@jbrowse/plugin-wiggle 2.5.0 → 2.6.1

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 };

package/dist/BigWigAdapter/BigWigAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BigWigAdapter.js","sourceRoot":"","sources":["../../src/BigWigAdapter/BigWigAdapter.ts"],"names":[],"mappings":";;AAAA,mCAAkC;AAClC,yEAGgD;AAEhD,8CAAoD;AACpD,6CAA0D;AAC1D,kDAA0D;AAC1D,oDAGiC;AAMjC,MAAqB,aAAc,SAAQ,oCAAsB;IAUvD,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,YAAM,CAAC;YACxB,UAAU,EAAE,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAAE,EAAE,CAAC;SAC7D,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,IAAA,mBAAY,EAC/B,2BAA2B,EAC3B,cAAc,EACd,GAAG,EAAE,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAC7B,CAAA;QACD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IAC3B,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,KAAa;;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAA,MAAM,CAAC,YAAY,CAAC,KAAK,CAAC,0CAAE,IAAI,CAAA;IACzC,CAAC;IAEM,KAAK,CAAC,cAAc,CAAC,IAAkB;QAC5C,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,IAAA,oBAAY,EAAC,MAAM,CAAC,YAA4C,CAAC,CAAA;IAC1E,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAsB,EAAE;QACzD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EACJ,OAAO,GAAG,CAAC,EACX,MAAM,EACN,UAAU,GAAG,CAAC,EACd,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,GAC1B,GAAG,IAAI,CAAA;QACR,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,cAAc,CAAC,yBAAyB,CAAC,CAAA;YACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;YACrC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACzC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBAC1D,GAAG,IAAI;gBACP,YAAY,EAAE,OAAO,GAAG,UAAU;aACnC,CAAC,CAAA;YAEF,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;gBACxB,IAAI,MAAM,EAAE;oBACV,mBAAmB;oBACnB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;iBACrB;gBACD,MAAM,QAAQ,GAAG,GAAG,MAAM,IAAI,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;gBACxE,mBAAmB;gBACnB,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;gBACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC;oBACZ,mBAAmB;oBACnB,GAAG,EAAE,CAAC,GAAW,EAAE,EAAE,CAAE,IAAgC,CAAC,GAAG,CAAC;oBAC5D,EAAE,EAAE,GAAG,EAAE,CAAC,QAAQ;oBAClB,mBAAmB;oBACnB,MAAM,EAAE,GAAG,EAAE,CAAC,IAAI;iBACnB,CAAC,CAAA;aACH;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,uEAAuE;IACvE,KAAK,CAAC,iCAAiC,CAAC,QAAkB;QACxD,OAAO,EAAE,cAAc,EAAE,CAAC,EAAE,CAAA;IAC9B,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,0BAAY,GAAG;IAC3B,eAAe;IACf,eAAe;IACf,gBAAgB;CACjB,CAAA;kBARkB,aAAa"}

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/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/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

@@ -1,6 +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/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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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearWiggleDisplay/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,yEAAuD;AACvD,2DAAyC;AACzC,iCAA4B;AAE5B,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,MAAM,UAAU,GAAG,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC,CAAA;QAC5D,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,mBAAmB;YAC9B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,qCAAqC,GAAC,CAAC;SAC1E,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,gDAAyD;AAAhD,mHAAA,OAAO,OAAW;AAC3B,8EAA+E;AAAtE,yIAAA,OAAO,OAAkB;AAClC,wCAAwD;AAA/C,sHAAA,OAAO,OAAgB"}

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
          */
@@ -96,7 +35,7 @@ function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
+        baseConfiguration: (0, configShared_1.default)(),
         explicitlyTyped: true,
     });
 }

package/dist/LinearWiggleDisplay/models/configSchema.js.map

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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/models/configSchema.ts"],"names":[],"mappings":";;;;;AAAA,+DAAiE;AACjE,qDAAuC;AAGvC,SAAS;AACT,6EAAiE;AAEjE;;GAEG;AACH,SAAwB,mBAAmB,CAAC,aAA4B;IACtE,MAAM,0BAA0B,GAC9B,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY,CAAA;IAC9D,MAAM,2BAA2B,GAC/B,aAAa,CAAC,eAAe,CAAC,iBAAiB,CAAC,CAAC,YAAY,CAAA;IAC/D,MAAM,4BAA4B,GAChC,aAAa,CAAC,eAAe,CAAC,kBAAkB,CAAC,CAAC,YAAY,CAAA;IAEhE,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,SAAS,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;YACpE,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,eAAe,EAAE,2BAA2B;YAC5C,cAAc,EAAE,0BAA0B;YAC1C,gBAAgB,EAAE,4BAA4B;SAC/C,CAAC;KACH,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,sBAAyB,GAAE;QAC9C,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AApCD,sCAoCC"}