Collapse introns

plugins/linear-genome-view/src/BaseLinearDisplay/components/LinearBlocks.tsx

@@ -87,8 +87,6 @@ const RenderedBlocks = observer(function ({
  )
 })
 
-export { RenderedBlocks }
-
 const LinearBlocks = observer(function ({
  model,
 }: {

plugins/linear-genome-view/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx

@@ -10,13 +10,20 @@ import {
  isSelectionContainer,
  isSessionModelWithWidgets,
  isFeature,
+ mergeIntervals,
  Feature,
 } from '@jbrowse/core/util'
 import { BaseBlock } from '@jbrowse/core/util/blockTypes'
 import CompositeMap from '@jbrowse/core/util/compositeMap'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
-import { autorun } from 'mobx'
-import { addDisposer, isAlive, types, Instance } from 'mobx-state-tree'
+import { autorun, when } from 'mobx'
+import {
+ addDisposer,
+ isAlive,
+ getSnapshot,
+ types,
+ Instance,
+} from 'mobx-state-tree'
 
 // icons
 import MenuOpenIcon from '@mui/icons-material/MenuOpen'
@@ -103,8 +110,8 @@ function stateModelFactory() {
  .views(self => ({
  /**
  * #getter
- * how many milliseconds to wait for the display to
- * "settle" before re-rendering a block
+ * how many milliseconds to wait for the display to "settle" before
+ * re-rendering a block
  */
  get renderDelay() {
  return 50
@@ -119,8 +126,8 @@ function stateModelFactory() {
 
  /**
  * #getter
- * returns a string feature ID if the globally-selected object
- * is probably a feature
+ * returns a string feature ID if the globally-selected object is
+ * probably a feature
  */
  get selectedFeatureId() {
  if (isAlive(self)) {
@@ -144,8 +151,8 @@ function stateModelFactory() {
  .views(self => ({
  /**
  * #getter
- * a CompositeMap of `featureId -> feature obj` that
- * just looks in all the block data for that feature
+ * a CompositeMap of `featureId -> feature obj` that just looks in all
+ * the block data for that feature
  */
  get features() {
  const featureMaps = []
@@ -303,6 +310,23 @@ function stateModelFactory() {
  * #method
  */
  contextMenuItems(): MenuItem[] {
+ const { contextMenuFeature } = self
+ const singleTranscript = contextMenuFeature?.get('subfeatures')?.[0]
+ const exons =
+ singleTranscript
+ ?.get('subfeatures')
+ ?.filter(
+ f => f.get('type') === 'exon' || f.get('type') === 'CDS',
+ ) || []
+ const cds =
+ singleTranscript
+ ?.get('subfeatures')
+ ?.filter(
+ f => f.get('type') === 'exon' || f.get('type') === 'CDS',
+ ) || []
+
+ // some GFF3 features have CDS and no exon subfeatures
+ const subs = exons.length ? exons : cds.length ? cds : []
  return [
  ...(self.contextMenuFeature
  ? [
@@ -324,6 +348,44 @@ function stateModelFactory() {
  }
  },
  },
+ ...(exons.length > 0 && contextMenuFeature
+ ? [
+ {
+ label: 'Collapse introns',
+ onClick: async () => {
+ const refName = contextMenuFeature.get('refName')
+ const view = getContainingView(self) as LGV
+ const w = 100
+ const res = mergeIntervals(
+ subs.map(f => ({
+ refName,
+ start: f.get('start') - w,
+ end: f.get('end') + w,
+ assemblyName: view.assemblyNames[0],
+ })),
+ w,
+ )
+
+ // need to strip ID before copying view snap
+ const { id, ...rest } = getSnapshot(view)
+ const newView = getSession(self).addView(
+ 'LinearGenomeView',
+ {
+ ...rest,
+ tracks: rest.tracks.map(track => {
+ const { id, ...rest } = track
+ return { ...rest }
+ }),
+ displayedRegions: res,
+ },
+ ) as LGV
+ await when(() => newView.initialized)
+
+ newView.showAllRegions()
+ },
+ },
+ ]
+ : []),
  ]
  : []),
  ]

plugins/svg/src/SvgFeatureRenderer/components/FeatureLabel.tsx

@@ -61,10 +61,10 @@ const FeatureLabel = observer(function ({
  const [labelVisible, setLabelVisible] = useState(exportSVG)
  const theme = useTheme()
 
- // we use an effect to set the label visible because there can be a
- // mismatch between the server and the client after hydration due to the
- // floating labels. if we are exporting an SVG we allow it as is though and
- // do not use the effect
+ // we use an effect to set the label visible because there can be a mismatch
+ // between the server and the client after hydration due to the floating
+ // labels. if we are exporting an SVG we allow it as is though and do not use
+ // the effect
  useEffect(() => {
  setLabelVisible(true)
  }, [])