@apollo-annotation/jbrowse-plugin-apollo 0.1.18 → 0.1.20

package/package.json

@@ -1,18 +1,18 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.1.18",
+  "version": "0.1.20",
   "description": "Apollo plugin for JBrowse 2",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
     "directory": "packages/jbrowse-plugin-apollo"
   },
-  "author": "JBrowse Team",
   "license": "Apache-2.0",
-  "keywords": [
-    "jbrowse",
-    "jbrowse2"
-  ],
+  "author": "JBrowse Team",
   "main": "dist/index.js",
   "module": "dist/index.esm.js",
   "typings": "dist/index.d.ts",
@@ -20,13 +20,6 @@
     "dist",
     "src"
   ],
-  "config": {
-    "jbrowse": {
-      "plugin": {
-        "name": "Apollo"
-      }
-    }
-  },
   "scripts": {
     "setup": "rimraf .jbrowse && jbrowse create .jbrowse",
     "clean": "rimraf dist",
@@ -47,13 +40,17 @@
     "prepack": "yarn build",
     "postversion": "git push --follow-tags"
   },
-  "jbrowse-plugin": {
-    "name": "Apollo"
+  "config": {
+    "jbrowse": {
+      "plugin": {
+        "name": "Apollo"
+      }
+    }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.1.18",
-    "@apollo-annotation/mst": "^0.1.18",
-    "@apollo-annotation/shared": "^0.1.18",
+    "@apollo-annotation/common": "^0.1.20",
+    "@apollo-annotation/mst": "^0.1.20",
+    "@apollo-annotation/shared": "^0.1.20",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "1.2.0",
@@ -74,21 +71,9 @@
     "socket.io-client": "^4.5.4",
     "tslib": "^2.3.1"
   },
-  "peerDependencies": {
-    "@jbrowse/core": "^2.7.0",
-    "@mui/material": "^5.11.14",
-    "mobx": "^6.6.1",
-    "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.1.7",
-    "prop-types": "^15.8.1",
-    "react": "^18.2.0",
-    "react-dom": "^18.2.0",
-    "rxjs": "^7.4.0",
-    "tss-react": "^4.6.1"
-  },
   "devDependencies": {
     "@jbrowse/cli": "^2.6.2",
-    "@jbrowse/core": "^2.7.0",
+    "@jbrowse/core": "^2.13.1",
     "@jbrowse/development-tools": "^2.1.1",
     "@jest/globals": "^29.0.3",
     "@mui/material": "^5.11.14",
@@ -97,7 +82,7 @@
     "@types/file-saver": "^2",
     "@types/node": "^18.14.2",
     "@types/prop-types": "^15",
-    "@types/react": "^17.0.34",
+    "@types/react": "^18.3.4",
     "@types/react-dom": "^18",
     "cypress": "12.17.3",
     "cypress-mongodb": "^6.2.0",
@@ -121,9 +106,24 @@
     "ts-jest": "^29.1.1",
     "ts-node": "^10.3.0",
     "tss-react": "^4.6.1",
-    "typescript": "^5.1.6"
+    "typescript": "^5.5.3"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.13.1",
+    "@mui/material": "^5.11.14",
+    "mobx": "^6.6.1",
+    "mobx-react": "^7.2.1",
+    "mobx-state-tree": "^5.1.7",
+    "prop-types": "^15.8.1",
+    "react": "^18.2.0",
+    "react-dom": "^18.2.0",
+    "rxjs": "^7.4.0",
+    "tss-react": "^4.6.1"
   },
   "publishConfig": {
     "access": "public"
+  },
+  "jbrowse-plugin": {
+    "name": "Apollo"
   }
 }

package/src/ApolloInternetAccount/addMenuItems.ts

@@ -2,6 +2,7 @@ import { AbstractMenuManager, AbstractSessionModel } from '@jbrowse/core/util'
 
 import {
   AddAssembly,
+  AddRefSeqAliases,
   DeleteAssembly,
   ImportFeatures,
   ManageUsers,
@@ -60,6 +61,23 @@ export function addMenuItems(rootModel: AbstractMenuManager) {
       )
     },
   })
+  rootModel.appendToMenu('Apollo', {
+    label: 'Add reference sequence aliases',
+    onClick: (session: ApolloSessionModel) => {
+      ;(session as unknown as AbstractSessionModel).queueDialog(
+        (doneCallback) => [
+          AddRefSeqAliases,
+          {
+            session,
+            handleClose: () => {
+              doneCallback()
+            },
+            changeManager: session.apolloDataStore.changeManager,
+          },
+        ],
+      )
+    },
+  })
   rootModel.appendToMenu('Apollo', {
     label: 'Manage Users',
     onClick: (session: ApolloSessionModel) => {

package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 import { isAbortException } from '@jbrowse/core/util'
 import {
   Button,

package/src/ApolloInternetAccount/configSchema.ts

@@ -21,6 +21,9 @@ const ApolloConfigSchema = ConfigurationSchema(
 
 export type ApolloInternetAccountConfigModel = typeof ApolloConfigSchema
 
-export type ApolloInternetAccountConfig =
-  Instance<ApolloInternetAccountConfigModel>
+// eslint disable because of
+// https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
+// eslint-disable-next-line @typescript-eslint/no-empty-interface
+export interface ApolloInternetAccountConfig
+  extends Instance<ApolloInternetAccountConfigModel> {}
 export default ApolloConfigSchema

package/src/ApolloInternetAccount/model.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unused-vars */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
@@ -27,7 +26,7 @@ import { autorun } from 'mobx'
 import { Instance, flow, getRoot, types } from 'mobx-state-tree'
 import { io } from 'socket.io-client'
 
-import { ApolloSessionModel, Collaborator } from '../session'
+import { Collaborator } from '../session'
 import { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 import { addMenuItems } from './addMenuItems'
@@ -36,7 +35,7 @@ import { ApolloInternetAccountConfigModel } from './configSchema'
 
 type AuthType = 'google' | 'microsoft' | 'guest'
 
-type Role = 'admin' | 'user' | 'readOnly'
+type Role = 'admin' | 'user' | 'readOnly' | 'none'
 
 const inWebWorker = typeof sessionStorage === 'undefined'
 
@@ -439,6 +438,13 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
             if (inWebWorker) {
               return
             }
+            const { session } = getRoot<ApolloRootModel>(self)
+            // This can be undefined if there is no session loaded, e.g. on
+            // the start screen
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            if (!session) {
+              return
+            }
             if (self.role) {
               await self.initialize(self.role)
               reaction.dispose()
@@ -454,5 +460,8 @@ export default stateModelFactory
 export type ApolloInternetAccountStateModel = ReturnType<
   typeof stateModelFactory
 >
-export type ApolloInternetAccountModel =
-  Instance<ApolloInternetAccountStateModel>
+// eslint disable because of
+// https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
+// eslint-disable-next-line @typescript-eslint/no-empty-interface
+export interface ApolloInternetAccountModel
+  extends Instance<ApolloInternetAccountStateModel> {}

package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts

@@ -0,0 +1,94 @@
+import { RefNameAliases } from './../BackendDrivers/BackendDriver'
+import {
+  BaseRefNameAliasAdapter,
+  BaseAdapter,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { readConfObject } from '@jbrowse/core/configuration'
+import { ApolloSessionModel } from '../session'
+import { BackendDriver } from '../BackendDrivers'
+import { nanoid } from 'nanoid'
+import RpcServer from 'librpc-web-mod/dist/server'
+
+declare global {
+  const rpcServer: RpcServer
+}
+
+interface ApolloRefNameAliasMessage {
+  apollo: true
+  messageId: string
+  refNameAliases: RefNameAliases[]
+}
+
+function isApolloRefNameAliasMessage(
+  data?: unknown,
+): data is ApolloRefNameAliasMessage {
+  return (
+    typeof data === 'object' &&
+    data !== null &&
+    'apollo' in data &&
+    data.apollo === true &&
+    'refNameAliases' in data
+  )
+}
+
+const isInWebWorker = typeof sessionStorage === 'undefined'
+
+export default class RefNameAliasAdapter
+  extends BaseAdapter
+  implements BaseRefNameAliasAdapter
+{
+  private refNameAliases: RefNameAliases[] | undefined
+
+  async getRefNameAliases() {
+    const assemblyId = readConfObject(this.config, 'assemblyId') as string
+    if (!isInWebWorker) {
+      const dataStore = (
+        this.pluginManager?.rootModel?.session as ApolloSessionModel | undefined
+      )?.apolloDataStore
+      if (!dataStore) {
+        throw new Error('No Apollo data store found')
+      }
+      const backendDriver = dataStore.getBackendDriver(
+        assemblyId,
+      ) as BackendDriver
+      const refNameAliases = await backendDriver.getRefNameAliases(assemblyId)
+      return refNameAliases
+    }
+    const refNameAliases = await new Promise(
+      (
+        resolve: (refNameAliases: RefNameAliases[]) => void,
+        reject: (reason: Error) => void,
+      ) => {
+        const timeoutId = setTimeout(() => {
+          reject(new Error('timeout'))
+        }, 20_000)
+        const messageId = nanoid()
+        const messageListener = (event: MessageEvent) => {
+          const data = event.data as ApolloRefNameAliasMessage
+          if (!isApolloRefNameAliasMessage(data)) {
+            return
+          }
+          if (data.messageId !== messageId) {
+            return
+          }
+          clearTimeout(timeoutId)
+          removeEventListener('message', messageListener)
+          resolve(data.refNameAliases)
+        }
+        addEventListener('message', messageListener)
+        rpcServer.emit('apollo', {
+          apollo: true,
+          method: 'getRefNameAliases',
+          assembly: assemblyId,
+          messageId,
+        })
+      },
+    )
+    this.refNameAliases = refNameAliases
+    return refNameAliases
+  }
+
+  async freeResources() {
+    // no resources to free
+  }
+}

package/src/ApolloRefNameAliasAdapter/configSchema.ts

@@ -0,0 +1,12 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default ConfigurationSchema(
+  'ApolloRefNameAliasAdapter',
+  {
+    assemblyId: {
+      type: 'string',
+      defaultValue: '',
+    },
+  },
+  { explicitlyTyped: true },
+)

package/src/ApolloRefNameAliasAdapter/index.ts

@@ -0,0 +1,21 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import configSchema from './configSchema'
+import ApolloRefNameAliasAdapter from './ApolloRefNameAliasAdapter'
+
+export function installApolloRefNameAliasAdapter(pluginManager: PluginManager) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'ApolloRefNameAliasAdapter',
+        configSchema,
+        adapterMetadata: {
+          category: undefined,
+          hiddenFromGUI: true,
+          description: undefined,
+        },
+        AdapterClass: ApolloRefNameAliasAdapter,
+      }),
+  )
+}

package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/prefer-promise-reject-errors */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */

package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx

@@ -5,7 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { AnnotationFeatureI } from '@apollo-annotation/mst'
+import { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
@@ -76,7 +76,7 @@ function selectColor(number: number) {
 function ApolloRendering(props: ApolloRenderingProps) {
   const [contextCoord, setContextCoord] = useState<Coord>()
   const [contextMenuFeature, setContextMenuFeature] =
-    useState<AnnotationFeatureI>()
+    useState<AnnotationFeature>()
 
   const canvasRef = useRef<HTMLCanvasElement>(null)
   const overlayCanvasRef = useRef<HTMLCanvasElement>(null)
@@ -86,7 +86,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
   // const [overEdge, setOverEdge] = useState<'start' | 'end'>()
   const [dragging, setDragging] = useState<{
     edge: 'start' | 'end'
-    feature: AnnotationFeatureI
+    feature: AnnotationFeature
     row: number
     bp: number
     px: number
@@ -187,9 +187,9 @@ function ApolloRendering(props: ApolloRenderingProps) {
     for (const [row, featureInfos] of featureLayout) {
       for (const [parentID, feature] of featureInfos) {
         const start = region.reversed
-          ? region.end - feature.end
-          : feature.start - region.start - 1
-        const end = feature.end - region.start - 1
+          ? region.end - feature.max
+          : feature.min - region.start - 1
+        const end = feature.max - region.start - 1
         const startPx = start / bpPerPx
         const endPx = end / bpPerPx
         const width = end - start
@@ -463,7 +463,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
   //   // eslint-disable-next-line @typescript-eslint/no-unused-vars
   //   const [parentID, feat] =
   //     layoutRow.find((f) => bp >= f[1].min && bp <= f[1].max) || []
-  //   let feature: AnnotationFeatureI | undefined = feat
+  //   let feature: AnnotationFeature | undefined = feat
   //   if (feature) {
   //     const topRow = row
   //     const startPx = (feature.start - region.start) / bpPerPx
@@ -473,7 +473,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
   //       y - topRow * height,
   //       bpPerPx,
   //       height,
-  //     ) as AnnotationFeatureI
+  //     ) as AnnotationFeature
   //   }
   //   if (feature) {
   //     // TODO: check reversed
@@ -526,7 +526,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
       let change: LocationEndChange | LocationStartChange
       if (edge === 'end') {
         const featureId = feature._id
-        const oldEnd = feature.end
+        const oldEnd = feature.max
         const newEnd = Math.round(bp)
         change = new LocationEndChange({
           typeName: 'LocationEndChange',
@@ -538,7 +538,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
         })
       } else {
         const featureId = feature._id
-        const oldStart = feature.start
+        const oldStart = feature.min
         const newStart = Math.round(bp)
         change = new LocationStartChange({
           typeName: 'LocationStartChange',

package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts

@@ -1,8 +1,4 @@
-/* eslint-disable @typescript-eslint/no-unsafe-return */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { readConfObject } from '@jbrowse/core/configuration'
 import {
   BaseAdapter,
@@ -10,58 +6,65 @@ import {
   BaseTextSearchArgs,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
+import { AbstractSessionModel, UriLocation } from '@jbrowse/core/util'
+import { ApolloSessionModel } from '../session'
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
 export class ApolloTextSearchAdapter
   extends BaseAdapter
   implements BaseTextSearchAdapter
 {
   get baseURL() {
-    return readConfObject(this.config, 'baseURL').uri
+    return (readConfObject(this.config, 'baseURL') as UriLocation).uri
   }
 
   get trackId() {
-    return readConfObject(this.config, 'trackId')
+    return readConfObject(this.config, 'trackId') as string
   }
 
   get assemblyNames() {
-    return readConfObject(this.config, 'assemblyNames')
+    return readConfObject(this.config, 'assemblyNames') as string[]
   }
 
   mapBaseResult(
-    features: {
-      refSeq: any // eslint-disable-line @typescript-eslint/no-explicit-any
-      start: number
-      end: number
-    }[],
+    features: AnnotationFeatureSnapshot[],
+    assembly: Assembly,
     query: string,
   ) {
-    return features.map(
-      (feature) =>
-        new BaseResult({
-          label: query,
-          trackId: this.trackId,
-          locString: `${feature.refSeq?.name}:${feature.start + 1}..${
-            feature.end
-          }`,
-        }),
-    )
+    return features.map((feature) => {
+      const refName = assembly.getCanonicalRefName(feature.refSeq)
+      return new BaseResult({
+        label: query,
+        trackId: this.trackId,
+        locString: `${refName}:${feature.min + 1}..${feature.max}`,
+      })
+    })
   }
 
   async searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]> {
-    const results = []
+    const query = args.queryString
+    const results: BaseResult[] = []
+    const session = this.pluginManager?.rootModel?.session as
+      | ApolloSessionModel
+      | undefined
+    if (!session) {
+      return results
+    }
+    const { apolloDataStore } = session
+    const { assemblyManager } = session as unknown as AbstractSessionModel
     for (const assemblyName of this.assemblyNames) {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const session = this.pluginManager?.rootModel?.session as any
-      const backendDriver =
-        session?.apolloDataStore.getBackendDriver(assemblyName)
-      const r = await backendDriver.searchFeatures(args.queryString, [
+      const backendDriver = apolloDataStore.getBackendDriver(assemblyName)
+      const assembly = assemblyManager.get(assemblyName)
+      if (!(backendDriver && assembly)) {
+        continue
+      }
+      const features = await backendDriver.searchFeatures(args.queryString, [
         assemblyName,
       ])
-      results.push(...r)
+      results.push(...this.mapBaseResult(features, assembly, query))
     }
 
-    const query = args.queryString
-    return this.mapBaseResult(results, query)
+    return results
   }
 
   // eslint-disable-next-line @typescript-eslint/no-empty-function

package/src/BackendDrivers/BackendDriver.ts

@@ -9,6 +9,12 @@ import { Region } from '@jbrowse/core/util'
 
 import { SubmitOpts } from '../ChangeManager'
 
+export interface RefNameAliases {
+  refName: string
+  aliases: string[]
+  uniqueId: string
+}
+
 export abstract class BackendDriver {
   constructor(protected clientStore: ClientDataStore) {}
 
@@ -22,6 +28,8 @@ export abstract class BackendDriver {
 
   abstract getAssemblies(internetAccountConfigId?: string): Assembly[]
 
+  abstract getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]>
+
   abstract submitChange(
     change: Change,
     opts: SubmitOpts,

package/src/BackendDrivers/CollaborationServerDriver.ts

@@ -18,7 +18,16 @@ import { Socket } from 'socket.io-client'
 
 import { ChangeManager, SubmitOpts } from '../ChangeManager'
 import { createFetchErrorMessage } from '../util'
-import { BackendDriver } from './BackendDriver'
+import { BackendDriver, RefNameAliases } from './BackendDriver'
+
+export interface ApolloRefSeqResponse {
+  _id: string
+  name: string
+  description?: string
+  aliases: string[]
+  length: string
+  assembly: string
+}
 
 export interface ApolloInternetAccount extends BaseInternetAccountModel {
   baseURL: string
@@ -235,6 +244,45 @@ export class CollaborationServerDriver extends BackendDriver {
     return seq
   }
 
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const { assemblyManager } = getSession(this.clientStore)
+    const assembly = assemblyManager.get(assemblyName)
+    if (!assembly) {
+      throw new Error(`Could not find assembly with name "${assemblyName}"`)
+    }
+    const internetAccount = this.clientStore.getInternetAccount(
+      assemblyName,
+    ) as ApolloInternetAccount
+    const { baseURL } = internetAccount
+    const url = new URL('refSeqs', baseURL)
+    const searchParams = new URLSearchParams({ assembly: assemblyName })
+    url.search = searchParams.toString()
+    const uri = url.toString()
+
+    const response = await this.fetch(internetAccount, uri)
+    if (!response.ok) {
+      let errorMessage
+      try {
+        errorMessage = await response.text()
+      } catch {
+        errorMessage = ''
+      }
+      throw new Error(
+        `getRefNameAliases failed: ${response.status} (${response.statusText})${
+          errorMessage ? ` (${errorMessage})` : ''
+        }`,
+      )
+    }
+    const refSeqs = (await response.json()) as ApolloRefSeqResponse[]
+    return refSeqs.map((refSeq) => {
+      return {
+        refName: refSeq.name,
+        aliases: [refSeq._id, ...refSeq.aliases],
+        uniqueId: `alias-${refSeq._id}`,
+      }
+    }) as RefNameAliases[]
+  }
+
   async getRegions(assemblyName: string): Promise<Region[]> {
     const { assemblyManager } = getSession(this.clientStore)
     const assembly = assemblyManager.get(assemblyName)

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -19,7 +19,7 @@ import { Region, getSession } from '@jbrowse/core/util'
 import { getSnapshot } from 'mobx-state-tree'
 
 import { checkFeatures, loadAssemblyIntoClient } from '../util'
-import { BackendDriver } from './BackendDriver'
+import { BackendDriver, RefNameAliases } from './BackendDriver'
 
 export class DesktopFileDriver extends BackendDriver {
   async loadAssembly(assemblyName: string) {
@@ -45,6 +45,19 @@ export class DesktopFileDriver extends BackendDriver {
     return assembly
   }
 
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const assembly = await this.getAssembly(assemblyName)
+    const refNameAliases: RefNameAliases[] = []
+    for (const [, refSeq] of assembly.refSeqs) {
+      refNameAliases.push({
+        refName: refSeq.name,
+        aliases: [refSeq._id],
+        uniqueId: `alias-${refSeq._id}`,
+      })
+    }
+    return refNameAliases
+  }
+
   async getFeatures(
     region: Region,
   ): Promise<[AnnotationFeatureSnapshot[], CheckResultSnapshot[]]> {

package/src/BackendDrivers/InMemoryFileDriver.ts

@@ -9,7 +9,7 @@ import { getConf } from '@jbrowse/core/configuration'
 import { Region, getSession } from '@jbrowse/core/util'
 
 import { SubmitOpts } from '../ChangeManager'
-import { BackendDriver } from './BackendDriver'
+import { BackendDriver, RefNameAliases } from './BackendDriver'
 
 export class InMemoryFileDriver extends BackendDriver {
   async getFeatures(): Promise<
@@ -32,6 +32,22 @@ export class InMemoryFileDriver extends BackendDriver {
     return { seq, refSeq: refName }
   }
 
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const assembly = this.clientStore.assemblies.get(assemblyName)
+    const refNameAliases: RefNameAliases[] = []
+    if (!assembly) {
+      return refNameAliases
+    }
+    for (const [, refSeq] of assembly.refSeqs) {
+      refNameAliases.push({
+        refName: refSeq.name,
+        aliases: [refSeq._id],
+        uniqueId: `alias-${refSeq._id}`,
+      })
+    }
+    return refNameAliases
+  }
+
   async getRegions(assemblyName: string): Promise<Region[]> {
     const assembly = this.clientStore.assemblies.get(assemblyName)
     if (!assembly) {