@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

package/src/BigWigAdapter/BigWigAdapter.ts

@@ -7,7 +7,10 @@ import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { updateStatus, Feature } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { rectifyStats, UnrectifiedFeatureStats } from '@jbrowse/core/util/stats'
+import {
+  rectifyStats,
+  UnrectifiedQuantitativeStats,
+} from '@jbrowse/core/util/stats'
 
 interface WiggleOptions extends BaseOptions {
   resolution?: number
@@ -25,11 +28,9 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
 
   private async setupPre(opts?: BaseOptions) {
     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',
@@ -61,7 +62,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
 
   public async getGlobalStats(opts?: BaseOptions) {
     const { header } = await this.setup(opts)
-    return rectifyStats(header.totalSummary as UnrectifiedFeatureStats)
+    return rectifyStats(header.totalSummary as UnrectifiedQuantitativeStats)
   }
 
   public getFeatures(region: Region, opts: WiggleOptions = {}) {
@@ -103,7 +104,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
   }
 
   // always render bigwig instead of calculating a feature density for it
-  async estimateRegionsStats(_regions: Region[]) {
+  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
     return { featureDensity: 0 }
   }
 

package/src/LinearWiggleDisplay/index.ts

@@ -3,7 +3,7 @@ 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) => {
   pluginManager.addDisplayType(() => {
@@ -16,7 +16,7 @@ export default (pluginManager: PluginManager) => {
       stateModel,
       trackType: 'QuantitativeTrack',
       viewType: 'LinearGenomeView',
-      ReactComponent,
+      ReactComponent: lazy(() => import('./components/WiggleDisplayComponent')),
     })
   })
 }

package/src/LinearWiggleDisplay/models/configSchema.ts

@@ -1,13 +1,13 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
 import { types } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 
+// locals
+import sharedWiggleConfigFactory from '../../shared/configShared'
+
 /**
  * #config LinearWiggleDisplay
  */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
 export default function WiggleConfigFactory(pluginManager: PluginManager) {
   const XYPlotRendererConfigSchema =
     pluginManager.getRendererType('XYPlotRenderer').configSchema
@@ -19,75 +19,6 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
   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']), // todo zscale
-        description: 'The type of scale to use',
-        defaultValue: 'linear',
-      },
-      /**
-       * #slot
-       */
-      inverted: {
-        type: 'boolean',
-        description: 'draw upside down',
-        defaultValue: false,
-      },
-
       /**
        * #slot
        */
@@ -109,7 +40,7 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
       /**
        * #baseConfiguration
        */
-      baseConfiguration: baseLinearDisplayConfigSchema,
+      baseConfiguration: sharedWiggleConfigFactory(),
       explicitlyTyped: true,
     },
   )