@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -3,12 +3,13 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { openLocation } from '@jbrowse/core/util/io';
 import { updateStatus } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { rectifyStats } from '@jbrowse/core/util/stats';
-export default class BigWigAdapter extends BaseFeatureDataAdapter {
+import { rectifyStats, } from '@jbrowse/core/util/stats';
+class BigWigAdapter extends BaseFeatureDataAdapter {
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
+        const pm = this.pluginManager;
         const bigwig = new BigWig({
-            filehandle: openLocation(this.getConf('bigWigLocation'), this.pluginManager),
+            filehandle: openLocation(this.getConf('bigWigLocation'), pm),
         });
         const header = await updateStatus('Downloading bigwig header', statusCallback, () => bigwig.getHeader(opts));
         return { bigwig, header };
@@ -67,7 +68,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
         }, signal);
     }
     // always render bigwig instead of calculating a feature density for it
-    async estimateRegionsStats(_regions) {
+    async getMultiRegionFeatureDensityStats(_regions) {
         return { featureDensity: 0 };
     }
     freeResources() { }
@@ -77,4 +78,5 @@ BigWigAdapter.capabilities = [
     'hasLocalStats',
     'hasGlobalStats',
 ];
+export default BigWigAdapter;
 //# sourceMappingURL=BigWigAdapter.js.map

package/esm/BigWigAdapter/BigWigAdapter.js.map

@@ -1 +1 @@
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package/esm/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/esm/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/esm/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/esm/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/esm/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/esm/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/esm/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/esm/LinearWiggleDisplay/index.js

@@ -1,7 +1,7 @@
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './models/configSchema';
 import modelFactory from './models/model';
-import ReactComponent from './components/WiggleDisplayComponent';
+import { lazy } from 'react';
 export default (pluginManager) => {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
@@ -13,7 +13,7 @@ export default (pluginManager) => {
             stateModel,
             trackType: 'QuantitativeTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent,
+            ReactComponent: lazy(() => import('./components/WiggleDisplayComponent')),
         });
     });
 };

package/esm/LinearWiggleDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearWiggleDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,MAAM,UAAU,GAAG,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;QAC5D,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,mBAAmB;YAC9B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,qCAAqC,CAAC,CAAC;SAC1E,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,sBAAsB,CAAA;AACzD,OAAO,EAAE,OAAO,IAAI,cAAc,EAAE,MAAM,qCAAqC,CAAA;AAC/E,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/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/esm/LinearWiggleDisplay/models/configSchema.js

@@ -1,79 +1,15 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
+// locals
+import sharedWiggleConfigFactory from '../../shared/configShared';
 /**
  * #config LinearWiggleDisplay
  */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export default function WiggleConfigFactory(pluginManager) {
     const XYPlotRendererConfigSchema = pluginManager.getRendererType('XYPlotRenderer').configSchema;
     const DensityRendererConfigSchema = pluginManager.getRendererType('DensityRenderer').configSchema;
     const LinePlotRendererConfigSchema = pluginManager.getRendererType('LinePlotRenderer').configSchema;
     return ConfigurationSchema('LinearWiggleDisplay', {
-        /**
-         * #slot
-         */
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: 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: 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
          */
@@ -94,7 +30,7 @@ export default function WiggleConfigFactory(pluginManager) {
         /**
          * #baseConfiguration
          */
-        baseConfiguration: baseLinearDisplayConfigSchema,
+        baseConfiguration: sharedWiggleConfigFactory(),
         explicitlyTyped: true,
     });
 }

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