@apollo-annotation/jbrowse-plugin-apollo 0.3.4 → 0.3.6

package/src/components/ViewChangeLog.tsx

@@ -13,22 +13,23 @@ import {
   DialogContentText,
   MenuItem,
   Select,
-  SelectChangeEvent,
+  type SelectChangeEvent,
 } from '@mui/material'
 import {
   DataGrid,
-  GridColDef,
-  GridRowsProp,
+  type GridColDef,
+  type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { Dialog } from './Dialog'
 
 interface ViewChangeLogProps {

package/src/components/ViewCheckResults.tsx

@@ -4,7 +4,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   Button,
   DialogActions,
@@ -12,21 +12,22 @@ import {
   DialogContentText,
   MenuItem,
   Select,
-  SelectChangeEvent,
+  type SelectChangeEvent,
 } from '@mui/material'
 import {
   DataGrid,
-  GridColDef,
-  GridRowsProp,
+  type GridColDef,
+  type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { Dialog } from './Dialog'
 
 interface ViewCheckResultsProps {

package/src/components/index.ts

@@ -9,7 +9,6 @@ export * from './ImportFeatures'
 export * from './LogOut'
 export * from './ManageChecks'
 export * from './ManageUsers'
-export * from './ModifyFeatureAttribute'
 export * from './OpenLocalFile'
 export * from './ViewChangeLog'
 export * from './AddRefSeqAliases'

package/src/extensions/annotationFromJBrowseFeature.test.ts

@@ -1,5 +1,6 @@
 import SimpleFeature from '@jbrowse/core/util/simpleFeature'
 import { describe, expect, it } from '@jest/globals'
+
 import { jbrowseFeatureToAnnotationFeature } from './annotationFromJBrowseFeature'
 
 describe('Convert JBrowse feature to annotation feature', () => {

package/src/extensions/annotationFromJBrowseFeature.ts

@@ -3,26 +3,28 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
-import AddIcon from '@mui/icons-material/Add'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
+import { type GFF3Feature } from '@gmod/gff'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
 import {
-  AbstractSessionModel,
+  type AbstractSessionModel,
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { type Feature } from '@jbrowse/core/util/simpleFeature'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import AddIcon from '@mui/icons-material/Add'
+
 import { CreateApolloAnnotation } from '../components/CreateApolloAnnotation'
-import { GFF3Feature } from '@gmod/gff'
-import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
 
 function simpleFeatureToGFF3Feature(
   feature: Feature,
   refSeqId: string,
 ): GFF3Feature {
+  // eslint-disable-next-line unicorn/prefer-structured-clone
   const xfeature = JSON.parse(JSON.stringify(feature))
   const children = xfeature.subfeatures
   const gff3Feature = [
@@ -130,11 +132,11 @@ export function annotationFromJBrowseFeature(
     }))
     .views((self) => {
       const superContextMenuItems = self.contextMenuItems
-      const session = getSession(self)
-      const assembly = self.getAssembly()
 
       return {
         contextMenuItems() {
+          const session = getSession(self)
+          const assembly = self.getAssembly()
           const feature = self.contextMenuFeature
           if (!feature) {
             return superContextMenuItems()

package/src/extensions/annotationFromPileup.ts

@@ -3,17 +3,17 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type DisplayType } from '@jbrowse/core/pluggableElementTypes'
+import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
 import { getContainingView, getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 import ObjectID from 'bson-objectid'
 
-import { ApolloSessionModel } from '../session'
+import { type ApolloSessionModel } from '../session'
 
 function parseCigar(cigar: string): [string | undefined, number][] {
   return (cigar.toUpperCase().match(/\d+\D/g) ?? []).map((op) => {

package/src/index.ts

@@ -9,41 +9,52 @@ import {
   changes,
   validationRegistry,
 } from '@apollo-annotation/shared'
+import Plugin from '@jbrowse/core/Plugin'
+import type PluginManager from '@jbrowse/core/PluginManager'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import {
   DisplayType,
   InternetAccountType,
-  PluggableElementType,
+  type PluggableElementType,
   TrackType,
-  ViewType,
+  type ViewType,
   WidgetType,
   createBaseTrackConfig,
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
 import {
-  AbstractSessionModel,
-  Region,
+  type AbstractSessionModel,
+  type Region,
   getSession,
   isAbstractMenuManager,
 } from '@jbrowse/core/util'
-import { LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
+import { type LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 
 import { version } from '../package.json'
+
 import {
   configSchema as apolloInternetAccountConfigSchema,
   modelFactory as apolloInternetAccountModelFactory,
 } from './ApolloInternetAccount'
+import { installApolloRefNameAliasAdapter } from './ApolloRefNameAliasAdapter'
 import { installApolloSequenceAdapter } from './ApolloSequenceAdapter'
-import {
-  ApolloSixFrameRenderer,
-  ReactComponent as ApolloSixFrameRendererReactComponent,
-  configSchema as apolloSixFrameRendererConfigSchema,
-} from './ApolloSixFrameRenderer'
 import { installApolloTextSearchAdapter } from './ApolloTextSearchAdapter'
-import { BackendDriver } from './BackendDrivers'
+import { type BackendDriver } from './BackendDrivers'
+import {
+  ApolloFeatureDetailsWidget,
+  ApolloFeatureDetailsWidgetModel,
+  ApolloTranscriptDetailsModel,
+  ApolloTranscriptDetailsWidget,
+} from './FeatureDetailsWidget'
+import {
+  configSchema as linearApolloDisplayConfigSchema,
+  stateModelFactory as LinearApolloDisplayStateModelFactory,
+} from './LinearApolloDisplay'
+import {
+  configSchema as linearApolloSixFrameDisplayConfigSchema,
+  stateModelFactory as LinearApolloSixFrameDisplayStateModelFactory,
+} from './LinearApolloSixFrameDisplay'
 import {
   AddFeature,
   DownloadGFF3,
@@ -55,29 +66,14 @@ import {
 } from './components'
 import ApolloPluginConfigurationSchema from './config'
 import {
-  annotationFromPileup,
   annotationFromJBrowseFeature,
+  annotationFromPileup,
 } from './extensions'
 import {
-  ApolloFeatureDetailsWidget,
-  ApolloFeatureDetailsWidgetModel,
-  ApolloTranscriptDetailsModel,
-  ApolloTranscriptDetailsWidget,
-} from './FeatureDetailsWidget'
-import {
-  stateModelFactory as LinearApolloDisplayStateModelFactory,
-  configSchema as linearApolloDisplayConfigSchema,
-} from './LinearApolloDisplay'
-import {
-  DisplayComponent,
-  makeSixFrameDisplayComponent,
+  LinearApolloDisplayComponent,
+  LinearApolloSixFrameDisplayComponent,
 } from './makeDisplayComponent'
-import { ApolloSessionModel, extendSession } from './session'
-import {
-  stateModelFactory as SixFrameFeatureDisplayStateModelFactory,
-  configSchemaFactory as sixFrameFeatureDisplayConfigSchemaFactory,
-} from './SixFrameFeatureDisplay'
-import { installApolloRefNameAliasAdapter } from './ApolloRefNameAliasAdapter'
+import { type ApolloSessionModel, extendSession } from './session'
 
 interface RpcHandle {
   on(event: string, listener: (event: MessageEvent) => void): this
@@ -186,38 +182,25 @@ export default class ApolloPlugin extends Plugin {
         ),
         trackType: 'ApolloTrack',
         viewType: 'LinearGenomeView',
-        ReactComponent: DisplayComponent,
+        ReactComponent: LinearApolloDisplayComponent,
       })
     })
 
     pluginManager.addDisplayType(() => {
-      const configSchema =
-        sixFrameFeatureDisplayConfigSchemaFactory(pluginManager)
-      const SixFrameDisplayComponent =
-        makeSixFrameDisplayComponent(pluginManager)
+      const configSchema = linearApolloSixFrameDisplayConfigSchema
       return new DisplayType({
-        name: 'SixFrameFeatureDisplay',
+        name: 'LinearApolloSixFrameDisplay',
         configSchema,
-        stateModel: SixFrameFeatureDisplayStateModelFactory(
+        stateModel: LinearApolloSixFrameDisplayStateModelFactory(
           pluginManager,
           configSchema,
         ),
         trackType: 'ApolloTrack',
         viewType: 'LinearGenomeView',
-        ReactComponent: SixFrameDisplayComponent,
+        ReactComponent: LinearApolloSixFrameDisplayComponent,
       })
     })
 
-    pluginManager.addRendererType(
-      () =>
-        new ApolloSixFrameRenderer({
-          name: 'ApolloSixFrameRenderer',
-          ReactComponent: ApolloSixFrameRendererReactComponent,
-          configSchema: apolloSixFrameRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
     pluginManager.addToExtensionPoint(
       'Core-extendSession',
       // @ts-expect-error not sure how to deal with snapshot model types

package/src/makeDisplayComponent.tsx

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-import PluginManager from '@jbrowse/core/PluginManager'
-import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
+import { getSession } from '@jbrowse/core/util'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import { Alert, Typography, alpha } from '@mui/material'
@@ -9,13 +8,11 @@ import React, { useCallback, useEffect, useRef } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
 import { LinearApolloDisplay } from './LinearApolloDisplay/components'
-import { LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
-import { TrackLines } from './SixFrameFeatureDisplay/components'
-import { SixFrameFeatureDisplay } from './SixFrameFeatureDisplay/stateModel'
+import { type LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
+import { LinearApolloSixFrameDisplay } from './LinearApolloSixFrameDisplay/components'
+import { type LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from './LinearApolloSixFrameDisplay/stateModel'
 import { TabularEditorPane } from './TabularEditor'
-
-import { getSession } from '@jbrowse/core/util'
-import { ApolloSessionModel } from './session'
+import { type ApolloSessionModel } from './session'
 
 const accordionControlHeight = 12
 
@@ -63,7 +60,7 @@ const useStyles = makeStyles()((theme) => ({
 }))
 
 function scrollSelectedFeatureIntoView(
-  model: LinearApolloDisplayI,
+  model: LinearApolloDisplayI | LinearApolloSixFrameDisplayI,
   scrollContainerRef: React.RefObject<HTMLDivElement>,
 ) {
   const { apolloRowHeight, selectedFeature } = model
@@ -157,7 +154,7 @@ const AccordionControl = observer(function AccordionControl({
   )
 })
 
-export const DisplayComponent = observer(function DisplayComponent({
+export const LinearApolloDisplayComponent = observer(function DisplayComponent({
   model,
   ...other
 }: {
@@ -171,7 +168,6 @@ export const DisplayComponent = observer(function DisplayComponent({
   const { classes } = useStyles()
 
   const {
-    detailsHeight,
     graphical,
     height: overallHeight,
     isShown,
@@ -187,7 +183,7 @@ export const DisplayComponent = observer(function DisplayComponent({
   }, [model, selectedFeature])
 
   const onDetailsResize = (delta: number) => {
-    model.setDetailsHeight(detailsHeight - delta)
+    model.setDetailsHeight(model.detailsHeight - delta)
   }
 
   if (!ontologyStore) {
@@ -199,9 +195,9 @@ export const DisplayComponent = observer(function DisplayComponent({
   }
 
   if (graphical && table) {
-    const tabularHeight = tabularEditor.isShown ? detailsHeight : 0
+    const tabularHeight = tabularEditor.isShown ? model.detailsHeight : 0
     const featureAreaHeight = isShown
-      ? overallHeight - detailsHeight - accordionControlHeight * 2
+      ? overallHeight - model.detailsHeight - accordionControlHeight * 2
       : 0
     return (
       <div style={{ height: overallHeight }}>
@@ -249,40 +245,96 @@ export const DisplayComponent = observer(function DisplayComponent({
   )
 })
 
-export function makeSixFrameDisplayComponent(pluginManager: PluginManager) {
-  const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin') as
-    | LinearGenomeViewPlugin
-    | undefined
-  if (!LGVPlugin) {
-    throw new Error('LinearGenomeView plugin not found')
-  }
-  const { BaseLinearDisplayComponent } = LGVPlugin.exports
-  function ApolloDisplayComponent({
+export const LinearApolloSixFrameDisplayComponent = observer(
+  function DisplayComponent({
     model,
     ...other
   }: {
-    model: SixFrameFeatureDisplay
+    model: LinearApolloSixFrameDisplayI
   }) {
+    const session = getSession(model) as unknown as ApolloSessionModel
+    const { ontologyManager } = session.apolloDataStore
+    const { featureTypeOntology } = ontologyManager
+    const ontologyStore = featureTypeOntology?.dataStore
+
     const { classes } = useStyles()
-    const { height, selectedFeature } = model
-    let { detailsHeight } = model
-    if (!selectedFeature) {
-      detailsHeight = 0
+
+    const {
+      detailsHeight,
+      graphical,
+      height: overallHeight,
+      isShown,
+      selectedFeature,
+      table,
+      tabularEditor,
+      toggleShown,
+    } = model
+
+    const canvasScrollContainerRef = useRef<HTMLDivElement>(null)
+    useEffect(() => {
+      scrollSelectedFeatureIntoView(model, canvasScrollContainerRef)
+    }, [model, selectedFeature])
+
+    const onDetailsResize = (delta: number) => {
+      model.setDetailsHeight(detailsHeight - delta)
     }
-    const featureAreaHeight = height - detailsHeight
-    return (
-      <div style={{ height: model.height }}>
-        <div className={classes.shading} style={{ height: featureAreaHeight }}>
-          <BaseLinearDisplayComponent model={model} {...other} />
+
+    if (!ontologyStore) {
+      return (
+        <div className={classes.alertContainer}>
+          <Alert severity="error">Could not load feature type ontology.</Alert>
+        </div>
+      )
+    }
+
+    if (graphical && table) {
+      const tabularHeight = tabularEditor.isShown ? detailsHeight : 0
+      const featureAreaHeight = isShown
+        ? overallHeight - detailsHeight - accordionControlHeight * 2
+        : 0
+      return (
+        <div style={{ height: overallHeight }}>
+          <AccordionControl
+            open={isShown}
+            title="Graphical"
+            onClick={toggleShown}
+          />
+          <div
+            className={classes.shading}
+            ref={canvasScrollContainerRef}
+            style={{ height: featureAreaHeight }}
+          >
+            <LinearApolloSixFrameDisplay model={model} {...other} />
+          </div>
+          <AccordionControl
+            title="Table"
+            open={tabularEditor.isShown}
+            onClick={tabularEditor.togglePane}
+            onResize={onDetailsResize}
+          />
+          <div className={classes.details} style={{ height: tabularHeight }}>
+            <TabularEditorPane model={model} />
+          </div>
         </div>
-        {/* <div className={classes.details} style={{ height: detailsHeight }}>
-          <ApolloDetails model={model} />
-        </div> */}
-        <div className="testTrackLines">
-          <TrackLines model={model} />
+      )
+    }
+
+    if (graphical) {
+      return (
+        <div
+          className={classes.shading}
+          ref={canvasScrollContainerRef}
+          style={{ height: overallHeight }}
+        >
+          <LinearApolloSixFrameDisplay model={model} {...other} />
         </div>
+      )
+    }
+
+    return (
+      <div className={classes.details} style={{ height: overallHeight }}>
+        <TabularEditorPane model={model} />
       </div>
     )
-  }
-  return observer(ApolloDisplayComponent)
-}
+  },
+)

package/src/session/ClientDataStore.ts

@@ -2,23 +2,27 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
+import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureModel,
-  AnnotationFeatureSnapshot,
+  type AnnotationFeatureModel,
+  type AnnotationFeatureSnapshot,
   ApolloAssembly,
-  ApolloAssemblySnapshot,
+  type ApolloAssemblySnapshot,
   ApolloRefSeq,
-  BackendDriverType,
+  type BackendDriverType,
   CheckResult,
-  CheckResultSnapshot,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/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 { type ConfigurationModel } from '@jbrowse/core/configuration/types'
+import { type Region, getSession, isElectron } from '@jbrowse/core/util'
 import {
-  Instance,
+  type LocalPathLocation,
+  type UriLocation,
+} from '@jbrowse/core/util/types/mst'
+import { autorun } from 'mobx'
+import {
+  type Instance,
   addDisposer,
   flow,
   getParentOfType,
@@ -28,21 +32,21 @@ import {
 } from 'mobx-state-tree'
 
 import {
-  ApolloInternetAccount,
+  type ApolloInternetAccount,
   CollaborationServerDriver,
   DesktopFileDriver,
   InMemoryFileDriver,
 } from '../BackendDrivers'
 import { ChangeManager } from '../ChangeManager'
-import ApolloPluginConfigurationSchema from '../config'
 import {
   OntologyManagerType,
-  OntologyRecordConfiguration,
-  TextIndexFieldDefinition,
+  type OntologyRecordConfiguration,
+  type TextIndexFieldDefinition,
 } from '../OntologyManager'
-import { ApolloRootModel } from '../types'
-import { autorun } from 'mobx'
-import { ApolloSessionModel } from './session'
+import type ApolloPluginConfigurationSchema from '../config'
+import { type ApolloRootModel } from '../types'
+
+import { type ApolloSessionModel } from './session'
 
 export function clientDataStoreFactory(
   AnnotationFeatureExtended: typeof AnnotationFeatureModel,

package/src/session/session.ts

@@ -1,27 +1,31 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
+import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
-  AnnotationFeature,
+  type AnnotationFeature,
   AnnotationFeatureModel,
 } from '@apollo-annotation/mst'
 import {
-  filterJBrowseConfig,
   ImportJBrowseConfigChange,
-  JBrowseConfig,
-  UserLocation,
+  type JBrowseConfig,
+  type UserLocation,
+  filterJBrowseConfig,
 } from '@apollo-annotation/shared'
-import { readConfObject, getConf } from '@jbrowse/core/configuration'
-import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AbstractSessionModel, SessionWithAddTracks } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type PluginManager from '@jbrowse/core/PluginManager'
+import { type AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
+import { getConf, readConfObject } from '@jbrowse/core/configuration'
+import { type BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+import {
+  type AbstractSessionModel,
+  type SessionWithAddTracks,
+} from '@jbrowse/core/util'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import SaveIcon from '@mui/icons-material/Save'
 import { autorun, observable } from 'mobx'
 import {
-  Instance,
-  SnapshotOut,
+  type Instance,
+  type SnapshotOut,
   applySnapshot,
   flow,
   getRoot,
@@ -29,13 +33,13 @@ import {
   types,
 } from 'mobx-state-tree'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { ApolloJobModel } from '../ApolloJobModel'
-import { ChangeManager } from '../ChangeManager'
-import { ApolloRootModel } from '../types'
+import { type ChangeManager } from '../ChangeManager'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { clientDataStoreFactory } from './ClientDataStore'
-import { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
 
 export interface ApolloSession extends AbstractSessionModel {
   apolloDataStore: ClientDataStoreType & { changeManager: ChangeManager }
@@ -119,16 +123,6 @@ export function extendSession(
                   : {}),
               },
             },
-            displays: [
-              {
-                type: 'LinearApolloDisplay',
-                displayId: `${trackId}-LinearApolloDisplay`,
-              },
-              {
-                type: 'SixFrameFeatureDisplay',
-                displayId: `${trackId}-SixFrameFeatureDisplay`,
-              },
-            ],
           })
         }
       },

package/src/types.ts

@@ -1,8 +1,8 @@
-import { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
-import { AppRootModel } from '@jbrowse/core/util'
+import { type BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
+import { type AppRootModel } from '@jbrowse/core/util'
 
-import { ApolloInternetAccountModel } from './ApolloInternetAccount/model'
-import { ApolloSessionModel } from './session'
+import { type ApolloInternetAccountModel } from './ApolloInternetAccount/model'
+import { type ApolloSessionModel } from './session'
 
 export interface ApolloRootModel extends Omit<AppRootModel, 'session'> {
   session: ApolloSessionModel