@jbrowse/plugin-wiggle 1.5.0 → 1.5.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "1.5.0",
+  "version": "1.5.4",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,9 +35,9 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/bbi": "^1.0.30",
+    "@gmod/bbi": "^1.0.31",
     "@material-ui/icons": "^4.11.2",
-    "@popperjs/core": "^2.9.3",
+    "@popperjs/core": "^2.11.0",
     "abortable-promise-cache": "^1.1.3",
     "color": "^3.1.1",
     "d3-scale": "^3.2.3",
@@ -60,5 +60,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "542025578a39bd170c8a166f2568ee7edbd54072"
+  "gitHead": "0c398214590969168694b4ed8e20b595178b9efd"
 }

package/src/BigWigAdapter/BigWigAdapter.test.ts

@@ -19,6 +19,7 @@ describe('adapter can fetch features from volvox.bw', () => {
       refName: 'ctgA',
       start: 0,
       end: 20000,
+      assemblyName: 'volvox',
     })
     expect(await adapter.refIdToName(0)).toBe('ctgA')
     expect(await adapter.refIdToName(1)).toBe(undefined)

package/src/BigWigAdapter/BigWigAdapter.ts

@@ -1,9 +1,9 @@
-import { BigWig, Feature as BBIFeature } from '@gmod/bbi'
+import { BigWig } from '@gmod/bbi'
 import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
@@ -66,7 +66,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     return rectifyStats(header.totalSummary as UnrectifiedFeatureStats)
   }
 
-  public getFeatures(region: NoAssemblyRegion, opts: WiggleOptions = {}) {
+  public getFeatures(region: Region, opts: WiggleOptions = {}) {
     const { refName, start, end } = region
     const {
       bpPerPx = 0,
@@ -82,7 +82,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
       })
       ob.pipe(
         mergeAll(),
-        map((record: BBIFeature) => {
+        map(record => {
           return new SimpleFeature({
             id: `${refName}:${record.start}-${record.end}`,
             data: { ...record, refName },

package/src/LinearWiggleDisplay/components/Tooltip.tsx

@@ -1,13 +1,15 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import React, { useMemo, useState } from 'react'
 import { observer } from 'mobx-react'
 import { makeStyles, alpha, Portal } from '@material-ui/core'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
+
+// locals
 import { YSCALEBAR_LABEL_OFFSET } from '../models/model'
 import { usePopper } from 'react-popper'
 
+// convert to number, apply shortened precision, and render
 function toP(s = 0) {
-  return parseFloat(s.toPrecision(6))
+  return +(+s).toPrecision(6)
 }
 
 function round(value: number) {
@@ -31,7 +33,6 @@ const useStyles = makeStyles(theme => ({
     lineHeight: `${round(14 / 10)}em`,
     maxWidth: 300,
     wordWrap: 'break-word',
-    fontWeight: theme.typography.fontWeightMedium,
   },
 
   hoverVertical: {
@@ -86,18 +87,19 @@ const Tooltip = observer(
     clientRect,
     TooltipContents,
   }: {
-    model: any
+    model: { featureUnderMouse: Feature }
     height: number
     clientMouseCoord: Coord
     offsetMouseCoord: Coord
     clientRect?: ClientRect
+
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     TooltipContents: React.FC<any>
   }) => {
     const { featureUnderMouse } = model
-    const classes = useStyles()
     const [width, setWidth] = useState(0)
-
-    const [popperElement, setPopperElement] = useState<any>(null)
+    const [anchorEl, setAnchorEl] = useState<HTMLDivElement | null>(null)
+    const classes = useStyles()
 
     // must be memoized a la https://github.com/popperjs/react-popper/issues/391
     const virtElement = useMemo(
@@ -120,13 +122,13 @@ const Tooltip = observer(
       }),
       [clientRect?.top, clientMouseCoord, width],
     )
-    const { styles, attributes } = usePopper(virtElement, popperElement)
+    const { styles, attributes } = usePopper(virtElement, anchorEl)
 
     return featureUnderMouse ? (
       <>
         <Portal>
           <div
-            ref={setPopperElement}
+            ref={setAnchorEl}
             className={classes.tooltip}
             // zIndex needed to go over widget drawer
             style={{ ...styles.popper, zIndex: 100000 }}
@@ -155,7 +157,7 @@ const Tooltip = observer(
 
 const WiggleTooltip = observer(
   (props: {
-    model: any
+    model: { featureUnderMouse: Feature }
     height: number
     offsetMouseCoord: Coord
     clientMouseCoord: Coord

package/src/WiggleRendering.tsx

@@ -14,6 +14,7 @@ function WiggleRendering(props: {
   onMouseLeave: Function
   onMouseMove: Function
   onFeatureClick: Function
+  blockKey: string
 }) {
   const {
     regions,

package/src/index.ts

@@ -9,6 +9,7 @@ import {
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes/models'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import { FileLocation } from '@jbrowse/core/util/types'
 import WiggleBaseRenderer from './WiggleBaseRenderer'
 import WiggleRendering from './WiggleRendering'
 import { configSchema as bigWigAdapterConfigSchema } from './BigWigAdapter'
@@ -35,6 +36,11 @@ import {
   WiggleGetGlobalStats,
   WiggleGetMultiRegionStats,
 } from './WiggleRPC/rpcMethods'
+import {
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
 
 export default class WigglePlugin extends Plugin {
   name = 'WigglePlugin'
@@ -86,6 +92,38 @@ export default class WigglePlugin extends Plugin {
             import('./BigWigAdapter/BigWigAdapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.(bw|bigwig)$/i
+          const adapterName = 'BigWigAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bigWigLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'BigWigAdapter') {
+            return 'QuantitativeTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
 
     pluginManager.addRendererType(
       () =>