1.jsx)(ui_1.PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }) }));
 });
 exports.default = HicRendering;

package/dist/HicRenderer/makeImageData.js

@@ -13,6 +13,8 @@ const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
 const viridis_1 = __importDefault(require("./viridis"));
 async function makeImageData(ctx, 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 (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
     const res = await dataAdapter.getResolution(bpPerPx / resolution);

package/dist/LinearHicDisplay/model.d.ts

@@ -34,7 +34,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -173,13 +173,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     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;
@@ -206,7 +206,7 @@ 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;
 } & {
     availableNormalizations: string[] | undefined;
@@ -287,7 +287,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/index.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const colord_1 = require("@jbrowse/core/util/colord");
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
 const HicAdapter_1 = __importDefault(require("./HicAdapter"));
 const HicRenderer_1 = __importDefault(require("./HicRenderer"));
 const HicTrack_1 = __importDefault(require("./HicTrack"));
@@ -20,31 +20,7 @@ class HicPlugin extends Plugin_1.default {
         (0, HicRenderer_1.default)(pluginManager);
         (0, HicTrack_1.default)(pluginManager);
         (0, LinearHicDisplay_1.default)(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.hic/i;
-                const adapterName = 'HicAdapter';
-                const fileName = (0, tracks_1.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);
-        });
+        (0, GuessAdapter_1.default)(pluginManager);
     }
     configure(pluginManager) {
         const { jexl } = pluginManager;

package/esm/GuessAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GuessAdapterF(pluginManager: PluginManager): void;

package/esm/GuessAdapter/index.js

@@ -0,0 +1,20 @@
+import { getFileName } from '@jbrowse/core/util/tracks';
+export default function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = getFileName(file);
+            return (/\.hic$/i.test(fileName) && !adapterHint) ||
+                adapterHint === 'HicAdapter'
+                ? {
+                    type: 'HicAdapter',
+                    hicLocation: file,
+                }
+                : adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => adapterName === 'HicAdapter'
+            ? 'HicTrack'
+            : trackTypeGuesser(adapterName);
+    });
+}

package/esm/HicAdapter/HicFilehandle.d.ts

@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { FileLocation } from '@jbrowse/core/util';
-import type { GenericFilehandle } from 'generic-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
 declare class HicFilehandle {
     private filehandle;
     constructor(filehandle: GenericFilehandle);

package/esm/HicAdapter/HicFilehandle.js

@@ -1,11 +1,10 @@
-import { Buffer } from 'buffer';
 import { openLocation } from '@jbrowse/core/util/io';
 class HicFilehandle {
     constructor(filehandle) {
         this.filehandle = filehandle;
     }
     async read(position, length) {
-        const { buffer } = await this.filehandle.read(Buffer.alloc(length), 0, length, position);
+        const buffer = await this.filehandle.read(length, position);
         return buffer.buffer.slice(buffer.byteOffset, buffer.byteOffset + buffer.byteLength);
     }
 }

package/esm/HicRenderer/HicRenderer.d.ts

@@ -33,18 +33,18 @@ export default class HicRenderer extends ServerSideRendererType {
         height: any;
         width: number;
         canvasRecordedData: any;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         height: any;
         width: number;
-        reactElement: React.JSX.Element;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         html?: string;
     } | {
         height: any;
         width: number;
         imageData: any;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     }>;
     getFeatures(args: RenderArgsDeserialized): Promise<any>;

package/esm/HicRenderer/components/HicRendering.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { Region } from '@jbrowse/core/util/types';
 declare const HicRendering: (props: {
     blockKey: string;
@@ -6,5 +5,5 @@ declare const HicRendering: (props: {
     height: number;
     regions: Region[];
     bpPerPx: number;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default HicRendering;

package/esm/HicRenderer/components/HicRendering.js

@@ -1,10 +1,9 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 const HicRendering = observer(function HicRendering(props) {
     const { width, height } = props;
     const canvasWidth = Math.ceil(width);
-    return (React.createElement("div", { style: { position: 'relative', width: canvasWidth, height } },
-        React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } })));
+    return (_jsx("div", { style: { position: 'relative', width: canvasWidth, height }, children: _jsx(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }) }));
 });
 export default HicRendering;

package/esm/HicRenderer/makeImageData.js

@@ -7,6 +7,8 @@ import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-sc
 import interpolateViridis from './viridis';
 export async function makeImageData(ctx, 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);

package/esm/LinearHicDisplay/model.d.ts

@@ -34,7 +34,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -173,13 +173,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     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;
@@ -206,7 +206,7 @@ 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;
 } & {
     availableNormalizations: string[] | undefined;
@@ -287,7 +287,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/esm/index.js

@@ -1,6 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { colord } from '@jbrowse/core/util/colord';
-import { getFileName } from '@jbrowse/core/util/tracks';
+import GuessAdapterF from './GuessAdapter';
 import HicAdapterF from './HicAdapter';
 import HicRendererF from './HicRenderer';
 import HicTrackF from './HicTrack';
@@ -15,31 +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": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }