@apollo-annotation/jbrowse-plugin-apollo 0.3.6 → 0.3.7

package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts

@@ -82,6 +82,9 @@ export function layoutsModelFactory(
       getGlyph(_feature: AnnotationFeature) {
         return geneGlyph
       },
+      featureLabelSpacer(elem: number): number {
+        return self.showFeatureLabels ? elem * 2 - 1 : elem
+      },
     }))
     .actions((self) => ({
       addSeenFeature(feature: AnnotationFeature) {
@@ -91,6 +94,11 @@ export function layoutsModelFactory(
         self.seenFeatures.delete(featureId)
       },
     }))
+    .views((self) => ({
+      get geneTrackRowNums() {
+        return [4, 5].map((elem) => self.featureLabelSpacer(elem))
+      },
+    }))
     .views((self) => ({
       get featureLayouts() {
         const { assemblyManager } =
@@ -120,7 +128,10 @@ export function layoutsModelFactory(
               throw new Error('featureTypeOntology is undefined')
             }
             if (feature.looksLikeGene) {
-              const rowNum = feature.strand == 1 ? 4 : 5
+              const rowNum =
+                feature.strand == 1
+                  ? self.geneTrackRowNums[0]
+                  : self.geneTrackRowNums[1]
               if (!featureLayout.get(rowNum)) {
                 featureLayout.set(rowNum, [])
               }
@@ -142,7 +153,10 @@ export function layoutsModelFactory(
                       if (!featureTypeOntology.isTypeOf(exon.type, 'exon')) {
                         continue
                       }
-                      const rowNum = exon.strand == 1 ? 4 : 5
+                      const rowNum =
+                        exon.strand == 1
+                          ? self.geneTrackRowNums[0]
+                          : self.geneTrackRowNums[1]
                       const layoutRow = featureLayout.get(rowNum)
                       layoutRow?.push({ rowNum, feature: exon, cds: null })
                     }
@@ -155,7 +169,9 @@ export function layoutsModelFactory(
                         strand ?? 1,
                         cds.phase,
                       )
-                      rowNum = rowNum < 0 ? -1 * rowNum + 5 : rowNum
+                      rowNum = self.featureLabelSpacer(
+                        rowNum < 0 ? -1 * rowNum + 5 : rowNum,
+                      )
                       if (!featureLayout.get(rowNum)) {
                         featureLayout.set(rowNum, [])
                       }

package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts

@@ -11,9 +11,10 @@ import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/con
 import { type MenuItem } from '@jbrowse/core/ui'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer } from 'mobx-state-tree'
+import { type Instance, addDisposer, cast } from 'mobx-state-tree'
 import { type CSSProperties } from 'react'
 
+import { type Edge, getPropagatedLocationChanges } from '../../util'
 import { type Coord } from '../components'
 import { type Glyph } from '../glyphs/Glyph'
 import { type CanvasMouseEvent } from '../types'
@@ -75,7 +76,8 @@ export function mouseEventsModelIntermediateFactory(
         start: MousePosition
         current: MousePosition
         feature: AnnotationFeature
-        edge: 'min' | 'max'
+        edge: Edge
+        shrinkParent: boolean
       } | null,
       cursor: undefined as CSSProperties['cursor'] | undefined,
       apolloHover: undefined as FeatureAndGlyphUnderMouse | undefined,
@@ -91,7 +93,7 @@ export function mouseEventsModelIntermediateFactory(
           return mousePosition
         }
         let foundFeature
-        if ([4, 5].includes(row)) {
+        if (self.geneTrackRowNums.includes(row)) {
           foundFeature = layoutRow.find(
             (f) =>
               f.feature.type == 'exon' &&
@@ -104,9 +106,16 @@ export function mouseEventsModelIntermediateFactory(
             )
           }
         } else {
-          foundFeature = layoutRow.find(
-            (f) => f.cds != null && bp >= f.cds.min && bp <= f.cds.max,
-          )
+          foundFeature = layoutRow.find((f) => {
+            const featureID = f.feature.attributes.get('gff_id')?.toString()
+            return (
+              f.cds != null &&
+              bp >= f.cds.min &&
+              bp <= f.cds.max &&
+              (featureID === undefined ||
+                !self.filteredTranscripts.includes(featureID))
+            )
+          })
         }
         if (!foundFeature) {
           return mousePosition
@@ -143,6 +152,9 @@ export function mouseEventsModelIntermediateFactory(
           self.cursor = cursor
         }
       },
+      updateFilteredTranscripts(forms: string[]): void {
+        self.filteredTranscripts = cast(forms)
+      },
     }))
     .actions(() => ({
       // onClick(event: CanvasMouseEvent) {
@@ -176,20 +188,23 @@ export function mouseEventsModelFactory(
       startDrag(
         mousePosition: MousePositionWithFeatureAndGlyph,
         feature: AnnotationFeature,
-        edge: 'min' | 'max',
+        edge: Edge,
+        shrinkParent = false,
       ) {
         self.apolloDragging = {
           start: mousePosition,
           current: mousePosition,
           feature,
           edge,
+          shrinkParent,
         }
       },
       endDrag() {
         if (!self.apolloDragging) {
           throw new Error('endDrag() called with no current drag in progress')
         }
-        const { current, edge, feature, start } = self.apolloDragging
+        const { current, edge, feature, start, shrinkParent } =
+          self.apolloDragging
         // don't do anything if it was only dragged a tiny bit
         if (Math.abs(current.x - start.x) <= 4) {
           self.setDragging()
@@ -199,33 +214,35 @@ export function mouseEventsModelFactory(
         const { displayedRegions } = self.lgv
         const region = displayedRegions[start.regionNumber]
         const assembly = self.getAssemblyId(region.assemblyName)
+        const changes = getPropagatedLocationChanges(
+          feature,
+          current.bp,
+          edge,
+          shrinkParent,
+        )
 
-        let change: LocationEndChange | LocationStartChange
-        if (edge === 'max') {
-          const featureId = feature._id
-          const oldEnd = feature.max
-          const newEnd = current.bp
-          change = new LocationEndChange({
-            typeName: 'LocationEndChange',
-            changedIds: [featureId],
-            featureId,
-            oldEnd,
-            newEnd,
-            assembly,
-          })
-        } else {
-          const featureId = feature._id
-          const oldStart = feature.min
-          const newStart = current.bp
-          change = new LocationStartChange({
-            typeName: 'LocationStartChange',
-            changedIds: [featureId],
-            featureId,
-            oldStart,
-            newStart,
-            assembly,
-          })
-        }
+        const change: LocationEndChange | LocationStartChange =
+          edge === 'max'
+            ? new LocationEndChange({
+                typeName: 'LocationEndChange',
+                changedIds: changes.map((c) => c.featureId),
+                changes: changes.map((c) => ({
+                  featureId: c.featureId,
+                  oldEnd: c.oldLocation,
+                  newEnd: c.newLocation,
+                })),
+                assembly,
+              })
+            : new LocationStartChange({
+                typeName: 'LocationStartChange',
+                changedIds: changes.map((c) => c.featureId),
+                changes: changes.map((c) => ({
+                  featureId: c.featureId,
+                  oldStart: c.oldLocation,
+                  newStart: c.newLocation,
+                })),
+                assembly,
+              })
         void self.changeManager.submit(change)
         self.setDragging()
         self.setCursor()
@@ -281,6 +298,8 @@ export function mouseEventsModelFactory(
             mousePosition,
             event,
           )
+        } else {
+          self.setSelectedFeature()
         }
 
         if (self.apolloDragging) {

package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts

@@ -4,7 +4,7 @@ import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/con
 import { doesIntersect2 } from '@jbrowse/core/util'
 import { type Theme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer } from 'mobx-state-tree'
+import { type Instance, addDisposer, types } from 'mobx-state-tree'
 
 import { type ApolloSessionModel } from '../../session'
 
@@ -29,6 +29,7 @@ export function renderingModelIntermediateFactory(
       detailsHeight: 200,
       lastRowTooltipBufferHeight: 80,
       isShown: true,
+      filteredTranscripts: types.array(types.string),
     })
     .volatile(() => ({
       canvas: null as HTMLCanvasElement | null,
@@ -38,8 +39,9 @@ export function renderingModelIntermediateFactory(
     }))
     .views((self) => ({
       get featuresHeight() {
+        const featureLabelSpacer = self.showFeatureLabels ? 2 : 1
         return (
-          (self.highestRow + 1) * self.apolloRowHeight +
+          featureLabelSpacer * ((self.highestRow + 1) * self.apolloRowHeight) +
           self.lastRowTooltipBufferHeight
         )
       },

package/src/OntologyManager/index.ts

@@ -15,6 +15,7 @@ import {
   flow,
   getRoot,
   getSnapshot,
+  isAlive,
   types,
 } from 'mobx-state-tree'
 
@@ -79,7 +80,9 @@ export const OntologyRecordType = types
       const equivalents: string[] = terms
         .map((term) => term.lbl)
         .filter((term) => term != undefined)
-      self.setEquivalentTypes(type, equivalents)
+      if (isAlive(self)) {
+        self.setEquivalentTypes(type, equivalents)
+      }
     }),
   }))
   .actions((self) => ({

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -68,6 +68,8 @@ function makeContextMenuItems(
     selectedFeature,
     session,
     setSelectedFeature,
+    filteredTranscripts,
+    updateFilteredTranscripts,
   } = display
   return featureContextMenuItems(
     feature,
@@ -77,6 +79,8 @@ function makeContextMenuItems(
     setSelectedFeature,
     session,
     changeManager,
+    filteredTranscripts,
+    updateFilteredTranscripts,
   )
 }
 

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -7,7 +7,14 @@ import {
 } from '@jbrowse/core/util'
 
 import { type ChangeManager } from '../../ChangeManager'
-import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
+import {
+  AddChildFeature,
+  CopyFeature,
+  DeleteFeature,
+  MergeExons,
+  MergeTranscripts,
+  SplitExon,
+} from '../../components'
 import { type ApolloSessionModel } from '../../session'
 import { getApolloInternetAccount } from '../../util'
 
@@ -19,6 +26,8 @@ export function featureContextMenuItems(
   setSelectedFeature: (f: AnnotationFeature | undefined) => void,
   session: ApolloSessionModel,
   changeManager: ChangeManager,
+  filteredTranscripts: string[],
+  updateFilteredTranscripts: (forms: string[]) => void,
 ) {
   const internetAccount = getApolloInternetAccount(session)
   const role = internetAccount ? internetAccount.role : 'admin'
@@ -26,6 +35,7 @@ export function featureContextMenuItems(
   const readOnly = !(role && ['admin', 'user'].includes(role))
   const menuItems: MenuItem[] = []
   if (feature) {
+    const featureID = feature.attributes.get('gff_id')?.toString()
     const sourceAssemblyId = getAssemblyId(region.assemblyName)
     const currentAssemblyId = getAssemblyId(region.assemblyName)
     menuItems.push(
@@ -111,6 +121,72 @@ export function featureContextMenuItems(
           )
         },
       },
+      {
+        label: 'Merge transcripts',
+        disabled: !admin,
+        onClick: () => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              MergeTranscripts,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager,
+                sourceFeature: feature,
+                sourceAssemblyId: currentAssemblyId,
+                selectedFeature,
+                setSelectedFeature,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Merge exons',
+        disabled: !admin,
+        onClick: () => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              MergeExons,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager,
+                sourceFeature: feature,
+                sourceAssemblyId: currentAssemblyId,
+                selectedFeature,
+                setSelectedFeature,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Split exon',
+        disabled: !admin,
+        onClick: () => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              SplitExon,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager,
+                sourceFeature: feature,
+                sourceAssemblyId: currentAssemblyId,
+                selectedFeature,
+                setSelectedFeature,
+              },
+            ],
+          )
+        },
+      },
     )
     const { featureTypeOntology } = session.apolloDataStore.ontologyManager
     if (!featureTypeOntology) {
@@ -121,22 +197,38 @@ export function featureContextMenuItems(
         featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')) &&
       isSessionModelWithWidgets(session)
     ) {
-      menuItems.push({
-        label: 'Edit transcript details',
-        onClick: () => {
-          const apolloTranscriptWidget = session.addWidget(
-            'ApolloTranscriptDetails',
-            'apolloTranscriptDetails',
-            {
-              feature,
-              assembly: currentAssemblyId,
-              changeManager,
-              refName: region.refName,
-            },
-          )
-          session.showWidget(apolloTranscriptWidget)
+      menuItems.push(
+        {
+          label: 'Edit transcript details',
+          onClick: () => {
+            const apolloTranscriptWidget = session.addWidget(
+              'ApolloTranscriptDetails',
+              'apolloTranscriptDetails',
+              {
+                feature,
+                assembly: currentAssemblyId,
+                changeManager,
+                refName: region.refName,
+              },
+            )
+            session.showWidget(apolloTranscriptWidget)
+          },
+        },
+        {
+          label: 'Visible',
+          type: 'checkbox',
+          checked:
+            featureID && filteredTranscripts.includes(featureID) ? false : true,
+          onClick: () => {
+            if (featureID) {
+              const newForms = filteredTranscripts.includes(featureID)
+                ? filteredTranscripts.filter((form) => form !== featureID)
+                : [...filteredTranscripts, featureID]
+              updateFilteredTranscripts(newForms)
+            }
+          },
         },
-      })
+      )
     }
   }
   return menuItems

package/src/components/AddAssemblyAliases.tsx

@@ -0,0 +1,114 @@
+import { AddAssemblyAliasesChange } from '@apollo-annotation/shared'
+import { Box, DialogContent, DialogContentText } from '@mui/material'
+import { DataGrid, type GridColDef, type GridRowModel } from '@mui/x-data-grid'
+import React from 'react'
+
+import {
+  type ApolloInternetAccount,
+  type CollaborationServerDriver,
+} from '../BackendDrivers'
+import { type ChangeManager } from '../ChangeManager'
+import { type ApolloSessionModel } from '../session'
+
+import { Dialog } from './Dialog'
+
+interface AddAssemblyAliasProps {
+  session: ApolloSessionModel
+  handleClose: () => void
+  changeManager: ChangeManager
+}
+
+const columns: GridColDef[] = [
+  {
+    field: 'name',
+    headerName: 'Assembly Name',
+    width: 150,
+    editable: false,
+  },
+  {
+    field: 'aliases',
+    headerName: 'Aliases',
+    width: 300,
+    editable: true,
+  },
+]
+
+interface AssemblyAlias {
+  id: string
+  name: string
+  aliases: string
+}
+
+export function AddAssemblyAliases({
+  changeManager,
+  handleClose,
+  session,
+}: AddAssemblyAliasProps) {
+  const { apolloDataStore } = session
+  const { collaborationServerDriver } = apolloDataStore as {
+    collaborationServerDriver: CollaborationServerDriver
+    getInternetAccount(
+      assemblyName?: string,
+      internetAccountId?: string,
+    ): ApolloInternetAccount
+  }
+  const assemblies = collaborationServerDriver.getAssemblies()
+
+  const rows: AssemblyAlias[] = assemblies.map((assembly) => {
+    return {
+      id: assembly.name,
+      name: assembly.displayName ?? assembly.name,
+      aliases: assembly.aliases.join(', '),
+    } as AssemblyAlias
+  })
+
+  const [errorMessage, setErrorMessage] = React.useState('')
+
+  const processRowUpdate = (newRow: GridRowModel, _oldRow: GridRowModel) => {
+    const change = new AddAssemblyAliasesChange({
+      typeName: 'AddAssemblyAliasesChange',
+      assembly: newRow.id as string,
+      aliases: (newRow.aliases as string).split(','),
+    })
+    void changeManager.submit(change).catch(() => {
+      setErrorMessage('Error submitting change')
+    })
+    handleClose()
+    return newRow
+  }
+
+  return (
+    <Dialog
+      open
+      title="Add assembly aliases"
+      handleClose={handleClose}
+      maxWidth={'sm'}
+      data-testid="add-assembly-alias"
+      fullWidth
+    >
+      <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
+        <Box sx={{ height: 400, width: '100%' }}>
+          <DataGrid
+            rows={rows}
+            columns={columns}
+            initialState={{
+              pagination: {
+                paginationModel: {
+                  pageSize: 5,
+                },
+              },
+            }}
+            pageSizeOptions={[5]}
+            processRowUpdate={processRowUpdate}
+            disableRowSelectionOnClick
+          />
+        </Box>
+      </DialogContent>
+      {errorMessage ? (
+        <DialogContent>
+          <DialogContentText color="error">{errorMessage}</DialogContentText>
+        </DialogContent>
+      ) : null}
+    </Dialog>
+  )
+}

package/src/components/AddChildFeature.tsx

@@ -1,8 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-/* eslint-disable @typescript-eslint/no-misused-promises */
+
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
-import { type AbstractSessionModel } from '@jbrowse/core/util'
 import {
   Button,
   DialogActions,
@@ -37,7 +36,6 @@ export function AddChildFeature({
   sourceAssemblyId,
   sourceFeature,
 }: AddChildFeatureProps) {
-  const { notify } = session as unknown as AbstractSessionModel
   const [end, setEnd] = useState(String(sourceFeature.max))
   const [start, setStart] = useState(String(sourceFeature.min + 1))
   const [type, setType] = useState('')
@@ -63,7 +61,7 @@ export function AddChildFeature({
     return terms
   }
 
-  async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
+  function onSubmit(event: React.FormEvent<HTMLFormElement>) {
     event.preventDefault()
     setErrorMessage('')
     const change = new AddFeatureChange({
@@ -79,8 +77,7 @@ export function AddChildFeature({
       },
       parentFeatureId: sourceFeature._id,
     })
-    await changeManager.submit(change)
-    notify('Feature added successfully', 'success')
+    void changeManager.submit(change)
     handleClose()
     event.preventDefault()
   }

package/src/components/AddFeature.tsx

@@ -1,12 +1,9 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/no-misused-promises */
+
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
-import {
-  type AbstractSessionModel,
-  type Region,
-} from '@jbrowse/core/util/types'
+import { type Region } from '@jbrowse/core/util/types'
 import InfoIcon from '@mui/icons-material/Info'
 import {
   Box,
@@ -96,7 +93,6 @@ export function AddFeature({
   region,
   session,
 }: AddFeatureProps) {
-  const { notify } = session as unknown as AbstractSessionModel
   const [end, setEnd] = useState(String(region.end))
   const [start, setStart] = useState(String(region.start + 1))
   const [type, setType] = useState<NewFeature>(NewFeature.GENE_AND_SUBFEATURES)
@@ -104,7 +100,7 @@ export function AddFeature({
   const [strand, setStrand] = useState<1 | -1 | undefined>()
   const [errorMessage, setErrorMessage] = useState('')
 
-  async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
+  function onSubmit(event: React.FormEvent<HTMLFormElement>) {
     event.preventDefault()
     setErrorMessage('')
 
@@ -120,7 +116,9 @@ export function AddFeature({
     }
 
     if (!refSeqId) {
-      setErrorMessage('Invalid refseq id')
+      setErrorMessage(
+        'Invalid refseq id. Make sure you have the Apollo annotation track open',
+      )
       return
     }
 
@@ -149,8 +147,7 @@ export function AddFeature({
           children,
         },
       })
-      await changeManager.submit(change)
-      notify('Feature added successfully', 'success')
+      void changeManager.submit(change)
       handleClose()
       return
     }
@@ -167,8 +164,7 @@ export function AddFeature({
         assembly: region.assemblyName,
         addedFeature: mRNA,
       })
-      await changeManager.submit(change)
-      notify('Feature added successfully', 'success')
+      void changeManager.submit(change)
       handleClose()
       return
     }
@@ -191,8 +187,7 @@ export function AddFeature({
         strand,
       },
     })
-    await changeManager.submit(change)
-    notify('Feature added successfully', 'success')
+    void changeManager.submit(change)
     handleClose()
     return
   }
@@ -231,7 +226,11 @@ export function AddFeature({
   }
 
   let submitDisabled: boolean = Boolean(error) || !(start && end && type)
-  if (type === NewFeature.CUSTOM && !customType) {
+  if (
+    (type === NewFeature.CUSTOM && !customType) ||
+    (!strand && type === NewFeature.GENE_AND_SUBFEATURES) ||
+    (!strand && type === NewFeature.TRANSCRIPT_AND_SUBFEATURES)
+  ) {
     submitDisabled = true
   }