@apollo-annotation/jbrowse-plugin-apollo 0.3.11 → 0.3.12

package/src/ChangeManager.ts

@@ -11,9 +11,9 @@ import {
   validationRegistry,
 } from '@apollo-annotation/shared'
 import { getSession } from '@jbrowse/core/util'
-import { type IAnyStateTreeNode } from 'mobx-state-tree'
+import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree'
 
-import { type ApolloSessionModel } from './session'
+import type { ApolloSessionModel } from './session'
 
 export interface SubmitOpts {
   /** defaults to true */
@@ -66,7 +66,12 @@ export class ChangeManager {
       statusMessage: 'Pre-validating',
       progressPct: 0,
       cancelCallback: () => {
-        controller.abort('ChangeManager')
+        controller.abort(
+          new DOMException(
+            `Cancelling change "${change.typeName}"`,
+            'AbortError',
+          ),
+        )
       },
     }
 

package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx

@@ -1,4 +1,5 @@
 import { getSession } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import {
   Accordion,
@@ -8,15 +9,14 @@ import {
 } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { Attributes } from './Attributes'
 import { BasicInformation } from './BasicInformation'
 import { FeatureDetailsNavigation } from './FeatureDetailsNavigation'
 import { Sequence } from './Sequence'
-import { type ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
+import type { ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
 
 const useStyles = makeStyles()((theme) => ({
   root: {

package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx

@@ -1,10 +1,12 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import styled from '@emotion/styled'
 import {
   type AbstractSessionModel,
   getEnv,
   getSession,
 } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import InfoIcon from '@mui/icons-material/Info'
 import {
@@ -15,19 +17,17 @@ import {
   Typography,
 } from '@mui/material'
 import { observer } from 'mobx-react'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 
 import { Attributes } from './Attributes'
 import { TranscriptSequence } from './TranscriptSequence'
 import { TranscriptWidgetEditLocation } from './TranscriptWidgetEditLocation'
 import { TranscriptWidgetSummary } from './TranscriptWidgetSummary'
-import { type ApolloTranscriptDetailsWidget as ApolloTranscriptDetailsWidgetState } from './model'
+import type { ApolloTranscriptDetailsWidget as ApolloTranscriptDetailsWidgetState } from './model'
 
 interface CustomComponentProps {
   session: AbstractSessionModel

package/src/FeatureDetailsWidget/AttributeKey.tsx

@@ -4,10 +4,10 @@ import {
   isGFFColumnInternal,
   isGFFInternalAttribute,
 } from '@apollo-annotation/shared'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import InfoIcon from '@mui/icons-material/Info'
 import { Chip, Tooltip, Typography } from '@mui/material'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()((theme) => ({
   attributeKey: {

package/src/FeatureDetailsWidget/AttributeKeySelector.tsx

@@ -12,7 +12,7 @@ import {
 import { observer } from 'mobx-react'
 import React, { useState } from 'react'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 const customKeyName = 'Custom'
 const gffKeys: Record<string, string | undefined> = {

package/src/FeatureDetailsWidget/Attributes.tsx

@@ -1,6 +1,8 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { FeatureAttributeChange } from '@apollo-annotation/shared'
 import { type AbstractSessionModel, getEnv } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import DeleteIcon from '@mui/icons-material/Delete'
 import EditIcon from '@mui/icons-material/Edit'
 import MoreHorizIcon from '@mui/icons-material/MoreHoriz'
@@ -18,11 +20,9 @@ import {
 } from '@mui/material'
 import { entries } from 'mobx'
 import { observer } from 'mobx-react'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { AttributeKey } from './AttributeKey'
 import { AttributeKeySelector } from './AttributeKeySelector'

package/src/FeatureDetailsWidget/BasicInformation.tsx

@@ -1,12 +1,12 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
   StrandChange,
   TypeChange,
 } from '@apollo-annotation/shared'
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
 import { TextField, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useState } from 'react'
@@ -15,7 +15,7 @@ import { isOntologyClass } from '../OntologyManager'
 import type OntologyStore from '../OntologyManager/OntologyStore'
 import { fetchValidDescendantTerms } from '../OntologyManager/util'
 import { OntologyTermAutocomplete } from '../components/OntologyTermAutocomplete'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { NumberTextField } from './NumberTextField'
 

package/src/FeatureDetailsWidget/DefaultAttributeEditor.tsx

@@ -4,7 +4,7 @@ import { Button, DialogActions, IconButton } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useState } from 'react'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { StringTextField } from './StringTextField'
 

package/src/FeatureDetailsWidget/FeatureDetailsNavigation.tsx

@@ -1,11 +1,11 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { Button, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import React from 'react'
 
 import { getFeatureNameOrId } from '../util'
 
-import { type ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
+import type { ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
 
 export const FeatureDetailsNavigation = observer(
   function FeatureDetailsNavigation(props: {

package/src/FeatureDetailsWidget/Sequence.tsx

@@ -1,11 +1,11 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { splitStringIntoChunks } from '@apollo-annotation/shared'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 function formatSequence(
   seq: string,

package/src/FeatureDetailsWidget/TranscriptSequence.tsx

@@ -1,4 +1,4 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { splitStringIntoChunks } from '@apollo-annotation/shared'
 import { defaultCodonTable, revcom } from '@jbrowse/core/util'
 import {
@@ -12,7 +12,7 @@ import {
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 import { copyToClipboard } from '../util/copyToClipboard'
 
 const SEQUENCE_WRAP_LENGTH = 60

package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx

@@ -3,10 +3,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import {
-  type AnnotationFeature,
-  type TranscriptPart,
-} from '@apollo-annotation/mst'
+import type { AnnotationFeature, TranscriptPart } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
@@ -32,8 +29,8 @@ import {
 import { observer } from 'mobx-react'
 import React, { useRef } from 'react'
 
-import { type OntologyRecord } from '../OntologyManager'
-import { type ApolloSessionModel } from '../session'
+import type { OntologyRecord } from '../OntologyManager'
+import type { ApolloSessionModel } from '../session'
 import { copyToClipboard } from '../util/copyToClipboard'
 
 import { StyledAccordionSummary } from './ApolloTranscriptDetailsWidget'

package/src/FeatureDetailsWidget/TranscriptWidgetSummary.tsx

@@ -1,4 +1,4 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import styled from '@emotion/styled'
 import { Table, TableBody, TableCell, TableRow } from '@mui/material'
 import { observer } from 'mobx-react'

package/src/FeatureDetailsWidget/model.ts

@@ -6,15 +6,15 @@ import {
 } from '@apollo-annotation/mst'
 import { getSession } from '@jbrowse/core/util'
 import { ElementId } from '@jbrowse/core/util/types/mst'
-import { autorun } from 'mobx'
 import {
   type Instance,
   type SnapshotIn,
   addDisposer,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { autorun } from 'mobx'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 export const ApolloFeatureDetailsWidgetModel = types
   .model('ApolloFeatureDetailsWidget', {

package/src/LinearApolloDisplay/components/CheckResultWarnings.tsx

@@ -1,4 +1,4 @@
-import { type CheckResultI } from '@apollo-annotation/mst'
+import type { CheckResultI } from '@apollo-annotation/mst'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import ErrorIcon from '@mui/icons-material/Error'
 import { Avatar, Badge, Box, Tooltip } from '@mui/material'
@@ -7,7 +7,7 @@ import React from 'react'
 
 import { clusterResultByMessage, useStyles } from '../../util/displayUtils'
 import { getLeftPx } from '../glyphs/util'
-import { type LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
+import type { LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
 
 export const CheckResultWarnings = observer(function CheckResultWarnings({
   display,

package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx

@@ -1,16 +1,17 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import { getContainingView } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import LockIcon from '@mui/icons-material/Lock'
 import { Alert, CircularProgress, Tooltip, useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
 
 import { type Coord, useStyles } from '../../util/displayUtils'
-import { type LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
+import type { LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
 
 import { CheckResultWarnings } from './CheckResultWarnings'
 
@@ -84,6 +85,8 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
             <CircularProgress size="18px" />
           </div>
         ) : null}
+        {/* This type is wrong in @jbrowse/core */}
+        {/* eslint-disable-next-line @typescript-eslint/no-unnecessary-condition */}
         {message ? (
           <Alert
             severity="warning"
@@ -156,7 +159,6 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
                   ? { top: contextCoord[1], left: contextCoord[0] }
                   : undefined
               }
-              style={{ zIndex: theme.zIndex.tooltip }}
               menuItems={contextMenuItems}
             />
           </>

package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts

@@ -1,5 +1,5 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { MenuItem } from '@jbrowse/core/ui'
 import { alpha } from '@mui/material'
 
 import {
@@ -9,12 +9,12 @@ import {
   isMousePositionWithFeature,
   isSelectedFeature,
 } from '../../util'
-import { type LinearApolloDisplay } from '../stateModel'
-import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
-import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
-import { type CanvasMouseEvent } from '../types'
+import type { LinearApolloDisplay } from '../stateModel'
+import type { LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
+import type { LinearApolloDisplayRendering } from '../stateModel/rendering'
+import type { CanvasMouseEvent } from '../types'
 
-import { type Glyph } from './Glyph'
+import type { Glyph } from './Glyph'
 
 function drawBoxOutline(
   ctx: CanvasRenderingContext2D,

package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -1,7 +1,7 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { readConfObject } from '@jbrowse/core/configuration'
-import { type BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
+import type { MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
   getContainingView,
@@ -9,11 +9,12 @@ import {
   intersection2,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { alpha } from '@mui/material'
 
-import { type OntologyRecord } from '../../OntologyManager'
+import type { OntologyRecord } from '../../OntologyManager'
 import { MergeExons, MergeTranscripts, SplitExon } from '../../components'
+import { DuplicateTranscript } from '../../components/DuplicateTranscript'
 import {
   type MousePosition,
   type MousePositionWithFeature,
@@ -30,13 +31,13 @@ import {
   selectFeatureAndOpenWidget,
 } from '../../util'
 import { getRelatedFeatures } from '../../util/annotationFeatureUtils'
-import { type LinearApolloDisplay } from '../stateModel'
-import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
-import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
-import { type CanvasMouseEvent } from '../types'
+import type { LinearApolloDisplay } from '../stateModel'
+import type { LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
+import type { LinearApolloDisplayRendering } from '../stateModel/rendering'
+import type { CanvasMouseEvent } from '../types'
 
 import { boxGlyph } from './BoxGlyph'
-import { type Glyph } from './Glyph'
+import type { Glyph } from './Glyph'
 
 let forwardFillLight: CanvasPattern | null = null
 let backwardFillLight: CanvasPattern | null = null
@@ -950,29 +951,54 @@ function getContextMenuItems(
         )
       }
       if (isTranscriptFeature(feature, session)) {
-        contextMenuItemsForFeature.push({
-          label: 'Merge transcript',
-          onClick: () => {
-            ;(session as unknown as AbstractSessionModel).queueDialog(
-              (doneCallback) => [
-                MergeTranscripts,
-                {
-                  session,
-                  handleClose: () => {
-                    doneCallback()
+        contextMenuItemsForFeature.push(
+          {
+            label: 'Merge transcript',
+            onClick: () => {
+              ;(session as unknown as AbstractSessionModel).queueDialog(
+                (doneCallback) => [
+                  MergeTranscripts,
+                  {
+                    session,
+                    handleClose: () => {
+                      doneCallback()
+                    },
+                    changeManager,
+                    sourceFeature: feature,
+                    sourceAssemblyId: currentAssemblyId,
+                    selectedFeature,
+                    setSelectedFeature: (feature?: AnnotationFeature) => {
+                      display.setSelectedFeature(feature)
+                    },
                   },
-                  changeManager,
-                  sourceFeature: feature,
-                  sourceAssemblyId: currentAssemblyId,
-                  selectedFeature,
-                  setSelectedFeature: (feature?: AnnotationFeature) => {
-                    display.setSelectedFeature(feature)
+                ],
+              )
+            },
+          },
+          {
+            label: 'Duplicate feature',
+            onClick: () => {
+              ;(session as unknown as AbstractSessionModel).queueDialog(
+                (doneCallback) => [
+                  DuplicateTranscript,
+                  {
+                    session,
+                    handleClose: () => {
+                      doneCallback()
+                    },
+                    changeManager,
+                    sourceFeature: feature,
+                    sourceAssemblyId: currentAssemblyId,
+                    selectedFeature,
+                    setSelectedFeature: (feature?: AnnotationFeature) => {
+                      display.setSelectedFeature(feature)
+                    },
                   },
-                },
-              ],
-            )
+                ],
+              )
+            },
           },
-        })
+        )
         if (isSessionModelWithWidgets(session)) {
           contextMenuItemsForFeature.splice(1, 0, {
             label: 'Open transcript editor',

package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts

@@ -1,5 +1,5 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { MenuItem } from '@jbrowse/core/ui'
 import { alpha } from '@mui/material'
 
 import {
@@ -8,12 +8,12 @@ import {
   isMousePositionWithFeature,
 } from '../../util'
 import { getRelatedFeatures } from '../../util/annotationFeatureUtils'
-import { type LinearApolloDisplay } from '../stateModel'
-import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
-import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
+import type { LinearApolloDisplay } from '../stateModel'
+import type { LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
+import type { LinearApolloDisplayRendering } from '../stateModel/rendering'
 
 import { boxGlyph, drawBox } from './BoxGlyph'
-import { type Glyph } from './Glyph'
+import type { Glyph } from './Glyph'
 
 function featuresForRow(feature: AnnotationFeature): AnnotationFeature[][] {
   const features = [[feature]]

package/src/LinearApolloDisplay/glyphs/Glyph.ts

@@ -1,11 +1,11 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { MenuItem } from '@jbrowse/core/ui'
 
-import { type OntologyRecord } from '../../OntologyManager'
-import { type MousePositionWithFeature } from '../../util'
-import { type LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
-import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
-import { type CanvasMouseEvent } from '../types'
+import type { OntologyRecord } from '../../OntologyManager'
+import type { MousePositionWithFeature } from '../../util'
+import type { LinearApolloDisplayMouseEvents } from '../stateModel/mouseEvents'
+import type { LinearApolloDisplayRendering } from '../stateModel/rendering'
+import type { CanvasMouseEvent } from '../types'
 
 export interface Glyph {
   /** @returns number of layout rows used by this glyph with this feature and zoom level */

package/src/LinearApolloDisplay/glyphs/util.ts

@@ -1,6 +1,6 @@
-import { type ContentBlock } from '@jbrowse/core/util/blockTypes'
+import type { ContentBlock } from '@jbrowse/core/util/blockTypes'
 
-import { type LinearApolloDisplay } from '../stateModel'
+import type { LinearApolloDisplay } from '../stateModel'
 
 export function getLeftPx(
   display: LinearApolloDisplay,

package/src/LinearApolloDisplay/stateModel/base.ts

@@ -3,10 +3,13 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  type AnyConfigurationSchemaType,
+  ConfigurationReference,
+  getConf,
+} from '@jbrowse/core/configuration'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
@@ -16,14 +19,20 @@ import {
 } from '@jbrowse/core/util'
 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 {
+  addDisposer,
+  cast,
+  getRoot,
+  getSnapshot,
+  types,
+} from '@jbrowse/mobx-state-tree'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree'
 
-import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
+import type { ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
 import { FilterFeatures } from '../../components/FilterFeatures'
-import { type ApolloSessionModel, type HoveredFeature } from '../../session'
-import { type ApolloRootModel } from '../../types'
+import type { ApolloSessionModel, HoveredFeature } from '../../session'
+import type { ApolloRootModel } from '../../types'
 import { EditZoomThresholdDialog } from '../../util/displayUtils'
 
 const minDisplayHeight = 20

package/src/LinearApolloDisplay/stateModel/index.ts

@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type Instance, types } from 'mobx-state-tree'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance, types } from '@jbrowse/mobx-state-tree'
 
 import { TabularEditorStateModelType } from '../../TabularEditor'
 

package/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -1,13 +1,13 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
-import { addDisposer, isAlive } from 'mobx-state-tree'
 
-import { type ApolloSessionModel } from '../../session'
+import type { ApolloSessionModel } from '../../session'
 import { boxGlyph, geneGlyph, genericChildGlyph } from '../glyphs'
 
 import { baseModelFactory } from './base'

package/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -1,14 +1,14 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import type { MenuItem } from '@jbrowse/core/ui'
+import { type Instance, addDisposer } from '@jbrowse/mobx-state-tree'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer } from 'mobx-state-tree'
-import { type CSSProperties } from 'react'
+import type { CSSProperties } from 'react'
 
 import {
   type Edge,
@@ -18,7 +18,7 @@ import {
   getPropagatedLocationChanges,
   isMousePositionWithFeature,
 } from '../../util'
-import { type CanvasMouseEvent } from '../types'
+import type { CanvasMouseEvent } from '../types'
 
 import { renderingModelFactory } from './rendering'