@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.6

package/src/FeatureDetailsWidget/DefaultAttributeEditor.tsx

@@ -0,0 +1,104 @@
+import AddBoxIcon from '@mui/icons-material/AddBox'
+import DeleteIcon from '@mui/icons-material/Delete'
+import { Button, DialogActions, IconButton } from '@mui/material'
+import { observer } from 'mobx-react'
+import React, { useState } from 'react'
+
+import { type ApolloSessionModel } from '../session'
+
+import { StringTextField } from './StringTextField'
+
+export interface AttributeEditorProps {
+  session: ApolloSessionModel
+  attributeValues?: string[]
+  setAttribute: (newAttribute?: string[]) => void
+  isNew?: boolean
+}
+
+export const DefaultAttributeEditor = observer(function DefaultAttributeEditor({
+  attributeValues,
+  setAttribute,
+  isNew = false,
+}: AttributeEditorProps) {
+  const [newValues, setNewValues] = useState<string[]>(
+    attributeValues && attributeValues.length > 0 ? attributeValues : [''],
+  )
+
+  function updateValue(idx: number, newValue: string) {
+    setNewValues((oldValues) => {
+      const newValues = [...oldValues]
+      newValues[idx] = newValue
+      return newValues
+    })
+  }
+  function deleteValue(idx: number) {
+    setNewValues((oldValues) => {
+      const newValues = [...oldValues]
+      newValues.splice(idx, 1)
+      return newValues
+    })
+  }
+  function addValue() {
+    setNewValues((oldValues) => {
+      const newValues = [...oldValues]
+      newValues.push('')
+      return newValues
+    })
+  }
+
+  return (
+    <>
+      {newValues.map((value, idx) => (
+        <div key={`${idx}-${value}`} style={{ display: 'flex' }}>
+          <StringTextField
+            value={value}
+            onChangeCommitted={(editedValue) => {
+              updateValue(idx, editedValue)
+            }}
+            variant="outlined"
+            fullWidth
+          />
+          <IconButton
+            aria-label="delete"
+            size="medium"
+            edge="end"
+            onClick={() => {
+              deleteValue(idx)
+            }}
+          >
+            <DeleteIcon fontSize="inherit" />
+          </IconButton>
+        </div>
+      ))}
+      <IconButton
+        aria-label="add"
+        size="medium"
+        color="secondary"
+        edge="start"
+        onClick={addValue}
+      >
+        <AddBoxIcon fontSize="inherit" />
+      </IconButton>
+      <DialogActions>
+        <Button
+          color="primary"
+          variant="contained"
+          onClick={() => {
+            setAttribute(newValues.filter(Boolean))
+          }}
+        >
+          {isNew ? 'Add' : 'Update'}
+        </Button>
+        <Button
+          variant="outlined"
+          type="submit"
+          onClick={() => {
+            setAttribute()
+          }}
+        >
+          Cancel
+        </Button>
+      </DialogActions>
+    </>
+  )
+})

package/src/FeatureDetailsWidget/DefaultAttributeViewer.tsx

@@ -0,0 +1,22 @@
+import { Typography } from '@mui/material'
+import React from 'react'
+
+export interface AttributeViewerProps {
+  values: string[] | undefined
+}
+
+export function DefaultAttributeViewer({ values }: AttributeViewerProps) {
+  return (
+    <>
+      {values?.map((value, idx) => (
+        <Typography
+          key={`${idx}.${value}`}
+          variant="body2"
+          color="textSecondary"
+        >
+          {value}
+        </Typography>
+      ))}
+    </>
+  )
+}

package/src/FeatureDetailsWidget/FeatureDetailsNavigation.tsx

@@ -1,12 +1,12 @@
-import React from 'react'
-
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { Button, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
+import React from 'react'
 
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
 import { getFeatureNameOrId } from '../util'
 
+import { type ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
+
 export const FeatureDetailsNavigation = observer(
   function FeatureDetailsNavigation(props: {
     model: ApolloFeatureDetails

package/src/FeatureDetailsWidget/NumberTextField.tsx

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { TextField, TextFieldProps } from '@mui/material'
+import { TextField, type TextFieldProps } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
 

package/src/FeatureDetailsWidget/Sequence.tsx

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

package/src/FeatureDetailsWidget/StringTextField.tsx

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { TextField, TextFieldProps } from '@mui/material'
+import { TextField, type TextFieldProps } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
 

package/src/FeatureDetailsWidget/TranscriptSequence.tsx

@@ -1,4 +1,4 @@
-import { 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 {
@@ -6,13 +6,13 @@ import {
   MenuItem,
   Paper,
   Select,
-  SelectChangeEvent,
+  type SelectChangeEvent,
   useTheme,
 } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
 
-import { ApolloSessionModel } from '../session'
+import { type ApolloSessionModel } from '../session'
 
 const SEQUENCE_WRAP_LENGTH = 60
 

package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx

@@ -3,11 +3,25 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import React, { useRef } from 'react'
-
-import { observer } from 'mobx-react'
-
+import {
+  type AnnotationFeature,
+  type TranscriptPart,
+} from '@apollo-annotation/mst'
+import {
+  LocationEndChange,
+  LocationStartChange,
+} from '@apollo-annotation/shared'
 import styled from '@emotion/styled'
+import {
+  type AbstractSessionModel,
+  defaultCodonTable,
+  revcom,
+} from '@jbrowse/core/util'
+import AddIcon from '@mui/icons-material/Add'
+import ContentCopyIcon from '@mui/icons-material/ContentCopy'
+import ContentCutIcon from '@mui/icons-material/ContentCut'
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
+import RemoveIcon from '@mui/icons-material/Remove'
 import {
   Accordion,
   AccordionDetails,
@@ -15,27 +29,13 @@ import {
   Tooltip,
   Typography,
 } from '@mui/material'
+import { observer } from 'mobx-react'
+import React, { useRef } from 'react'
 
-import AddIcon from '@mui/icons-material/Add'
-import RemoveIcon from '@mui/icons-material/Remove'
-import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
-import ContentCopyIcon from '@mui/icons-material/ContentCopy'
-import ContentCutIcon from '@mui/icons-material/ContentCut'
-
-import { AnnotationFeature, TranscriptPart } from '@apollo-annotation/mst'
+import { type ApolloSessionModel } from '../session'
 
 import { StyledAccordionSummary } from './ApolloTranscriptDetailsWidget'
 import { NumberTextField } from './NumberTextField'
-import { ApolloSessionModel } from '../session'
-import {
-  AbstractSessionModel,
-  defaultCodonTable,
-  revcom,
-} from '@jbrowse/core/util'
-import {
-  LocationEndChange,
-  LocationStartChange,
-} from '@apollo-annotation/shared'
 
 const StyledTextField = styled(NumberTextField)(() => ({
   '&.MuiFormControl-root': {

package/src/FeatureDetailsWidget/TranscriptWidgetSummary.tsx

@@ -1,10 +1,10 @@
+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'
 import React from 'react'
 
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { observer } from 'mobx-react'
 import { getFeatureId, getFeatureName, getStrand } from '../util'
-import { Table, TableBody, TableCell, TableRow } from '@mui/material'
-import styled from '@emotion/styled'
 
 const HeaderTableCell = styled(TableCell)(() => ({
   fontWeight: 'bold',

package/src/FeatureDetailsWidget/model.ts

@@ -1,15 +1,20 @@
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  AnnotationFeature,
+  type AnnotationFeature,
   AnnotationFeatureModel,
 } from '@apollo-annotation/mst'
 import { getSession } from '@jbrowse/core/util'
 import { ElementId } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
-import { Instance, SnapshotIn, addDisposer, types } from 'mobx-state-tree'
+import {
+  type Instance,
+  type SnapshotIn,
+  addDisposer,
+  types,
+} from 'mobx-state-tree'
 
-import { ApolloSessionModel } from '../session'
+import { type ApolloSessionModel } from '../session'
 
 export const ApolloFeatureDetailsWidgetModel = types
   .model('ApolloFeatureDetailsWidget', {

package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx

@@ -1,13 +1,13 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { Menu, MenuItem } from '@jbrowse/core/ui'
+import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import {
-  AbstractSessionModel,
+  type AbstractSessionModel,
   doesIntersect2,
   getContainingView,
 } from '@jbrowse/core/util'
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import ErrorIcon from '@mui/icons-material/Error'
 import {
   Alert,
@@ -20,7 +20,7 @@ import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
+import { type LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
 
 interface LinearApolloDisplayProps {
   model: LinearApolloDisplayI
@@ -95,7 +95,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
   const { assemblyManager } = session as unknown as AbstractSessionModel
   return (
     <>
-      {lgv.bpPerPx <= 3 ? (
+      {3 / lgv.bpPerPx >= 1 ? (
         <div
           className={classes.canvasContainer}
           style={{
@@ -238,7 +238,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
                           pointerEvents: apolloDragging ? 'none' : 'auto',
                         }}
                       >
-                        <ErrorIcon />
+                        <ErrorIcon data-testid="ErrorIcon" />
                       </Avatar>
                     </Tooltip>
                   )

package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts

@@ -1,25 +1,24 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { Theme, alpha } from '@mui/material'
-import { MenuItem } from '@jbrowse/core/ui'
-
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { type MenuItem } from '@jbrowse/core/ui'
 import {
-  AbstractSessionModel,
+  type AbstractSessionModel,
+  type SessionWithWidgets,
   isSessionModelWithWidgets,
-  SessionWithWidgets,
 } from '@jbrowse/core/util'
+import { type Theme, alpha } from '@mui/material'
 
 import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
-
-import { LinearApolloDisplay } from '../stateModel'
+import { type LinearApolloDisplay } from '../stateModel'
 import {
+  type LinearApolloDisplayMouseEvents,
+  type MousePosition,
+  type MousePositionWithFeatureAndGlyph,
   isMousePositionWithFeatureAndGlyph,
-  LinearApolloDisplayMouseEvents,
-  MousePosition,
-  MousePositionWithFeatureAndGlyph,
 } from '../stateModel/mouseEvents'
-import { CanvasMouseEvent } from '../types'
-import { Glyph } from './Glyph'
-import { LinearApolloDisplayRendering } from '../stateModel/rendering'
+import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
+import { type CanvasMouseEvent } from '../types'
+
+import { type Glyph } from './Glyph'
 
 function drawBoxOutline(
   ctx: CanvasRenderingContext2D,

package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -1,18 +1,19 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { getFrame, intersection2 } from '@jbrowse/core/util'
 import { alpha } from '@mui/material'
 
-import { LinearApolloDisplay } from '../stateModel'
+import { type OntologyRecord } from '../../OntologyManager'
+import { type LinearApolloDisplay } from '../stateModel'
 import {
+  type MousePosition,
+  type MousePositionWithFeatureAndGlyph,
   isMousePositionWithFeatureAndGlyph,
-  MousePosition,
-  MousePositionWithFeatureAndGlyph,
 } from '../stateModel/mouseEvents'
-import { CanvasMouseEvent } from '../types'
-import { Glyph } from './Glyph'
+import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
+import { type CanvasMouseEvent } from '../types'
+
 import { boxGlyph } from './BoxGlyph'
-import { LinearApolloDisplayRendering } from '../stateModel/rendering'
-import { OntologyRecord } from '../../OntologyManager'
+import { type Glyph } from './Glyph'
 
 let forwardFillLight: CanvasPattern | null = null
 let backwardFillLight: CanvasPattern | null = null
@@ -225,7 +226,6 @@ function draw(
               apolloSelectedFeature && _id === apolloSelectedFeature._id
                 ? 'rgb(0,0,0)'
                 : cdsColorCode
-            ctx.fillStyle = cdsColorCode
             ctx.fillRect(
               cdsStartPx + 1,
               cdsTop + 1,

package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts

@@ -1,9 +1,10 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 
-import { LinearApolloDisplay } from '../stateModel'
-import { boxGlyph, isSelectedFeature, drawBox } from './BoxGlyph'
-import { Glyph } from './Glyph'
-import { LinearApolloDisplayRendering } from '../stateModel/rendering'
+import { type LinearApolloDisplay } from '../stateModel'
+import { type LinearApolloDisplayRendering } from '../stateModel/rendering'
+
+import { boxGlyph, drawBox, isSelectedFeature } from './BoxGlyph'
+import { type Glyph } from './Glyph'
 
 function featuresForRow(feature: AnnotationFeature): AnnotationFeature[][] {
   const features = [[feature]]

package/src/LinearApolloDisplay/glyphs/Glyph.ts

@@ -1,13 +1,13 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { 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 {
-  LinearApolloDisplayMouseEvents,
-  MousePositionWithFeatureAndGlyph,
+  type LinearApolloDisplayMouseEvents,
+  type MousePositionWithFeatureAndGlyph,
 } from '../stateModel/mouseEvents'
-import { LinearApolloDisplayRendering } from '../stateModel/rendering'
-import { CanvasMouseEvent } from '../types'
-import { OntologyRecord } from '../../OntologyManager'
+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/stateModel/base.ts

@@ -3,26 +3,26 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { 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 { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
 import {
-  AbstractSessionModel,
+  type AbstractSessionModel,
   getContainingView,
   getSession,
 } 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 { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, cast, getRoot, types, getSnapshot } from 'mobx-state-tree'
+import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree'
 
-import { ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../../session'
-import { ApolloRootModel } from '../../types'
+import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
 import { FilterFeatures } from '../../components/FilterFeatures'
+import { type ApolloSessionModel } from '../../session'
+import { type ApolloRootModel } from '../../types'
 
 const minDisplayHeight = 20
 
@@ -36,6 +36,9 @@ export function baseModelFactory(
       configuration: ConfigurationReference(configSchema),
       graphical: true,
       table: false,
+      showStartCodons: false,
+      showStopCodons: true,
+      highContrast: false,
       heightPreConfig: types.maybe(
         types.refinement(
           'displayHeight',
@@ -168,6 +171,15 @@ export function baseModelFactory(
         self.graphical = true
         self.table = true
       },
+      toggleShowStartCodons() {
+        self.showStartCodons = !self.showStartCodons
+      },
+      toggleShowStopCodons() {
+        self.showStopCodons = !self.showStopCodons
+      },
+      toggleHighContrast() {
+        self.highContrast = !self.highContrast
+      },
       updateFilteredFeatureTypes(types: string[]) {
         self.filteredFeatureTypes = cast(types)
       },
@@ -179,7 +191,13 @@ export function baseModelFactory(
       const { filteredFeatureTypes, trackMenuItems: superTrackMenuItems } = self
       return {
         trackMenuItems() {
-          const { graphical, table } = self
+          const {
+            graphical,
+            table,
+            showStartCodons,
+            showStopCodons,
+            highContrast,
+          } = self
           return [
             ...superTrackMenuItems(),
             {
@@ -210,6 +228,30 @@ export function baseModelFactory(
                     self.showGraphicalAndTable()
                   },
                 },
+                {
+                  label: 'Show start codons',
+                  type: 'checkbox',
+                  checked: showStartCodons,
+                  onClick: () => {
+                    self.toggleShowStartCodons()
+                  },
+                },
+                {
+                  label: 'Show stop codons',
+                  type: 'checkbox',
+                  checked: showStopCodons,
+                  onClick: () => {
+                    self.toggleShowStopCodons()
+                  },
+                },
+                {
+                  label: 'Use high contrast colors',
+                  type: 'checkbox',
+                  checked: highContrast,
+                  onClick: () => {
+                    self.toggleHighContrast()
+                  },
+                },
               ],
             },
             {

package/src/LinearApolloDisplay/stateModel/index.ts

@@ -1,8 +1,9 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { Instance, types } from 'mobx-state-tree'
+import type PluginManager from '@jbrowse/core/PluginManager'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type Instance, types } from 'mobx-state-tree'
 
 import { TabularEditorStateModelType } from '../../TabularEditor'
+
 import { mouseEventsModelFactory } from './mouseEvents'
 
 export function stateModelFactory(

package/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -1,16 +1,17 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type PluginManager from '@jbrowse/core/PluginManager'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import { autorun, observable } from 'mobx'
 import { addDisposer, isAlive } from 'mobx-state-tree'
 
-import { ApolloSessionModel } from '../../session'
-import { baseModelFactory } from './base'
+import { type ApolloSessionModel } from '../../session'
 import { boxGlyph, geneGlyph, genericChildGlyph } from '../glyphs'
 
+import { baseModelFactory } from './base'
+
 function getRowsForFeature(
   startingRow: number,
   rowCount: number,
@@ -62,7 +63,7 @@ export function layoutsModelFactory(
         return self.seenFeatures.get(id)
       },
       getGlyph(feature: AnnotationFeature) {
-        if (this.looksLikeGene(feature)) {
+        if (feature.looksLikeGene) {
           return geneGlyph
         }
         if (feature.children?.size) {
@@ -70,38 +71,6 @@ export function layoutsModelFactory(
         }
         return boxGlyph
       },
-      looksLikeGene(feature: AnnotationFeature): boolean {
-        const { featureTypeOntology } =
-          self.session.apolloDataStore.ontologyManager
-        if (!featureTypeOntology) {
-          return false
-        }
-        const { children } = feature
-        if (!children?.size) {
-          return false
-        }
-        const isGene =
-          featureTypeOntology.isTypeOf(feature.type, 'gene') ||
-          featureTypeOntology.isTypeOf(feature.type, 'pseudogene')
-        if (!isGene) {
-          return false
-        }
-        for (const [, child] of children) {
-          if (
-            featureTypeOntology.isTypeOf(child.type, 'transcript') ||
-            featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
-          ) {
-            const { children: grandChildren } = child
-            if (!grandChildren?.size) {
-              return false
-            }
-            return [...grandChildren.values()].some((grandchild) =>
-              featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
-            )
-          }
-        }
-        return false
-      },
     }))
     .actions((self) => ({
       addSeenFeature(feature: AnnotationFeature) {