@jbrowse/plugin-wiggle 2.5.0 → 2.6.2

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 };
@@ -80,4 +81,3 @@ BigWigAdapter.capabilities = [
     'hasGlobalStats',
 ];
 exports.default = BigWigAdapter;
-//# sourceMappingURL=BigWigAdapter.js.map

package/dist/BigWigAdapter/configSchema.js

@@ -26,4 +26,3 @@ const BigWigAdapter = (0, configuration_1.ConfigurationSchema)('BigWigAdapter',
     },
 }, { explicitlyTyped: true });
 exports.default = BigWigAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BigWigAdapter/index.js

@@ -41,4 +41,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigWigAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts

@@ -1,8 +1,9 @@
+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/CreateMultiWiggleExtension/ConfirmDialog.js

@@ -51,4 +51,3 @@ const ConfirmDialog = ({ tracks, onClose, }) => {
             react_1.default.createElement(material_1.Button, { onClick: () => onClose(true, { name: val }), color: "primary", variant: "contained", autoFocus: true }, "Submit"))));
 };
 exports.default = ConfirmDialog;
-//# sourceMappingURL=ConfirmDialog.js.map

package/dist/CreateMultiWiggleExtension/index.js

@@ -80,4 +80,3 @@ function default_1(pm) {
     });
 }
 exports.default = default_1;
-//# sourceMappingURL=index.js.map

package/dist/DensityRenderer/DensityRenderer.js

@@ -11,4 +11,3 @@ class DensityRenderer extends WiggleBaseRenderer_1.default {
     }
 }
 exports.default = DensityRenderer;
-//# sourceMappingURL=DensityRenderer.js.map

package/dist/DensityRenderer/configSchema.js

@@ -17,4 +17,3 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('DensityRenderer',
     explicitlyTyped: true,
 });
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/DensityRenderer/index.js

@@ -14,4 +14,3 @@ exports.default = (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/LinePlotRenderer/LinePlotRenderer.js

@@ -16,4 +16,3 @@ class LinePlotRenderer extends WiggleBaseRenderer_1.default {
     }
 }
 exports.default = LinePlotRenderer;
-//# sourceMappingURL=LinePlotRenderer.js.map

package/dist/LinePlotRenderer/configSchema.js

@@ -26,4 +26,3 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('LinePlotRenderer'
     explicitlyTyped: true,
 });
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinePlotRenderer/index.js

@@ -14,4 +14,3 @@ exports.default = (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

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

@@ -1,3 +1,4 @@
+import React from 'react';
 declare function SetColorDialog({ model, handleClose, }: {
     model: {
         color?: string;
@@ -8,6 +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/SetColorDialog.js

@@ -57,4 +57,3 @@ function SetColorDialog({ model, handleClose, }) {
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: () => handleClose() }, "Submit"))));
 }
 exports.default = (0, mobx_react_1.observer)(SetColorDialog);
-//# sourceMappingURL=SetColorDialog.js.map

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/Tooltip.js

@@ -38,4 +38,3 @@ const WiggleTooltip = (0, mobx_react_1.observer)(function (props) {
 exports.default = WiggleTooltip;
 var Tooltip_2 = require("../../Tooltip");
 Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_2).default; } });
-//# sourceMappingURL=Tooltip.js.map

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

@@ -1,6 +1,7 @@
+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/components/WiggleDisplayComponent.js

@@ -33,4 +33,3 @@ const LinearWiggleDisplay = (0, mobx_react_1.observer)((props) => {
 exports.default = LinearWiggleDisplay;
 var YScaleBar_2 = require("../../shared/YScaleBar");
 Object.defineProperty(exports, "YScaleBar", { enumerable: true, get: function () { return __importDefault(YScaleBar_2).default; } });
-//# sourceMappingURL=WiggleDisplayComponent.js.map

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 +42,13 @@ 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/models/configSchema.d.ts

@@ -1,79 +1,62 @@
 import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LinearWiggleDisplay
+ */
 export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
-    autoscale: {
+    defaultRendering: {
         type: string;
-        defaultValue: string;
         model: import("mobx-state-tree").ISimpleType<string>;
-        description: 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;
     };
-    /**
-     * #slot
-     */
     minScore: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot
-     */
     maxScore: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     numStdDev: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     scaleType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     inverted: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #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<{
     maxFeatureScreenDensity: {
         type: string;
@@ -96,4 +79,4 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         defaultValue: string;
         contextVariable: string[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
+}, 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
          */
@@ -96,9 +35,8 @@ function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
+        baseConfiguration: (0, configShared_1.default)(),
         explicitlyTyped: true,
     });
 }
 exports.default = WiggleConfigFactory;
-//# sourceMappingURL=configSchema.js.map