@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

package/dist/BigWigAdapter/BigWigAdapter.d.ts

@@ -15,9 +15,9 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refIdToName(refId: number): Promise<any>;
-    getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").FeatureStats>;
+    getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").QuantitativeStats>;
     getFeatures(region: Region, opts?: WiggleOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(_regions: Region[]): Promise<{
+    getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
     freeResources(): void;

package/dist/BigWigAdapter/BigWigAdapter.js

@@ -9,8 +9,9 @@ const stats_1 = require("@jbrowse/core/util/stats");
 class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
+        const pm = this.pluginManager;
         const bigwig = new bbi_1.BigWig({
-            filehandle: (0, io_1.openLocation)(this.getConf('bigWigLocation'), this.pluginManager),
+            filehandle: (0, io_1.openLocation)(this.getConf('bigWigLocation'), pm),
         });
         const header = await (0, util_1.updateStatus)('Downloading bigwig header', statusCallback, () => bigwig.getHeader(opts));
         return { bigwig, header };
@@ -69,15 +70,15 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }, signal);
     }
     // always render bigwig instead of calculating a feature density for it
-    async estimateRegionsStats(_regions) {
+    async getMultiRegionFeatureDensityStats(_regions) {
         return { featureDensity: 0 };
     }
     freeResources() { }
 }
-exports.default = BigWigAdapter;
 BigWigAdapter.capabilities = [
     'hasResolution',
     'hasLocalStats',
     'hasGlobalStats',
 ];
+exports.default = BigWigAdapter;
 //# sourceMappingURL=BigWigAdapter.js.map

package/dist/BigWigAdapter/BigWigAdapter.js.map

@@ -1 +1 @@
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package/dist/BigWigAdapter/configSchema.d.ts

@@ -1,2 +1,21 @@
-declare const BigWigAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const BigWigAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    bigWigLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    source: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BigWigAdapter;

package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const ConfirmDialog: ({ tracks, onClose, }: {
     tracks: AnyConfigurationModel[];
     onClose: (arg: boolean, arg1?: {
         name: string;
     }) => void;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default ConfirmDialog;

package/dist/DensityRenderer/configSchema.d.ts

@@ -1,2 +1,34 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/dist/LinePlotRenderer/configSchema.d.ts

@@ -1,2 +1,45 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string; /**
+         * #baseConfiguration
+         */
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

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

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 declare function SetColorDialog({ model, handleClose, }: {
     model: {
         color?: string;
@@ -9,6 +9,6 @@ declare function SetColorDialog({ model, handleClose, }: {
         setNegColor: (arg?: string) => void;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SetColorDialog;
 export default _default;

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

@@ -15,6 +15,6 @@ declare const WiggleTooltip: (props: {
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
     TooltipContents?: TooltipContentsComponent;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default WiggleTooltip;
 export { default as Tooltip } from '../../Tooltip';

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

@@ -1,7 +1,7 @@
-/// <reference types="react" />
+import React from 'react';
 import { WiggleDisplayModel } from '../models/model';
 declare const LinearWiggleDisplay: (props: {
     model: WiggleDisplayModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default LinearWiggleDisplay;
 export { default as YScaleBar } from '../../shared/YScaleBar';

package/dist/LinearWiggleDisplay/index.js

@@ -1,4 +1,27 @@
 "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 };
 };
@@ -7,7 +30,7 @@ exports.modelFactory = exports.ReactComponent = exports.Tooltip = void 0;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const model_1 = __importDefault(require("./models/model"));
-const WiggleDisplayComponent_1 = __importDefault(require("./components/WiggleDisplayComponent"));
+const react_1 = require("react");
 exports.default = (pluginManager) => {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
@@ -19,14 +42,14 @@ exports.default = (pluginManager) => {
             stateModel,
             trackType: 'QuantitativeTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent: WiggleDisplayComponent_1.default,
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/WiggleDisplayComponent')))),
         });
     });
 };
 var Tooltip_1 = require("./components/Tooltip");
 Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
-var WiggleDisplayComponent_2 = require("./components/WiggleDisplayComponent");
-Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(WiggleDisplayComponent_2).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");
 Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
 //# sourceMappingURL=index.js.map

package/dist/LinearWiggleDisplay/index.js.map

@@ -1 +1 @@
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package/dist/LinearWiggleDisplay/models/configSchema.d.ts

@@ -1,2 +1,82 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+/**
+ * #config LinearWiggleDisplay
+ */
+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;
+        LinePlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    minimalTicks: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    numStdDev: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/dist/LinearWiggleDisplay/models/configSchema.js

@@ -1,81 +1,20 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 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");
+// locals
+const configShared_1 = __importDefault(require("../../shared/configShared"));
 /**
  * #config LinearWiggleDisplay
  */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 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
-         */
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: mobx_state_tree_1.types.enumeration('Autoscale type', [
-                'global',
-                'local',
-                'globalsd',
-                'localsd',
-                'zscore',
-            ]),
-            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
-        },
-        /**
-         * #slot
-         */
-        minimalTicks: {
-            type: 'boolean',
-            defaultValue: false,
-            description: 'use the minimal amount of ticks',
-        },
-        /**
-         * #slot
-         */
-        minScore: {
-            type: 'number',
-            defaultValue: Number.MIN_VALUE,
-            description: 'minimum value for the y-scale',
-        },
-        /**
-         * #slot
-         */
-        maxScore: {
-            type: 'number',
-            description: 'maximum value for the y-scale',
-            defaultValue: Number.MAX_VALUE,
-        },
-        /**
-         * #slot
-         */
-        numStdDev: {
-            type: 'number',
-            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
-            defaultValue: 3,
-        },
-        /**
-         * #slot
-         */
-        scaleType: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
-            description: 'The type of scale to use',
-            defaultValue: 'linear',
-        },
-        /**
-         * #slot
-         */
-        inverted: {
-            type: 'boolean',
-            description: 'draw upside down',
-            defaultValue: false,
-        },
         /**
          * #slot
          */
@@ -96,7 +35,7 @@ function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
+        baseConfiguration: (0, configShared_1.default)(),
         explicitlyTyped: true,
     });
 }

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