@jbrowse/plugin-hic 2.6.2 → 2.7.0

package/dist/HicAdapter/HicAdapter.js

@@ -51,7 +51,6 @@ class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getResolution(bpPerPx, opts) {
         const { resolutions } = await this.setup(opts);
-        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
         let chosenResolution = resolutions.at(-1);
         for (let i = resolutions.length - 1; i >= 0; i -= 1) {
             const r = resolutions[i];

package/dist/HicRenderer/HicRenderer.js

@@ -1,27 +1,4 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : 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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -32,6 +9,7 @@ const offscreenCanvasUtils_1 = require("@jbrowse/core/util/offscreenCanvasUtils"
 const operators_1 = require("rxjs/operators");
 const configuration_1 = require("@jbrowse/core/configuration");
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const colord_1 = require("@jbrowse/core/util/colord");
 class HicRenderer extends ServerSideRendererType_1.default {
     constructor() {
         super(...arguments);
@@ -42,17 +20,15 @@ class HicRenderer extends ServerSideRendererType_1.default {
         const [region] = regions;
         const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
         const res = await dataAdapter.getResolution(bpPerPx / resolution);
-        const Color = await Promise.resolve().then(() => __importStar(require('color'))).then(f => f.default);
         const w = res / (bpPerPx * Math.sqrt(2));
-        const baseColor = Color((0, configuration_1.readConfObject)(config, 'baseColor'));
+        const baseColor = (0, colord_1.colord)((0, configuration_1.readConfObject)(config, 'baseColor'));
         if (features.length) {
             const offset = features[0].bin1;
             let maxScore = 0;
             let minBin = 0;
             let maxBin = 0;
             await (0, util_1.abortBreakPoint)(signal);
-            for (let i = 0; i < features.length; i++) {
-                const { bin1, bin2, counts } = features[i];
+            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);
@@ -68,8 +44,7 @@ class HicRenderer extends ServerSideRendererType_1.default {
             }
             ctx.rotate(-Math.PI / 4);
             let start = Date.now();
-            for (let i = 0; i < features.length; i++) {
-                const { bin1, bin2, counts } = features[i];
+            for (const { bin1, bin2, counts } of features) {
                 ctx.fillStyle = (0, configuration_1.readConfObject)(config, 'color', {
                     count: counts,
                     maxScore,

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

@@ -1,10 +1,10 @@
 import React from 'react';
 import { Region } from '@jbrowse/core/util/types';
-declare const _default: (props: {
+declare const HicRendering: (props: {
     blockKey: string;
     width: number;
     height: number;
     regions: Region[];
     bpPerPx: number;
 }) => React.JSX.Element;
-export default _default;
+export default HicRendering;

package/dist/HicRenderer/components/HicRendering.js

@@ -6,10 +6,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
-exports.default = (0, mobx_react_1.observer)(function HicRendering(props) {
+const HicRendering = (0, mobx_react_1.observer)(function HicRendering(props) {
     const { width, height } = props;
     const canvasWidth = Math.ceil(width);
     // need to call this in render so we get the right observer behavior
     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 } })));
 });
+exports.default = HicRendering;

package/dist/index.js

@@ -4,6 +4,7 @@ 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 HicRenderer_1 = __importDefault(require("./HicRenderer"));
 const HicTrack_1 = __importDefault(require("./HicTrack"));
 const LinearHicDisplay_1 = __importDefault(require("./LinearHicDisplay"));
@@ -47,9 +48,10 @@ class HicPlugin extends Plugin_1.default {
         });
     }
     configure(pluginManager) {
-        pluginManager.jexl.addFunction('alpha', (color, value) => color.alpha(value));
-        pluginManager.jexl.addFunction('hsl', (color) => color.hsl());
-        pluginManager.jexl.addFunction('colorString', (color) => color.string());
+        const { jexl } = pluginManager;
+        jexl.addFunction('alpha', (color, n) => color.alpha(n));
+        jexl.addFunction('hsl', (color) => (0, colord_1.colord)(color.toHsl()));
+        jexl.addFunction('colorString', (color) => color.toHex());
     }
 }
 exports.default = HicPlugin;

package/esm/HicAdapter/HicAdapter.js

@@ -44,7 +44,6 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
     }
     async getResolution(bpPerPx, opts) {
         const { resolutions } = await this.setup(opts);
-        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
         let chosenResolution = resolutions.at(-1);
         for (let i = resolutions.length - 1; i >= 0; i -= 1) {
             const r = resolutions[i];

package/esm/HicRenderer/HicRenderer.js

@@ -4,6 +4,7 @@ import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'
 import { toArray } from 'rxjs/operators';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { colord } from '@jbrowse/core/util/colord';
 export default class HicRenderer extends ServerSideRendererType {
     constructor() {
         super(...arguments);
@@ -14,17 +15,15 @@ export default class HicRenderer extends ServerSideRendererType {
         const [region] = regions;
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
         const res = await dataAdapter.getResolution(bpPerPx / resolution);
-        const Color = await import('color').then(f => f.default);
         const w = res / (bpPerPx * Math.sqrt(2));
-        const baseColor = Color(readConfObject(config, 'baseColor'));
+        const baseColor = colord(readConfObject(config, 'baseColor'));
         if (features.length) {
             const offset = features[0].bin1;
             let maxScore = 0;
             let minBin = 0;
             let maxBin = 0;
             await abortBreakPoint(signal);
-            for (let i = 0; i < features.length; i++) {
-                const { bin1, bin2, counts } = features[i];
+            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);
@@ -40,8 +39,7 @@ export default class HicRenderer extends ServerSideRendererType {
             }
             ctx.rotate(-Math.PI / 4);
             let start = Date.now();
-            for (let i = 0; i < features.length; i++) {
-                const { bin1, bin2, counts } = features[i];
+            for (const { bin1, bin2, counts } of features) {
                 ctx.fillStyle = readConfObject(config, 'color', {
                     count: counts,
                     maxScore,

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

@@ -1,10 +1,10 @@
 import React from 'react';
 import { Region } from '@jbrowse/core/util/types';
-declare const _default: (props: {
+declare const HicRendering: (props: {
     blockKey: string;
     width: number;
     height: number;
     regions: Region[];
     bpPerPx: number;
 }) => React.JSX.Element;
-export default _default;
+export default HicRendering;

package/esm/HicRenderer/components/HicRendering.js

@@ -1,10 +1,11 @@
 import React from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
-export default observer(function HicRendering(props) {
+const HicRendering = observer(function HicRendering(props) {
     const { width, height } = props;
     const canvasWidth = Math.ceil(width);
     // need to call this in render so we get the right observer behavior
     return (React.createElement("div", { style: { position: 'relative', width: canvasWidth, height } },
         React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } })));
 });
+export default HicRendering;

package/esm/index.js

@@ -1,4 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
+import { colord } from '@jbrowse/core/util/colord';
 import HicRendererF from './HicRenderer';
 import HicTrackF from './HicTrack';
 import LinearHicDisplayF from './LinearHicDisplay';
@@ -42,8 +43,9 @@ export default class HicPlugin extends Plugin {
         });
     }
     configure(pluginManager) {
-        pluginManager.jexl.addFunction('alpha', (color, value) => color.alpha(value));
-        pluginManager.jexl.addFunction('hsl', (color) => color.hsl());
-        pluginManager.jexl.addFunction('colorString', (color) => color.string());
+        const { jexl } = pluginManager;
+        jexl.addFunction('alpha', (color, n) => color.alpha(n));
+        jexl.addFunction('hsl', (color) => colord(color.toHsl()));
+        jexl.addFunction('colorString', (color) => color.toHex());
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,6 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "color": "^3.1.3",
     "hic-straw": "^2.0.3"
   },
   "peerDependencies": {
@@ -44,7 +43,7 @@
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
-    "mobx-react": "^7.0.0",
+    "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
     "rxjs": "^7.0.0"
@@ -55,5 +54,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }