Fix gene without subfeatures not being displayed in sequence feature …

…details (#3593)
GMOD · May 18, 2023 · f0d5995 · f0d5995
1 parent dba0801
commit f0d5995
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Showing 6 changed files with 10 additions and 17 deletions.
diff --git a/packages/core/BaseFeatureWidget/SequenceFeatureDetails.tsx b/packages/core/BaseFeatureWidget/SequenceFeatureDetails.tsx
@@ -41,9 +41,7 @@ const useStyles = makeStyles()(theme => ({
   formControl: {
     margin: 0,
   },
-  container: {
-    margin: theme.spacing(1),
-  },
+
   container2: {
     marginTop: theme.spacing(1),
   },
@@ -56,13 +54,10 @@ const BPLIMIT = 500_000
 // to not be 100% accurate
 export default function SequenceFeatureDetails({ model, feature }: BaseProps) {
   const { classes } = useStyles()
-  const parentFeature = feature as unknown as ParentFeat
-  const hasCDS = !!parentFeature.subfeatures?.find(sub => sub.type === 'CDS')
-  const isGene = feature.type === 'gene'
   const [shown, setShown] = useState(false)
   const [helpShown, setHelpShown] = useState(false)
 
-  return (isGene && !hasCDS) || !model ? null : (
+  return !model ? null : (
     <div className={classes.container2}>
       <Button variant="contained" onClick={() => setShown(!shown)}>
         {shown ? 'Hide feature sequence' : 'Show feature sequence'}
@@ -181,7 +176,7 @@ function FeatureSequence({ model, feature }: BaseProps) {
   const attemptGeneType =
     feature.type === 'CDS'
       ? sequenceTypes.includes('CDS') && !feature.parentId
-      : sequenceTypes.includes(feature.type)
+      : sequenceTypes.includes(feature.type) && feature.subfeatures?.length
   const val = attemptGeneType ? (hasCDS ? 'cds' : 'cdna') : 'genomic'
 
   // this useEffect is needed to reset the mode/setMode useState because the

diff --git a/plugins/arc/src/LinearArcDisplay/index.ts b/plugins/arc/src/LinearArcDisplay/index.ts
@@ -10,6 +10,7 @@ export default (pluginManager: PluginManager) => {
     const configSchema = configSchemaFactory(pluginManager)
     return new DisplayType({
       name: 'LinearArcDisplay',
+      displayName: 'Arc display',
       configSchema,
       stateModel: stateModelFactory(configSchema),
       trackType: 'FeatureTrack',

diff --git a/plugins/linear-genome-view/src/LinearBareDisplay/index.ts b/plugins/linear-genome-view/src/LinearBareDisplay/index.ts
@@ -12,6 +12,7 @@ export default (pluginManager: PluginManager) => {
     return new DisplayType({
       name: 'LinearBareDisplay',
       configSchema,
+      displayName: 'Bare feature display',
       stateModel: stateModelFactory(configSchema),
       trackType: 'BasicTrack',
       viewType: 'LinearGenomeView',

diff --git a/plugins/linear-genome-view/src/LinearBasicDisplay/components/SetMaxHeight.tsx b/plugins/linear-genome-view/src/LinearBasicDisplay/components/SetMaxHeight.tsx
@@ -10,23 +10,19 @@ import {
 } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 
-const useStyles = makeStyles()(theme => ({
+const useStyles = makeStyles()({
   root: {
     width: 500,
   },
-
-  field: {
-    margin: theme.spacing(2),
-  },
-}))
+})
 
 function SetMaxHeightDlg({
   model,
   handleClose,
 }: {
   model: {
     maxHeight?: number
-    setMaxHeight: Function
+    setMaxHeight: (arg?: number) => void
   }
   handleClose: () => void
 }) {

diff --git a/plugins/linear-genome-view/src/LinearBasicDisplay/index.ts b/plugins/linear-genome-view/src/LinearBasicDisplay/index.ts
@@ -11,7 +11,7 @@ export default (pluginManager: PluginManager) => {
     const config = configSchema(pluginManager)
     return new DisplayType({
       name: 'LinearBasicDisplay',
-      displayName: 'Basic deature display',
+      displayName: 'Basic feature display',
       configSchema: config,
       stateModel: modelFactory(config),
       trackType: 'FeatureTrack',

diff --git a/plugins/linear-genome-view/src/LinearBasicDisplay/model.ts b/plugins/linear-genome-view/src/LinearBasicDisplay/model.ts
@@ -137,7 +137,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
       /**
        * #action
        */
-      setMaxHeight(val: number) {
+      setMaxHeight(val?: number) {
         self.trackMaxHeight = val
       },
     }))