@jbrowse/plugin-hic 2.13.1 → 2.15.0

package/dist/HicAdapter/HicAdapter.js

@@ -70,7 +70,7 @@ class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
             statusCallback('');
             observer.complete();
-        }, opts.signal); // eslint-disable-line @typescript-eslint/no-explicit-any
+        }, opts.signal);
     }
     // don't do feature stats estimation, similar to bigwigadapter
     async getMultiRegionFeatureDensityStats(_regions) {

package/dist/HicRenderer/HicRenderer.d.ts

@@ -28,7 +28,7 @@ export type ResultsSerialized = ServerSideResultsSerialized;
 export type ResultsDeserialized = ServerSideResultsDeserialized;
 export default class HicRenderer extends ServerSideRendererType {
     supportsSVG: boolean;
-    makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
+    makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;
     render(renderProps: RenderArgsDeserialized): Promise<{
         height: any;
         width: number;

package/dist/HicRenderer/HicRenderer.js

@@ -11,9 +11,9 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const colord_1 = require("@jbrowse/core/util/colord");
 const rxjs_1 = require("rxjs");
-const d3_scale_1 = require("d3-scale");
-const d3_scale_chromatic_1 = require("d3-scale-chromatic");
-const d3_interpolate_1 = require("d3-interpolate");
+const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
+const viridis_1 = __importDefault(require("./viridis"));
+const d3_interpolate_1 = require("@mui/x-charts-vendor/d3-interpolate");
 class HicRenderer extends ServerSideRendererType_1.default {
     constructor() {
         super(...arguments);
@@ -21,7 +21,7 @@ class HicRenderer extends ServerSideRendererType_1.default {
     }
     async makeImageData(ctx, props) {
         const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, } = props;
-        const [region] = regions;
+        const region = regions[0];
         const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
         const res = await dataAdapter.getResolution(bpPerPx / resolution);
         const width = (region.end - region.start) / bpPerPx;
@@ -54,7 +54,7 @@ class HicRenderer extends ServerSideRendererType_1.default {
                     'rgb(128, 0, 38)',
                     'rgb(0, 0, 0)',
                 ]),
-                viridis: d3_scale_chromatic_1.interpolateViridis,
+                viridis: viridis_1.default,
             };
             const m = useLogScale ? maxScore : maxScore / 20;
             // @ts-expect-error
@@ -85,10 +85,11 @@ class HicRenderer extends ServerSideRendererType_1.default {
             }
             ctx.restore();
         }
+        return undefined;
     }
     async render(renderProps) {
         const { config, regions, bpPerPx } = renderProps;
-        const [region] = regions;
+        const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
         const height = (0, configuration_1.readConfObject)(config, 'maxHeight');
         const features = await this.getFeatures(renderProps);
@@ -120,7 +121,6 @@ class HicRenderer extends ServerSideRendererType_1.default {
         // cast to any to avoid return-type conflict, because the
         // types of features returned by our getFeatures are quite
         // different from the base interface
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return features;
     }
 }

package/dist/HicRenderer/configSchema.js

@@ -21,7 +21,7 @@ const HicRenderer = (0, configuration_1.ConfigurationSchema)('HicRenderer', {
     color: {
         type: 'color',
         description: 'the color of each feature in a hic alignment',
-        defaultValue: `jexl:interpolate(count,scale)`,
+        defaultValue: 'jexl:interpolate(count,scale)',
         contextVariable: ['count', 'maxScore', 'baseColor', 'scale'],
     },
     /**

package/dist/HicRenderer/viridis.d.ts

@@ -0,0 +1,2 @@
+declare const _default: (t: any) => any;
+export default _default;

package/dist/HicRenderer/viridis.js

@@ -0,0 +1,35 @@
+"use strict";
+// @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
+Object.defineProperty(exports, "__esModule", { value: true });
+// 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);
+    let i = 0;
+    while (i < n) {
+        colors[i] = `#${specifier.slice(i * 6, ++i * 6)}`;
+    }
+    return colors;
+}
+function ramp(range) {
+    const n = range.length;
+    return function (t) {
+        return range[Math.max(0, Math.min(n - 1, Math.floor(t * n)))];
+    };
+}
+exports.default = ramp(colors('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'));

package/dist/LinearHicDisplay/model.d.ts

@@ -129,7 +129,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{

package/dist/LinearHicDisplay/model.js

@@ -105,7 +105,9 @@ function stateModelFactory(configSchema) {
                         label: 'Use log scale',
                         type: 'checkbox',
                         checked: self.useLogScale,
-                        onClick: () => self.setUseLogScale(!self.useLogScale),
+                        onClick: () => {
+                            self.setUseLogScale(!self.useLogScale);
+                        },
                     },
                     {
                         label: 'Color scheme',
@@ -113,19 +115,27 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Fall',
-                                onClick: () => self.setColorScheme('fall'),
+                                onClick: () => {
+                                    self.setColorScheme('fall');
+                                },
                             },
                             {
                                 label: 'Viridis',
-                                onClick: () => self.setColorScheme('viridis'),
+                                onClick: () => {
+                                    self.setColorScheme('viridis');
+                                },
                             },
                             {
                                 label: 'Juicebox',
-                                onClick: () => self.setColorScheme('juicebox'),
+                                onClick: () => {
+                                    self.setColorScheme('juicebox');
+                                },
                             },
                             {
                                 label: 'Clear',
-                                onClick: () => self.setColorScheme(undefined),
+                                onClick: () => {
+                                    self.setColorScheme(undefined);
+                                },
                             },
                         ],
                     },
@@ -134,11 +144,15 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Finer resolution',
-                                onClick: () => self.setResolution(self.resolution * 2),
+                                onClick: () => {
+                                    self.setResolution(self.resolution * 2);
+                                },
                             },
                             {
                                 label: 'Coarser resolution',
-                                onClick: () => self.setResolution(self.resolution / 2),
+                                onClick: () => {
+                                    self.setResolution(self.resolution / 2);
+                                },
                             },
                         ],
                     },

package/esm/HicAdapter/HicAdapter.js

@@ -64,7 +64,7 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
             }
             statusCallback('');
             observer.complete();
-        }, opts.signal); // eslint-disable-line @typescript-eslint/no-explicit-any
+        }, opts.signal);
     }
     // don't do feature stats estimation, similar to bigwigadapter
     async getMultiRegionFeatureDensityStats(_regions) {

package/esm/HicRenderer/HicRenderer.d.ts

@@ -28,7 +28,7 @@ export type ResultsSerialized = ServerSideResultsSerialized;
 export type ResultsDeserialized = ServerSideResultsDeserialized;
 export default class HicRenderer extends ServerSideRendererType {
     supportsSVG: boolean;
-    makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
+    makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;
     render(renderProps: RenderArgsDeserialized): Promise<{
         height: any;
         width: number;

package/esm/HicRenderer/HicRenderer.js

@@ -6,9 +6,9 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { colord } from '@jbrowse/core/util/colord';
 import { firstValueFrom } from 'rxjs';
-import { scaleSequential, scaleSequentialLog } from 'd3-scale';
-import { interpolateViridis } from 'd3-scale-chromatic';
-import { interpolateRgbBasis } from 'd3-interpolate';
+import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-scale';
+import interpolateViridis from './viridis';
+import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
 export default class HicRenderer extends ServerSideRendererType {
     constructor() {
         super(...arguments);
@@ -16,7 +16,7 @@ export default class HicRenderer extends ServerSideRendererType {
     }
     async makeImageData(ctx, props) {
         const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, } = props;
-        const [region] = regions;
+        const region = regions[0];
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
         const res = await dataAdapter.getResolution(bpPerPx / resolution);
         const width = (region.end - region.start) / bpPerPx;
@@ -80,10 +80,11 @@ export default class HicRenderer extends ServerSideRendererType {
             }
             ctx.restore();
         }
+        return undefined;
     }
     async render(renderProps) {
         const { config, regions, bpPerPx } = renderProps;
-        const [region] = regions;
+        const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
         const height = readConfObject(config, 'maxHeight');
         const features = await this.getFeatures(renderProps);
@@ -115,7 +116,6 @@ export default class HicRenderer extends ServerSideRendererType {
         // cast to any to avoid return-type conflict, because the
         // types of features returned by our getFeatures are quite
         // different from the base interface
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return features;
     }
 }

package/esm/HicRenderer/configSchema.js

@@ -19,7 +19,7 @@ const HicRenderer = ConfigurationSchema('HicRenderer', {
     color: {
         type: 'color',
         description: 'the color of each feature in a hic alignment',
-        defaultValue: `jexl:interpolate(count,scale)`,
+        defaultValue: 'jexl:interpolate(count,scale)',
         contextVariable: ['count', 'maxScore', 'baseColor', 'scale'],
     },
     /**

package/esm/HicRenderer/viridis.d.ts

@@ -0,0 +1,2 @@
+declare const _default: (t: any) => any;
+export default _default;

package/esm/HicRenderer/viridis.js

@@ -0,0 +1,33 @@
+// @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);
+    let i = 0;
+    while (i < n) {
+        colors[i] = `#${specifier.slice(i * 6, ++i * 6)}`;
+    }
+    return colors;
+}
+function ramp(range) {
+    const n = range.length;
+    return function (t) {
+        return range[Math.max(0, Math.min(n - 1, Math.floor(t * n)))];
+    };
+}
+export default ramp(colors('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'));

package/esm/LinearHicDisplay/model.d.ts

@@ -129,7 +129,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{

package/esm/LinearHicDisplay/model.js

@@ -102,7 +102,9 @@ export default function stateModelFactory(configSchema) {
                         label: 'Use log scale',
                         type: 'checkbox',
                         checked: self.useLogScale,
-                        onClick: () => self.setUseLogScale(!self.useLogScale),
+                        onClick: () => {
+                            self.setUseLogScale(!self.useLogScale);
+                        },
                     },
                     {
                         label: 'Color scheme',
@@ -110,19 +112,27 @@ export default function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Fall',
-                                onClick: () => self.setColorScheme('fall'),
+                                onClick: () => {
+                                    self.setColorScheme('fall');
+                                },
                             },
                             {
                                 label: 'Viridis',
-                                onClick: () => self.setColorScheme('viridis'),
+                                onClick: () => {
+                                    self.setColorScheme('viridis');
+                                },
                             },
                             {
                                 label: 'Juicebox',
-                                onClick: () => self.setColorScheme('juicebox'),
+                                onClick: () => {
+                                    self.setColorScheme('juicebox');
+                                },
                             },
                             {
                                 label: 'Clear',
-                                onClick: () => self.setColorScheme(undefined),
+                                onClick: () => {
+                                    self.setColorScheme(undefined);
+                                },
                             },
                         ],
                     },
@@ -131,11 +141,15 @@ export default function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Finer resolution',
-                                onClick: () => self.setResolution(self.resolution * 2),
+                                onClick: () => {
+                                    self.setResolution(self.resolution * 2);
+                                },
                             },
                             {
                                 label: 'Coarser resolution',
-                                onClick: () => self.setResolution(self.resolution / 2),
+                                onClick: () => {
+                                    self.setResolution(self.resolution / 2);
+                                },
                             },
                         ],
                     },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "2.13.1",
+  "version": "2.15.0",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/hic",
+    "test": "cd ../..; jest --passWithNoTests plugins/hic",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -36,14 +36,13 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "d3-interpolate": "^2.0.1",
-    "d3-scale-chromatic": "^2.0.0",
+    "@mui/x-charts-vendor": "^7.12.0",
     "hic-straw": "^2.0.3"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
-    "@mui/material": "^5.0.0",
+    "@mui/material": "^6.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -56,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
 }