@jbrowse/plugin-wiggle 2.16.1 → 2.18.0

package/dist/BigWigAdapter/BigWigAdapter.d.ts

@@ -1,7 +1,8 @@
 import { BigWig } from '@gmod/bbi';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 interface WiggleOptions extends BaseOptions {
     resolution?: number;
 }

package/dist/BigWigAdapter/BigWigAdapter.js

@@ -2,8 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const bbi_1 = require("@gmod/bbi");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const stats_1 = require("@jbrowse/core/util/stats");
 class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -40,7 +40,7 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     getFeatures(region, opts = {}) {
         const { refName, start, end } = region;
-        const { bpPerPx = 0, signal, resolution = 1, statusCallback = () => { }, } = opts;
+        const { bpPerPx = 0, stopToken, resolution = 1, statusCallback = () => { }, } = opts;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             statusCallback('Downloading bigwig data');
             const source = this.getConf('source');
@@ -52,25 +52,20 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             });
             for (const data of feats) {
                 if (source) {
-                    // @ts-expect-error
                     data.source = source;
                 }
                 const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`;
-                // @ts-expect-error
                 data.refName = refName;
                 data.uniqueId = uniqueId;
                 observer.next({
-                    // @ts-expect-error
                     get: (str) => data[str],
                     id: () => uniqueId,
-                    // @ts-expect-error
                     toJSON: () => data,
                 });
             }
             observer.complete();
-        }, signal);
+        }, stopToken);
     }
-    // always render bigwig instead of calculating a feature density for it
     async getMultiRegionFeatureDensityStats(_regions) {
         return { featureDensity: 0 };
     }

package/dist/BigWigAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BigWigAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bigWigLocation: {
         type: string;
         defaultValue: {
@@ -9,17 +6,11 @@ declare const BigWigAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     source: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     resolutionMultiplier: {
         type: string;
         defaultValue: number;

package/dist/BigWigAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BigWigAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BigWigAdapter = (0, configuration_1.ConfigurationSchema)('BigWigAdapter', {
-    /**
-     * #slot
-     */
     bigWigLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,17 +10,11 @@ const BigWigAdapter = (0, configuration_1.ConfigurationSchema)('BigWigAdapter',
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     source: {
         type: 'string',
         defaultValue: '',
         description: 'Used for multiwiggle',
     },
-    /**
-     * #slot
-     */
     resolutionMultiplier: {
         type: 'number',
         defaultValue: 1,

package/dist/BigWigAdapter/index.d.ts

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

package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const ConfirmDialog: ({ tracks, onClose, }: {
     tracks: AnyConfigurationModel[];
     onClose: (arg: boolean, arg1?: {

package/dist/CreateMultiWiggleExtension/ConfirmDialog.js

@@ -27,9 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
 const configuration_1 = require("@jbrowse/core/configuration");
+const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
+const material_1 = require("@mui/material");
 const ConfirmDialog = ({ tracks, onClose, }) => {
     const [val, setVal] = (0, react_1.useState)(`MultiWiggle ${Date.now()}`);
     const allQuant = tracks.every(t => t.type === 'QuantitativeTrack');

package/dist/CreateMultiWiggleExtension/index.d.ts

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

package/dist/CreateMultiWiggleExtension/index.js

@@ -28,6 +28,31 @@ const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const ConfirmDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ConfirmDialog'))));
+function makeTrack({ model, arg, }) {
+    const tracks = model.selection;
+    const trackIds = tracks.map(c => (0, configuration_1.readConfObject)(c, 'name'));
+    const subadapters = tracks
+        .map(c => (0, configuration_1.readConfObject)(c, 'adapter'))
+        .map((c, idx) => ({ ...c, source: trackIds[idx] }));
+    const now = +Date.now();
+    const trackId = `multitrack-${now}-sessionTrack`;
+    const session = (0, util_1.getSession)(model);
+    if ((0, util_1.isSessionWithAddTracks)(session)) {
+        session.addTrackConf({
+            type: 'MultiQuantitativeTrack',
+            trackId,
+            name: arg.name,
+            assemblyNames: [
+                ...new Set(tracks.flatMap(c => (0, configuration_1.readConfObject)(c, 'assemblyNames'))),
+            ],
+            adapter: {
+                type: 'MultiWiggleAdapter',
+                subadapters,
+            },
+        });
+        model.view.showTrack(trackId);
+    }
+}
 function CreateMultiWiggleExtensionF(pm) {
     pm.addToExtensionPoint('TrackSelector-multiTrackMenuItems', (items, props) => {
         const { session } = props;
@@ -39,38 +64,13 @@ function CreateMultiWiggleExtensionF(pm) {
                         label: 'Create multi-wiggle track',
                         onClick: (model) => {
                             const tracks = model.selection;
-                            const trackIds = tracks.map(c => (0, configuration_1.readConfObject)(c, 'name'));
-                            function makeTrack(arg) {
-                                const subadapters = tracks
-                                    .map(c => (0, configuration_1.readConfObject)(c, 'adapter'))
-                                    .map((c, idx) => ({ ...c, source: trackIds[idx] }));
-                                const assemblyNames = [
-                                    ...new Set(tracks.flatMap(c => (0, configuration_1.readConfObject)(c, 'assemblyNames'))),
-                                ];
-                                const now = +Date.now();
-                                const trackId = `multitrack-${now}-sessionTrack`;
-                                const session = (0, util_1.getSession)(model);
-                                if ((0, util_1.isSessionWithAddTracks)(session)) {
-                                    session.addTrackConf({
-                                        type: 'MultiQuantitativeTrack',
-                                        trackId,
-                                        name: arg.name,
-                                        assemblyNames,
-                                        adapter: {
-                                            type: 'MultiWiggleAdapter',
-                                            subadapters,
-                                        },
-                                    });
-                                    model.view.showTrack(trackId);
-                                }
-                            }
                             (0, util_1.getSession)(model).queueDialog(handleClose => [
                                 ConfirmDialog,
                                 {
                                     tracks,
                                     onClose: (arg, arg1) => {
                                         if (arg && arg1) {
-                                            makeTrack(arg1);
+                                            makeTrack({ model, arg: arg1 });
                                         }
                                         handleClose();
                                     },

package/dist/DensityRenderer/DensityRenderer.d.ts

@@ -1,4 +1,5 @@
-import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import type { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export default class DensityRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
         reducedFeatures: import("@jbrowse/core/util").Feature[];

package/dist/DensityRenderer/DensityRenderer.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const drawDensity_1 = require("../drawDensity");
 const WiggleBaseRenderer_1 = __importDefault(require("../WiggleBaseRenderer"));
+const drawDensity_1 = require("../drawDensity");
 class DensityRenderer extends WiggleBaseRenderer_1.default {
     async draw(ctx, props) {
         return (0, drawDensity_1.drawDensity)(ctx, props);

package/dist/DensityRenderer/configSchema.js

@@ -5,14 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const configSchema_1 = __importDefault(require("../configSchema"));
-/**
- * #config DensityRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('DensityRenderer', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: configSchema_1.default,
     explicitlyTyped: true,
 });

package/dist/DensityRenderer/index.d.ts

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

package/dist/DensityRenderer/index.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = DensityRendererF;
-const configSchema_1 = __importDefault(require("./configSchema"));
 const DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 const WiggleRendering_1 = __importDefault(require("../WiggleRendering"));
 function DensityRendererF(pluginManager) {
     pluginManager.addRendererType(() => new DensityRenderer_1.default({

package/dist/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -1,5 +1,6 @@
-import { Feature } from '@jbrowse/core/util';
-import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import type { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+import type { Feature } from '@jbrowse/core/util';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
         reducedFeatures: Feature[];

package/dist/LinePlotRenderer/LinePlotRenderer.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const WiggleBaseRenderer_1 = __importDefault(require("../WiggleBaseRenderer"));
-const util_1 = require("../util");
 const drawLine_1 = require("../drawLine");
+const util_1 = require("../util");
 class LinePlotRenderer extends WiggleBaseRenderer_1.default {
     async draw(ctx, props) {
         const { config } = props;

package/dist/LinePlotRenderer/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     displayCrossHatches: {
         type: string;
         description: string;

package/dist/LinePlotRenderer/configSchema.js

@@ -5,23 +5,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const configSchema_1 = __importDefault(require("../configSchema"));
-/**
- * #config LinePlotRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('LinePlotRenderer', {
-    /**
-     * #slot
-     */
     displayCrossHatches: {
         type: 'boolean',
         description: 'choose to draw cross hatches (sideways lines)',
         defaultValue: false,
     },
 }, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: configSchema_1.default,
     explicitlyTyped: true,
 });

package/dist/LinePlotRenderer/index.d.ts

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

package/dist/LinearWiggleDisplay/components/SetColorDialog.js

@@ -24,10 +24,10 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
 const ColorPicker_1 = require("@jbrowse/core/ui/ColorPicker");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const SetColorDialog = (0, mobx_react_1.observer)(function SetColorDialog({ model, handleClose, }) {
     const [posneg, setPosNeg] = (0, react_1.useState)(false);
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set color" },

package/dist/LinearWiggleDisplay/components/Tooltip.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-import { TooltipContentsComponent } from '../../Tooltip';
+import type { TooltipContentsComponent } from '../../Tooltip';
+import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const WiggleTooltip: (props: {
     model: {

package/dist/LinearWiggleDisplay/components/Tooltip.js

@@ -6,12 +6,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.Tooltip = void 0;
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
-// locals
 const Tooltip_1 = __importDefault(require("../../Tooltip"));
 const util_1 = require("../../util");
 const en = (n) => n.toLocaleString('en-US');
 const TooltipContents = react_1.default.forwardRef(function TooltipContents2({ feature }, ref) {
-    const start = feature.get('start');
+    const start = feature.get('start') + 1;
     const end = feature.get('end');
     const refName = feature.get('refName');
     const name = feature.get('name');

package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../models/model';
+import type { WiggleDisplayModel } from '../model';
 declare const LinearWiggleDisplay: (props: {
     model: WiggleDisplayModel;
 }) => React.JSX.Element;

package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_react_1 = require("mobx-react");
 const YScaleBar_1 = __importDefault(require("../../shared/YScaleBar"));
 const LinearWiggleDisplay = (0, mobx_react_1.observer)((props) => {
     const { model } = props;

package/dist/LinearWiggleDisplay/{models/configSchema.d.ts → configSchema.d.ts}

@@ -1,21 +1,10 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearWiggleDisplay
- * extends
- * - [SharedWiggleDisplay](../sharedwiggledisplay)
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         DensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         XYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LinearWiggleDisplay/{models/configSchema.js → configSchema.js}

@@ -6,39 +6,24 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = WiggleConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
-const configShared_1 = __importDefault(require("../../shared/configShared"));
-/**
- * #config LinearWiggleDisplay
- * extends
- * - [SharedWiggleDisplay](../sharedwiggledisplay)
- */
+const SharedWiggleConfigSchema_1 = __importDefault(require("../shared/SharedWiggleConfigSchema"));
 function WiggleConfigFactory(pluginManager) {
     const XYPlotRendererConfigSchema = pluginManager.getRendererType('XYPlotRenderer').configSchema;
     const DensityRendererConfigSchema = pluginManager.getRendererType('DensityRenderer').configSchema;
     const LinePlotRendererConfigSchema = pluginManager.getRendererType('LinePlotRenderer').configSchema;
     return (0, configuration_1.ConfigurationSchema)('LinearWiggleDisplay', {
-        /**
-         * #slot
-         */
         defaultRendering: {
             type: 'stringEnum',
             model: mobx_state_tree_1.types.enumeration('Rendering', ['density', 'xyplot', 'line']),
             defaultValue: 'xyplot',
         },
-        /**
-         * #slot
-         */
         renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
             DensityRenderer: DensityRendererConfigSchema,
             XYPlotRenderer: XYPlotRendererConfigSchema,
             LinePlotRenderer: LinePlotRendererConfigSchema,
         }),
     }, {
-        /**
-         * #baseConfiguration
-         */
-        baseConfiguration: (0, configShared_1.default)(),
+        baseConfiguration: (0, SharedWiggleConfigSchema_1.default)(),
         explicitlyTyped: true,
     });
 }

package/dist/LinearWiggleDisplay/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearWiggleDisplayF(pluginManager: PluginManager): void;
 export { default as Tooltip } from './components/Tooltip';
 export { default as ReactComponent } from './components/WiggleDisplayComponent';
-export { default as modelFactory } from './models/model';
+export { default as modelFactory } from './model';

package/dist/LinearWiggleDisplay/index.js

@@ -28,10 +28,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.modelFactory = exports.ReactComponent = exports.Tooltip = void 0;
 exports.default = LinearWiggleDisplayF;
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const configSchema_1 = __importDefault(require("./models/configSchema"));
-const model_1 = __importDefault(require("./models/model"));
 const react_1 = require("react");
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 function LinearWiggleDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
@@ -51,5 +51,5 @@ var Tooltip_1 = require("./components/Tooltip");
 Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
 var WiggleDisplayComponent_1 = require("./components/WiggleDisplayComponent");
 Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(WiggleDisplayComponent_1).default; } });
-var model_2 = require("./models/model");
+var model_2 = require("./model");
 Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });