@apollo-annotation/jbrowse-plugin-apollo 0.1.0 → 0.1.5

package/src/LinearApolloDisplay/stateModel/base.ts

@@ -1,3 +1,4 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
@@ -10,7 +11,6 @@ import {
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { AnnotationFeatureI } from 'apollo-mst'
 import { autorun } from 'mobx'
 import { addDisposer, getRoot, types } from 'mobx-state-tree'
 

package/src/LinearApolloDisplay/stateModel/getGlyph.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatureI } from 'apollo-mst'
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 
 import {
   BoxGlyph,

package/src/LinearApolloDisplay/stateModel/glyphs.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatureI } from 'apollo-mst'
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { ObservableMap, observable } from 'mobx'
 import { types } from 'mobx-state-tree'
 

package/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -1,7 +1,7 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
-import { AnnotationFeatureI } from 'apollo-mst'
 import { autorun, observable } from 'mobx'
 import { addDisposer, isAlive } from 'mobx-state-tree'
 

package/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -1,9 +1,9 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { MenuItem } from '@jbrowse/core/ui'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { Theme } from '@mui/material'
-import { AnnotationFeatureI } from 'apollo-mst'
 import { autorun } from 'mobx'
 import { Instance, addDisposer } from 'mobx-state-tree'
 import type { CSSProperties } from 'react'

package/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -9,6 +9,29 @@ import { ApolloSessionModel } from '../../session'
 import { getGlyph } from './getGlyph'
 import { layoutsModelFactory } from './layouts'
 
+export type Frame = 1 | 2 | 3 | -1 | -2 | -3
+
+export function getFrame(
+  start: number,
+  end: number,
+  strand: 1 | -1,
+  phase: 0 | 1 | 2,
+): Frame {
+  return strand === 1
+    ? ((((start + phase) % 3) + 1) as 1 | 2 | 3)
+    : ((-1 * ((end - phase) % 3) - 1) as -1 | -2 | -3)
+}
+
+export const frameColors: [
+  null,
+  string,
+  string,
+  string,
+  string,
+  string,
+  string,
+] = [null, '#FF8080', '#80FF80', '#8080FF', '#8080FF', '#80FF80', '#FF8080']
+
 export function renderingModelIntermediateFactory(
   pluginManager: PluginManager,
   configSchema: AnyConfigurationSchemaType,
@@ -145,13 +168,17 @@ function colorCode(letter: string, theme?: Theme) {
   )
 }
 
-function codonColorCode(letter: string) {
+function codonColorCode(letter: string, rowColorCode: string, bpPerPx: number) {
   const colorMap: Record<string, string> = {
     M: '#33ee33',
     '*': '#f44336',
   }
 
-  return colorMap[letter?.toUpperCase()] || 'lightgray'
+  if (colorMap[letter?.toUpperCase()] !== undefined) {
+    return colorMap[letter?.toUpperCase()]
+  }
+
+  return bpPerPx <= 0.1 ? rowColorCode : 'lightgray'
 }
 
 function reverseCodonSeq(seq: string): string {
@@ -186,6 +213,7 @@ function drawTranslation(
   seq: string,
   i: number,
   reverse: boolean,
+  rowColorCode: string,
 ) {
   let codonSeq: string = seq.slice(i, i + 3).toUpperCase()
   if (reverse) {
@@ -197,7 +225,7 @@ function drawTranslation(
     return
   }
   seqTrackctx.beginPath()
-  seqTrackctx.fillStyle = codonColorCode(codonLetter)
+  seqTrackctx.fillStyle = codonColorCode(codonLetter, rowColorCode, bpPerPx)
   seqTrackctx.rect(trnslStartPx, trnslY, trnslWidthPx, sequenceRowHeight)
   seqTrackctx.fill()
   if (bpPerPx <= 0.1) {
@@ -266,6 +294,7 @@ export function sequenceRenderingModelFactory(
 
                 // Draw translation forward
                 for (let j = 2; j >= 0; j--) {
+                  const color = frameColors.at(j + 1) ?? '#ffffff'
                   if ((region.start + i) % 3 === j) {
                     drawTranslation(
                       seqTrackctx,
@@ -277,6 +306,7 @@ export function sequenceRenderingModelFactory(
                       seq,
                       i,
                       false,
+                      color,
                     )
                   }
                 }
@@ -339,6 +369,7 @@ export function sequenceRenderingModelFactory(
 
                 // Draw translation reverse
                 for (let k = 0; k <= 2; k++) {
+                  const color = frameColors.at(-(k + 1)) ?? '#ffffff'
                   const rowOffset = self.lgv.bpPerPx <= 1 ? 5 : 3
                   if ((region.start + i) % 3 === k) {
                     drawTranslation(
@@ -351,6 +382,7 @@ export function sequenceRenderingModelFactory(
                       seq,
                       i,
                       true,
+                      color,
                     )
                   }
                 }

package/src/OntologyManager/util.ts

@@ -0,0 +1,33 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
+
+import OntologyStore from './OntologyStore'
+import { isOntologyClass } from '.'
+
+export async function fetchValidDescendantTerms(
+  parentFeature: AnnotationFeatureI | undefined,
+  ontologyStore: OntologyStore,
+  _signal: AbortSignal,
+) {
+  if (!parentFeature) {
+    return
+  }
+  // since this is a child of an existing feature, restrict the autocomplete choices to valid
+  // parts of that feature
+  const parentTypeTerms = await ontologyStore.getTermsWithLabelOrSynonym(
+    parentFeature.type,
+    { includeSubclasses: false },
+  )
+  // eslint-disable-next-line unicorn/no-array-callback-reference
+  const parentTypeClassTerms = parentTypeTerms.filter(isOntologyClass)
+  if (parentTypeTerms.length === 0) {
+    return
+  }
+  const subpartTerms = await ontologyStore.getClassesThat(
+    'part_of',
+    parentTypeClassTerms,
+  )
+  if (subpartTerms.length === 0) {
+    return
+  }
+  return subpartTerms
+}

package/src/SixFrameFeatureDisplay/stateModel.ts

@@ -1,3 +1,4 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { ConfigurationReference } from '@jbrowse/core/configuration'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
@@ -13,7 +14,6 @@ import { BaseBlock } from '@jbrowse/core/util/blockTypes'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { AnnotationFeatureI } from 'apollo-mst'
 import { autorun } from 'mobx'
 import { Instance, addDisposer, types } from 'mobx-state-tree'
 

package/src/TabularEditor/HybridGrid/ChangeHandling.ts

@@ -1,11 +1,11 @@
-import type { AnnotationFeatureI } from 'apollo-mst'
+import type { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import {
   DiscontinuousLocationEndChange,
   DiscontinuousLocationStartChange,
   LocationEndChange,
   LocationStartChange,
   TypeChange,
-} from 'apollo-shared'
+} from '@apollo-annotation/apollo-shared'
 
 import type { ChangeManager } from '../../ChangeManager'
 

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -1,5 +1,5 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AbstractSessionModel } from '@jbrowse/core/util'
-import { AnnotationFeatureI } from 'apollo-mst'
 import { observer } from 'mobx-react'
 import React from 'react'
 import { makeStyles } from 'tss-react/mui'
@@ -144,8 +144,8 @@ export const Feature = observer(function Feature({
           (isSelected
             ? ` ${selectedFeatureClass}`
             : isHovered
-            ? ` ${classes.hoveredFeature}`
-            : '')
+              ? ` ${classes.hoveredFeature}`
+              : '')
         }
         onClick={(e) => {
           e.stopPropagation()

package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx

@@ -1,4 +1,4 @@
-import { AnnotationFeatureI } from 'apollo-mst'
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { observer } from 'mobx-react'
 import { getSnapshot } from 'mobx-state-tree'
 import React from 'react'

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -1,6 +1,6 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { MenuItem } from '@jbrowse/core/ui'
 import { AbstractSessionModel } from '@jbrowse/core/util'
-import { AnnotationFeatureI } from 'apollo-mst'
 
 import { ChangeManager } from '../../ChangeManager'
 import {

package/src/components/AddAssembly.tsx

@@ -1,3 +1,8 @@
+import {
+  AddAssemblyAndFeaturesFromFileChange,
+  AddAssemblyFromExternalChange,
+  AddAssemblyFromFileChange,
+} from '@apollo-annotation/apollo-shared'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import LinkIcon from '@mui/icons-material/Link'
@@ -22,11 +27,6 @@ import {
 } from '@mui/material'
 import InputAdornment from '@mui/material/InputAdornment'
 import LinearProgress from '@mui/material/LinearProgress'
-import {
-  AddAssemblyAndFeaturesFromFileChange,
-  AddAssemblyFromExternalChange,
-  AddAssemblyFromFileChange,
-} from 'apollo-shared'
 import ObjectID from 'bson-objectid'
 import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'

package/src/components/AddChildFeature.tsx

@@ -1,3 +1,5 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
+import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import {
   Button,
@@ -11,14 +13,13 @@ import {
   SelectChangeEvent,
   TextField,
 } from '@mui/material'
-import { AnnotationFeatureI } from 'apollo-mst'
-import { AddFeatureChange } from 'apollo-shared'
 import ObjectID from 'bson-objectid'
 import React, { useState } from 'react'
 
 import { ChangeManager } from '../ChangeManager'
 import { isOntologyClass } from '../OntologyManager'
 import OntologyStore from '../OntologyManager/OntologyStore'
+import { fetchValidDescendantTerms } from '../OntologyManager/util'
 import { ApolloSessionModel } from '../session'
 import { Dialog } from './Dialog'
 import { OntologyTermAutocomplete } from './OntologyTermAutocomplete'
@@ -54,37 +55,23 @@ export function AddChildFeature({
   const [errorMessage, setErrorMessage] = useState('')
   const [typeWarningText, setTypeWarningText] = useState('')
 
-  async function fetchValidDescendantTerms(
+  async function fetchValidTerms(
     parentFeature: AnnotationFeatureI | undefined,
     ontologyStore: OntologyStore,
     _signal: AbortSignal,
   ) {
-    if (!parentFeature) {
-      return
-    }
-    // since this is a child of an existing feature, restrict the autocomplete choices to valid
-    // parts of that feature
-    const parentTypeTerms = await ontologyStore.getTermsWithLabelOrSynonym(
-      parentFeature.type,
-      { includeSubclasses: false },
-    )
-    // eslint-disable-next-line unicorn/no-array-callback-reference
-    const parentTypeClassTerms = parentTypeTerms.filter(isOntologyClass)
-    if (parentTypeTerms.length === 0) {
-      return
-    }
-    const subpartTerms = await ontologyStore.getClassesThat(
-      'part_of',
-      parentTypeClassTerms,
+    const terms = await fetchValidDescendantTerms(
+      parentFeature,
+      ontologyStore,
+      _signal,
     )
-    if (subpartTerms.length > 0) {
-      setTypeWarningText('')
-    } else {
+    if (!terms) {
       setTypeWarningText(
-        `Type "${parentFeature.type}" does not have any children in the ontology`,
+        `Type "${parentFeature?.type}" does not have any children in the ontology`,
       )
+      return
     }
-    return subpartTerms
+    return terms
   }
 
   async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
@@ -193,10 +180,7 @@ export function AddChildFeature({
             style={{ width: 170 }}
             value={type}
             filterTerms={isOntologyClass}
-            fetchValidTerms={fetchValidDescendantTerms.bind(
-              null,
-              sourceFeature,
-            )}
+            fetchValidTerms={fetchValidTerms.bind(null, sourceFeature)}
             renderInput={(params) => (
               <TextField
                 {...params}

package/src/components/AddFeature.tsx

@@ -1,3 +1,4 @@
+import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel, Region } from '@jbrowse/core/util/types'
 import {
   Button,
@@ -11,7 +12,6 @@ import {
   SelectChangeEvent,
   TextField,
 } from '@mui/material'
-import { AddFeatureChange } from 'apollo-shared'
 import ObjectID from 'bson-objectid'
 import React, { useState } from 'react'
 

package/src/components/CopyFeature.tsx

@@ -1,3 +1,8 @@
+import {
+  AnnotationFeatureI,
+  AnnotationFeatureSnapshot,
+} from '@apollo-annotation/apollo-mst'
+import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import {
@@ -10,8 +15,6 @@ import {
   SelectChangeEvent,
   TextField,
 } from '@mui/material'
-import { AnnotationFeatureI, AnnotationFeatureSnapshot } from 'apollo-mst'
-import { AddFeatureChange } from 'apollo-shared'
 import ObjectID from 'bson-objectid'
 import { IKeyValueMap } from 'mobx'
 import { getSnapshot } from 'mobx-state-tree'

package/src/components/DeleteAssembly.tsx

@@ -1,3 +1,4 @@
+import { DeleteAssemblyChange } from '@apollo-annotation/apollo-shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   Button,
@@ -11,7 +12,6 @@ import {
   Select,
   SelectChangeEvent,
 } from '@mui/material'
-import { DeleteAssemblyChange } from 'apollo-shared'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 

package/src/components/DeleteFeature.tsx

@@ -1,3 +1,5 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
+import { DeleteFeatureChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import {
   Button,
@@ -5,8 +7,6 @@ import {
   DialogContent,
   DialogContentText,
 } from '@mui/material'
-import { AnnotationFeatureI } from 'apollo-mst'
-import { DeleteFeatureChange } from 'apollo-shared'
 import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 

package/src/components/DownloadGFF3.tsx

@@ -1,3 +1,5 @@
+import { ApolloAssembly } from '@apollo-annotation/apollo-mst'
+import { makeGFF3Feature } from '@apollo-annotation/apollo-shared'
 import gff, { GFF3Item } from '@gmod/gff'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
@@ -10,8 +12,6 @@ import {
   Select,
   SelectChangeEvent,
 } from '@mui/material'
-import { ApolloAssembly } from 'apollo-mst'
-import { makeGFF3Feature } from 'apollo-shared'
 import { saveAs } from 'file-saver'
 import { IMSTMap, getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'

package/src/components/ImportFeatures.tsx

@@ -1,3 +1,4 @@
+import { AddFeaturesFromFileChange } from '@apollo-annotation/apollo-shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
 import {
@@ -12,7 +13,6 @@ import {
 import Checkbox from '@mui/material/Checkbox'
 import FormControlLabel from '@mui/material/FormControlLabel'
 import LinearProgress from '@mui/material/LinearProgress'
-import { AddFeaturesFromFileChange } from 'apollo-shared'
 import React, { useEffect, useState } from 'react'
 
 import {

package/src/components/ManageUsers.tsx

@@ -1,3 +1,4 @@
+import { DeleteUserChange, UserChange } from '@apollo-annotation/apollo-shared'
 import { AbstractRootModel } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
 import {
@@ -19,7 +20,6 @@ import {
   GridRowParams,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { DeleteUserChange, UserChange } from 'apollo-shared'
 import { getRoot } from 'mobx-state-tree'
 import React, { useCallback, useEffect, useState } from 'react'
 

package/src/components/ModifyFeatureAttribute.tsx

@@ -1,3 +1,5 @@
+import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
+import { FeatureAttributeChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
 import {
@@ -16,8 +18,6 @@ import {
   TextField,
   Typography,
 } from '@mui/material'
-import { AnnotationFeatureI } from 'apollo-mst'
-import { FeatureAttributeChange } from 'apollo-shared'
 import { getRoot, getSnapshot } from 'mobx-state-tree'
 import React, { useMemo, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'

package/src/components/ViewChangeLog.tsx

@@ -1,3 +1,4 @@
+import { changeRegistry } from '@apollo-annotation/apollo-common'
 import {
   Button,
   DialogActions,
@@ -13,7 +14,6 @@ import {
   GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { changeRegistry } from 'apollo-common'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
@@ -76,9 +76,11 @@ export function ViewChangeLog({ handleClose, session }: ViewChangeLogProps) {
       headerName: 'Change JSON',
       width: 600,
       renderCell: ({ value }) => (
-        <textarea className={classes.changeTextarea} readOnly>
-          {JSON.stringify(value)}
-        </textarea>
+        <textarea
+          className={classes.changeTextarea}
+          value={JSON.stringify(value)}
+          readOnly
+        />
       ),
       valueFormatter: ({ value }) => JSON.stringify(value),
     },
@@ -88,7 +90,7 @@ export function ViewChangeLog({ handleClose, session }: ViewChangeLogProps) {
       headerName: 'Time',
       width: 160,
       type: 'dateTime',
-      valueGetter: ({ value }) => value && new Date(value),
+      valueGetter: (value) => value && new Date(value),
     },
   ]
 

package/src/extensions/annotationFromPileup.ts

@@ -1,11 +1,11 @@
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/apollo-mst'
+import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
 import PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
 import { getContainingView, getSession } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
-import { AnnotationFeatureSnapshot } from 'apollo-mst'
-import { AddFeatureChange } from 'apollo-shared'
 import ObjectID from 'bson-objectid'
 
 import { ApolloSessionModel } from '../session'

package/src/index.ts

@@ -1,3 +1,11 @@
+import { changeRegistry, checkRegistry } from '@apollo-annotation/apollo-common'
+import {
+  CDSCheck,
+  CoreValidation,
+  ParentChildValidation,
+  changes,
+  validationRegistry,
+} from '@apollo-annotation/apollo-shared'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import {
   DisplayType,
@@ -5,6 +13,7 @@ import {
   PluggableElementType,
   TrackType,
   ViewType,
+  WidgetType,
   createBaseTrackConfig,
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes'
@@ -18,14 +27,6 @@ import {
 } from '@jbrowse/core/util'
 import { LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
-import { changeRegistry, checkRegistry } from 'apollo-common'
-import {
-  CDSCheck,
-  CoreValidation,
-  ParentChildValidation,
-  changes,
-  validationRegistry,
-} from 'apollo-shared'
 
 import { version } from '../package.json'
 import {
@@ -50,6 +51,10 @@ import { AddFeature } from './components/AddFeature'
 import { ViewCheckResults } from './components/ViewCheckResults'
 import ApolloPluginConfigurationSchema from './config'
 import { annotationFromPileup } from './extensions'
+import {
+  ApolloFeatureDetailsWidget,
+  ApolloFeatureDetailsWidgetModel,
+} from './FeatureDetailsWidget'
 import {
   stateModelFactory as LinearApolloDisplayStateModelFactory,
   configSchemaFactory as linearApolloDisplayConfigSchemaFactory,
@@ -106,6 +111,19 @@ export default class ApolloPlugin extends Plugin {
   install(pluginManager: PluginManager) {
     installApolloSequenceAdapter(pluginManager)
     installApolloTextSearchAdapter(pluginManager)
+
+    pluginManager.addWidgetType(() => {
+      const configSchema = ConfigurationSchema('ApolloFeatureDetailsWidget', {})
+      const widgetType = new WidgetType({
+        name: 'ApolloFeatureDetailsWidget',
+        heading: 'Apollo feature details',
+        configSchema,
+        stateModel: ApolloFeatureDetailsWidgetModel,
+        ReactComponent: ApolloFeatureDetailsWidget,
+      })
+      return widgetType
+    })
+
     pluginManager.addTrackType(() => {
       const configSchema = ConfigurationSchema(
         'ApolloTrack',

package/src/makeDisplayComponent.tsx

@@ -2,8 +2,7 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
-import { Typography } from '@mui/material'
-import { alpha } from '@mui/material/styles'
+import { Typography, alpha } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useCallback, useEffect, useRef } from 'react'
 import { makeStyles } from 'tss-react/mui'

package/src/session/ClientDataStore.ts

@@ -1,8 +1,4 @@
-import { getConf, readConfObject } from '@jbrowse/core/configuration'
-import { ConfigurationModel } from '@jbrowse/core/configuration/types'
-import { Region, getSession, isElectron } from '@jbrowse/core/util'
-import { LocalPathLocation, UriLocation } from '@jbrowse/core/util/types/mst'
-import { ClientDataStore as ClientDataStoreType } from 'apollo-common'
+import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/apollo-common'
 import {
   AnnotationFeature,
   AnnotationFeatureSnapshot,
@@ -10,7 +6,11 @@ import {
   ApolloRefSeq,
   CheckResult,
   CheckResultSnapshot,
-} from 'apollo-mst'
+} from '@apollo-annotation/apollo-mst'
+import { getConf, readConfObject } from '@jbrowse/core/configuration'
+import { ConfigurationModel } from '@jbrowse/core/configuration/types'
+import { Region, getSession, isElectron } from '@jbrowse/core/util'
+import { LocalPathLocation, UriLocation } from '@jbrowse/core/util/types/mst'
 import {
   Instance,
   SnapshotOut,

package/src/session/session.ts

@@ -1,3 +1,9 @@
+import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/apollo-common'
+import {
+  AnnotationFeature,
+  AnnotationFeatureI,
+} from '@apollo-annotation/apollo-mst'
+import { UserLocation } from '@apollo-annotation/apollo-shared'
 import { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
 import { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
@@ -7,9 +13,6 @@ import {
   SessionWithConfigEditing,
 } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { ClientDataStore as ClientDataStoreType } from 'apollo-common'
-import { AnnotationFeature, AnnotationFeatureI } from 'apollo-mst'
-import { UserLocation } from 'apollo-shared'
 import { autorun, observable } from 'mobx'
 import { Instance, flow, getRoot, types } from 'mobx-state-tree'
 

package/src/util/loadAssemblyIntoClient.ts

@@ -1,10 +1,13 @@
-import gff, { GFF3Comment, GFF3Feature, GFF3Sequence } from '@gmod/gff'
-import { ClientDataStore, checkRegistry } from 'apollo-common'
+import {
+  ClientDataStore,
+  checkRegistry,
+} from '@apollo-annotation/apollo-common'
 import {
   AnnotationFeatureSnapshot,
   ApolloAssemblyI,
   CheckResultSnapshot,
-} from 'apollo-mst'
+} from '@apollo-annotation/apollo-mst'
+import gff, { GFF3Comment, GFF3Feature, GFF3Sequence } from '@gmod/gff'
 import { getSnapshot } from 'mobx-state-tree'
 import { nanoid } from 'nanoid'