Bump deps

Author: cmdcolin

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

@@ -11,16 +11,20 @@ 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, 
-
+import { autorun, when } from 'mobx'
+import {
+  addDisposer,
+  isAlive,
   getSnapshot,
-Instance } from 'mobx-state-tree'
+  types,
+  Instance,
+} from 'mobx-state-tree'
 
 // icons
 import MenuOpenIcon from '@mui/icons-material/MenuOpen'
@@ -33,7 +37,6 @@ import BlockState from './serverSideRenderedBlock'
 import configSchema from './configSchema'
 import TrackHeightMixin from './TrackHeightMixin'
 import FeatureDensityMixin from './FeatureDensityMixin'
-import { nanoid } from '@jbrowse/core/util/nanoid'
 
 type LGV = LinearGenomeViewModel
 
@@ -306,6 +309,23 @@ 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
             ? [
@@ -327,47 +347,44 @@ function stateModelFactory() {
                     }
                   },
                 },
-                {
-                  label: 'Collapse introns',
-                  onClick: async () => {
-                    const { contextMenuFeature } = self
-                    if (contextMenuFeature) {
-                      const refName = contextMenuFeature.get('refName')
-                      const view = getContainingView(self) as LGV
-                      const singleTranscript =
-                        contextMenuFeature.get('subfeatures')?.[0]
-                      const res =
-                        singleTranscript
-                          ?.get('subfeatures')
-                          ?.filter(f => f.get('type') === 'exon')
-                          .map(f => ({
-                            refName,
-                            start: f.get('start') - 100,
-                            end: f.get('end') + 100,
-                            assemblyName: view.assemblyNames[0],
-                          })) || []
-                      res.sort((a, b) => a.start - b.start)
+                ...(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,
-                          id: nanoid(),
-                          tracks: rest.tracks.map(track => {
-                            const { id, ...rest } = track
-                            return { ...rest, id: nanoid() }
-                          }),
-                          displayedRegions: res,
-                        },
-                      ) as LGV
-                      await when(() => newView.initialized)
+                          // 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()
-                    }
-                  },
-                },
+                          newView.showAllRegions()
+                        },
+                      },
+                    ]
+                  : []),
               ]
             : []),
         ]

plugins/linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts

@@ -242,12 +242,6 @@ export function renderBlockData(
     const layoutId = getContainingView(display).id
     const cannotBeRenderedReason = display.regionCannotBeRendered(self.region)
 
-    const asm = assemblyManager.get(regionAsm)!
-    const regions = [getSnapshot(self.region)]
-    const parentRegions = regions.map(region => {
-      const r = asm?.getCanonicalRefName(region.refName)
-      return asm.regions?.find(b => b.refName === r)
-    })
     return {
       rendererType,
       rpcManager,
@@ -261,8 +255,7 @@ export function renderBlockData(
           }
         },
         assemblyName: self.region.assemblyName,
-        regions,
-        parentRegions,
+        regions: [getSnapshot(self.region)],
         adapterConfig,
         rendererType: rendererType.name,
         sessionId,

plugins/linear-genome-view/src/LinearGenomeView/components/Header.tsx

@@ -112,11 +112,14 @@ const Controls = ({ model }: { model: LGV }) => {
 }
 
 const LinearGenomeViewHeader = observer(({ model }: { model: LGV }) => {
-  const Wrapper = model.hideHeaderOverview ? React.Fragment : OverviewScalebar
   return !model.hideHeader ? (
-    <Wrapper model={model}>
+    model.hideHeaderOverview ? (
       <Controls model={model} />
-    </Wrapper>
+    ) : (
+      <OverviewScalebar model={model}>
+        <Controls model={model} />
+      </OverviewScalebar>
+    )
   ) : null
 })
 

plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx

@@ -7,7 +7,6 @@ import DivRenderingConfigSchema from '../configSchema'
 test('renders with one, zoomed way out', () => {
   const { container } = render(
     <DivSequenceRendering
-      rowHeight={13}
       regions={[
         { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
       ]}
@@ -39,7 +38,6 @@ test('renders with one, zoomed way out', () => {
 test('renders with one feature with no seq, zoomed in, should throw', () => {
   const { container } = render(
     <DivSequenceRendering
-      rowHeight={13}
       regions={[
         { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
       ]}
@@ -70,7 +68,6 @@ test('renders with one feature with no seq, zoomed in, should throw', () => {
 test('renders with one feature with an incorrect seq, zoomed in, should throw', () => {
   const { container } = render(
     <DivSequenceRendering
-      rowHeight={13}
       regions={[
         { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
       ]}
@@ -102,7 +99,6 @@ test('renders with one feature with an incorrect seq, zoomed in, should throw',
 test('renders with one feature with a correct seq, zoomed in, should render nicely', () => {
   const { container } = render(
     <DivSequenceRendering
-      rowHeight={13}
       regions={[
         { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
       ]}
@@ -134,7 +130,6 @@ test('renders with one feature with a correct seq, zoomed in, should render nice
 test('renders with one feature reversed with a correct seq, zoomed in, should render nicely', () => {
   const { container } = render(
     <DivSequenceRendering
-      rowHeight={13}
       regions={[
         {
           assemblyName: 'volvox',

plugins/sequence/src/LinearReferenceSequenceDisplay/components/SetHeightDialog.tsx

@@ -20,7 +20,6 @@ export interface Glyph
     selected?: boolean
     config: AnyConfigurationModel
     region: Region
-    parentRegion: Region
     bpPerPx: number
     topLevel?: boolean
     [key: string]: unknown