@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.7

package/src/components/ViewChangeLog.tsx

@@ -13,22 +13,23 @@ import {
   DialogContentText,
   MenuItem,
   Select,
-  SelectChangeEvent,
+  type SelectChangeEvent,
 } from '@mui/material'
 import {
   DataGrid,
-  GridColDef,
-  GridRowsProp,
+  type GridColDef,
+  type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { Dialog } from './Dialog'
 
 interface ViewChangeLogProps {

package/src/components/ViewCheckResults.tsx

@@ -4,7 +4,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   Button,
   DialogActions,
@@ -12,21 +12,22 @@ import {
   DialogContentText,
   MenuItem,
   Select,
-  SelectChangeEvent,
+  type SelectChangeEvent,
 } from '@mui/material'
 import {
   DataGrid,
-  GridColDef,
-  GridRowsProp,
+  type GridColDef,
+  type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { Dialog } from './Dialog'
 
 interface ViewCheckResultsProps {

package/src/components/index.ts

@@ -9,7 +9,10 @@ export * from './ImportFeatures'
 export * from './LogOut'
 export * from './ManageChecks'
 export * from './ManageUsers'
+export * from './MergeExons'
+export * from './MergeTranscripts'
 export * from './OpenLocalFile'
 export * from './ViewChangeLog'
 export * from './AddRefSeqAliases'
 export * from './ViewCheckResults'
+export * from './SplitExon'

package/src/config.ts

@@ -10,6 +10,11 @@ const ApolloPluginConfigurationSchema = ConfigurationSchema('ApolloPlugin', {
     type: 'string',
     defaultValue: 'Sequence Ontology',
   },
+  hasRole: {
+    description: 'Flag used internally by jbrowse-plugin-apollo',
+    type: 'boolean',
+    defaultValue: false,
+  },
 })
 
 export default ApolloPluginConfigurationSchema

package/src/extensions/annotationFromJBrowseFeature.test.ts

@@ -1,5 +1,6 @@
 import SimpleFeature from '@jbrowse/core/util/simpleFeature'
 import { describe, expect, it } from '@jest/globals'
+
 import { jbrowseFeatureToAnnotationFeature } from './annotationFromJBrowseFeature'
 
 describe('Convert JBrowse feature to annotation feature', () => {

package/src/extensions/annotationFromJBrowseFeature.ts

@@ -3,21 +3,22 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
-import AddIcon from '@mui/icons-material/Add'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
+import { type GFF3Feature } from '@gmod/gff'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
 import {
-  AbstractSessionModel,
+  type AbstractSessionModel,
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { type Feature } from '@jbrowse/core/util/simpleFeature'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import AddIcon from '@mui/icons-material/Add'
+
 import { CreateApolloAnnotation } from '../components/CreateApolloAnnotation'
-import { GFF3Feature } from '@gmod/gff'
-import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
 
 function simpleFeatureToGFF3Feature(
   feature: Feature,
@@ -136,6 +137,7 @@ export function annotationFromJBrowseFeature(
         contextMenuItems() {
           const session = getSession(self)
           const assembly = self.getAssembly()
+          const region = self.getFirstRegion()
           const feature = self.contextMenuFeature
           if (!feature) {
             return superContextMenuItems()
@@ -157,6 +159,7 @@ export function annotationFromJBrowseFeature(
                       annotationFeature: self.getAnnotationFeature(assembly),
                       assembly,
                       refSeqId: self.getRefSeqId(assembly),
+                      region,
                     },
                   ],
                 )

package/src/extensions/annotationFromPileup.ts

@@ -3,22 +3,31 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { AddFeatureChange } from '@apollo-annotation/shared'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
-import { getContainingView, getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type DisplayType } from '@jbrowse/core/pluggableElementTypes'
+import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
+import {
+  type AbstractSessionModel,
+  getContainingView,
+  getSession,
+} from '@jbrowse/core/util'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 import ObjectID from 'bson-objectid'
 
-import { ApolloSessionModel } from '../session'
+import { CreateApolloAnnotation } from '../components/CreateApolloAnnotation'
 
-function parseCigar(cigar: string): [string | undefined, number][] {
-  return (cigar.toUpperCase().match(/\d+\D/g) ?? []).map((op) => {
-    return [(/\D/.exec(op) ?? [])[0], Number.parseInt(op, 10)]
-  })
+function parseCigar(cigar: string): [string, number][] {
+  const regex = /(\d+)([MIDNSHPX=])/g
+  const result: [string, number][] = []
+  let match
+
+  while ((match = regex.exec(cigar)) !== null) {
+    result.push([match[2], Number.parseInt(match[1], 10)])
+  }
+
+  return result
 }
 
 export function annotationFromPileup(pluggableElement: PluggableElementBase) {
@@ -62,55 +71,87 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
         }
         return refSeqId
       },
-      createFeature() {
+      getAnnotationFeature() {
         const feature = self.contextMenuFeature
         const assembly = self.getAssembly()
         const refSeqId = self.getRefSeqId(assembly)
+        const start: number = feature.get('start')
+        const end: number = feature.get('end')
+        const strand = feature.get('strand')
+        const name = feature.get('name')
+
         const cigarData: string = feature.get('CIGAR')
         const ops = parseCigar(cigarData)
-        let currOffset = 0
-        const start: number = feature.get('start')
-        let openStart: number | undefined
+        let position = start
+        let currentExonStart: number | undefined
         const exons: {
           start: number
           end: number
         }[] = []
+
+        // Example: [[96,S], [4,M], [4216,N], [357,M], [1,I], [628,M], [94,S]]
+        // Results in 2 exons
+        // M, = and X are matches -> exon
+        // N is a gap in the reference sequence -> intron
+        // I, S, H and P -> not counted in reference position
         for (const [op, len] of ops) {
-          // open or continue open
-          if (op === 'M' || op === '=') {
-            // if it was closed, then open with start, strand, type
-            if (openStart === undefined) {
-              // add subfeature
-              openStart = currOffset + start
+          switch (op) {
+            case 'M':
+            case '=':
+            case 'X': {
+              if (currentExonStart === undefined) {
+                currentExonStart = position
+              }
+              position += len
+              break
+            }
+
+            case 'N': {
+              if (currentExonStart !== undefined) {
+                exons.push({
+                  start: currentExonStart,
+                  end: position,
+                })
+                currentExonStart = undefined
+              }
+              position += len
+              break
+            }
+            case 'D': {
+              position += len
+              break
+            }
+            case 'I':
+            case 'S':
+            case 'H':
+            case 'P': {
+              // These operations do not affect the position in the reference sequence
+              break
+            }
+            default: {
+              throw new Error(`Unknown CIGAR operation: ${op}`)
             }
-          } else if (op === 'N' && openStart !== undefined) {
-            // if it was open, then close and add the subfeature
-            exons.push({
-              start: openStart,
-              end: currOffset + openStart,
-            })
-            openStart = undefined
-          }
-          if (op !== 'I') {
-            // we ignore insertions when calculating potential exon length
-            currOffset += len
           }
         }
-        // if we are still open, then close with the final length and add subfeature
-        if (openStart !== undefined) {
+
+        // If still in exon at end
+        if (currentExonStart !== undefined) {
           exons.push({
-            start: openStart,
-            end: currOffset + start,
+            start: currentExonStart,
+            end: position,
           })
         }
 
         const newFeature: AnnotationFeatureSnapshot = {
           _id: ObjectID().toHexString(),
           refSeq: refSeqId,
-          min: feature.get('start'),
-          max: feature.get('end'),
+          min: start,
+          max: end,
           type: 'mRNA',
-          strand: feature.get('strand'),
+          strand,
+          attributes: {
+            name: [name],
+          },
         }
         if (exons.length === 0) {
           return newFeature
@@ -118,75 +159,28 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
 
         const children: Record<string, AnnotationFeatureSnapshot> = {}
         newFeature.children = children
-        const [firstExon] = exons
-        const cdsFeature: AnnotationFeatureSnapshot = {
-          _id: ObjectID().toHexString(),
-          refSeq: refSeqId,
-          min: firstExon.start,
-          max: firstExon.end,
-          type: 'CDS',
-          strand: feature.get('strand'),
-        }
-        newFeature.children[cdsFeature._id] = cdsFeature
-        if (exons.length === 1) {
-          const exon: AnnotationFeatureSnapshot = {
-            _id: ObjectID().toHexString(),
-            refSeq: refSeqId,
-            min: firstExon.start,
-            max: firstExon.end,
-            type: 'exon',
-            strand: feature.get('strand'),
-          }
-          newFeature.children[exon._id] = exon
-          return newFeature
-        }
 
-        const discontinuousLocations: {
-          start: number
-          end: number
-          phase: 0 | 1 | 2
-        }[] = []
-        let phase: 0 | 1 | 2 = 0
         for (const exon of exons) {
-          cdsFeature.min = Math.min(cdsFeature.min, exon.start)
-          cdsFeature.max = Math.max(cdsFeature.max, exon.end)
-          const { end, start } = exon
-          discontinuousLocations.push({ start, end, phase })
-          const localPhase = (end - start) % 3
-          phase = ((phase + localPhase) % 3) as 0 | 1 | 2
           const newExon: AnnotationFeatureSnapshot = {
             _id: ObjectID().toHexString(),
             refSeq: refSeqId,
-            min: start,
-            max: end,
+            min: exon.start,
+            max: exon.end,
             type: 'exon',
-            strand: feature.get('strand'),
+            strand,
           }
           newFeature.children[newExon._id] = newExon
         }
         return newFeature
       },
-      async onPileupFeatureContext() {
-        const newFeature = self.createFeature()
-        const assembly = self.getAssembly()
-        const assemblyId = assembly.name
-        const change = new AddFeatureChange({
-          changedIds: [newFeature._id],
-          typeName: 'AddFeatureChange',
-          assembly: assemblyId,
-          addedFeature: newFeature,
-        })
-        const session = getSession(self)
-        await (
-          session as unknown as ApolloSessionModel
-        ).apolloDataStore.changeManager.submit(change)
-        session.notify('Annotation added successfully', 'success')
-      },
     }))
     .views((self) => {
       const superContextMenuItems = self.contextMenuItems
       return {
         contextMenuItems() {
+          const session = getSession(self)
+          const assembly = self.getAssembly()
+          const region = self.getFirstRegion()
           const feature = self.contextMenuFeature
           if (!feature) {
             return superContextMenuItems()
@@ -196,7 +190,23 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
             {
               label: 'Create Apollo annotation',
               icon: AddIcon,
-              onClick: self.onPileupFeatureContext,
+              onClick: () => {
+                ;(session as unknown as AbstractSessionModel).queueDialog(
+                  (doneCallback) => [
+                    CreateApolloAnnotation,
+                    {
+                      session,
+                      handleClose: () => {
+                        doneCallback()
+                      },
+                      annotationFeature: self.getAnnotationFeature(assembly),
+                      assembly,
+                      refSeqId: self.getRefSeqId(assembly),
+                      region,
+                    },
+                  ],
+                )
+              },
             },
           ]
         },

package/src/index.ts

@@ -9,41 +9,52 @@ import {
   changes,
   validationRegistry,
 } from '@apollo-annotation/shared'
+import Plugin from '@jbrowse/core/Plugin'
+import type PluginManager from '@jbrowse/core/PluginManager'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import {
   DisplayType,
   InternetAccountType,
-  PluggableElementType,
+  type PluggableElementType,
   TrackType,
-  ViewType,
+  type ViewType,
   WidgetType,
   createBaseTrackConfig,
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
 import {
-  AbstractSessionModel,
-  Region,
+  type AbstractSessionModel,
+  type Region,
   getSession,
   isAbstractMenuManager,
 } from '@jbrowse/core/util'
-import { LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
+import { type LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 
 import { version } from '../package.json'
+
 import {
   configSchema as apolloInternetAccountConfigSchema,
   modelFactory as apolloInternetAccountModelFactory,
 } from './ApolloInternetAccount'
+import { installApolloRefNameAliasAdapter } from './ApolloRefNameAliasAdapter'
 import { installApolloSequenceAdapter } from './ApolloSequenceAdapter'
-import {
-  ApolloSixFrameRenderer,
-  ReactComponent as ApolloSixFrameRendererReactComponent,
-  configSchema as apolloSixFrameRendererConfigSchema,
-} from './ApolloSixFrameRenderer'
 import { installApolloTextSearchAdapter } from './ApolloTextSearchAdapter'
-import { BackendDriver } from './BackendDrivers'
+import { type BackendDriver } from './BackendDrivers'
+import {
+  ApolloFeatureDetailsWidget,
+  ApolloFeatureDetailsWidgetModel,
+  ApolloTranscriptDetailsModel,
+  ApolloTranscriptDetailsWidget,
+} from './FeatureDetailsWidget'
+import {
+  configSchema as linearApolloDisplayConfigSchema,
+  stateModelFactory as LinearApolloDisplayStateModelFactory,
+} from './LinearApolloDisplay'
+import {
+  configSchema as linearApolloSixFrameDisplayConfigSchema,
+  stateModelFactory as LinearApolloSixFrameDisplayStateModelFactory,
+} from './LinearApolloSixFrameDisplay'
 import {
   AddFeature,
   DownloadGFF3,
@@ -55,29 +66,14 @@ import {
 } from './components'
 import ApolloPluginConfigurationSchema from './config'
 import {
-  annotationFromPileup,
   annotationFromJBrowseFeature,
+  annotationFromPileup,
 } from './extensions'
 import {
-  ApolloFeatureDetailsWidget,
-  ApolloFeatureDetailsWidgetModel,
-  ApolloTranscriptDetailsModel,
-  ApolloTranscriptDetailsWidget,
-} from './FeatureDetailsWidget'
-import {
-  stateModelFactory as LinearApolloDisplayStateModelFactory,
-  configSchema as linearApolloDisplayConfigSchema,
-} from './LinearApolloDisplay'
-import {
-  DisplayComponent,
-  makeSixFrameDisplayComponent,
+  LinearApolloDisplayComponent,
+  LinearApolloSixFrameDisplayComponent,
 } from './makeDisplayComponent'
-import { ApolloSessionModel, extendSession } from './session'
-import {
-  stateModelFactory as SixFrameFeatureDisplayStateModelFactory,
-  configSchemaFactory as sixFrameFeatureDisplayConfigSchemaFactory,
-} from './SixFrameFeatureDisplay'
-import { installApolloRefNameAliasAdapter } from './ApolloRefNameAliasAdapter'
+import { type ApolloSessionModel, extendSession } from './session'
 
 interface RpcHandle {
   on(event: string, listener: (event: MessageEvent) => void): this
@@ -186,38 +182,25 @@ export default class ApolloPlugin extends Plugin {
         ),
         trackType: 'ApolloTrack',
         viewType: 'LinearGenomeView',
-        ReactComponent: DisplayComponent,
+        ReactComponent: LinearApolloDisplayComponent,
       })
     })
 
     pluginManager.addDisplayType(() => {
-      const configSchema =
-        sixFrameFeatureDisplayConfigSchemaFactory(pluginManager)
-      const SixFrameDisplayComponent =
-        makeSixFrameDisplayComponent(pluginManager)
+      const configSchema = linearApolloSixFrameDisplayConfigSchema
       return new DisplayType({
-        name: 'SixFrameFeatureDisplay',
+        name: 'LinearApolloSixFrameDisplay',
         configSchema,
-        stateModel: SixFrameFeatureDisplayStateModelFactory(
+        stateModel: LinearApolloSixFrameDisplayStateModelFactory(
           pluginManager,
           configSchema,
         ),
         trackType: 'ApolloTrack',
         viewType: 'LinearGenomeView',
-        ReactComponent: SixFrameDisplayComponent,
+        ReactComponent: LinearApolloSixFrameDisplayComponent,
       })
     })
 
-    pluginManager.addRendererType(
-      () =>
-        new ApolloSixFrameRenderer({
-          name: 'ApolloSixFrameRenderer',
-          ReactComponent: ApolloSixFrameRendererReactComponent,
-          configSchema: apolloSixFrameRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
     pluginManager.addToExtensionPoint(
       'Core-extendSession',
       // @ts-expect-error not sure how to deal with snapshot model types