@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

package/src/session/session.ts

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import type { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
   type AnnotationFeature,
   AnnotationFeatureModel,
@@ -12,8 +11,12 @@ import {
   filterJBrowseConfig,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import type { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
-import { getConf, readConfObject } from '@jbrowse/core/configuration'
+import type assemblyManager from '@jbrowse/core/assemblyManager'
+import {
+  type AnyConfigurationModel,
+  getConf,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import type { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
 import type {
   AbstractSessionModel,
@@ -34,15 +37,17 @@ import { autorun, flow, observable, when } from 'mobx'
 
 import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { ApolloJobModel } from '../ApolloJobModel'
-import type { ChangeManager } from '../ChangeManager'
 import type ApolloPluginConfigurationSchema from '../config'
-import type { ApolloRootModel } from '../types'
+import { type ApolloRootModel, isApolloInternetAccount } from '../types'
 import { createFetchErrorMessage } from '../util'
 
-import { clientDataStoreFactory } from './ClientDataStore'
+import {
+  type ClientDataStoreModel,
+  clientDataStoreFactory,
+} from './ClientDataStore'
 
 export interface ApolloSession extends AbstractSessionModel {
-  apolloDataStore: ClientDataStoreType & { changeManager: ChangeManager }
+  apolloDataStore: ClientDataStoreModel
   apolloSelectedFeature?: AnnotationFeature
   apolloSetSelectedFeature(feature?: AnnotationFeature): void
 }
@@ -58,6 +63,8 @@ export interface HoveredFeature {
   bp: number
 }
 
+type Assembly = Instance<ReturnType<typeof assemblyManager>>['assemblies'][0]
+
 export function extendSession(
   pluginManager: PluginManager,
   sessionModel: ReturnType<typeof types.model>,
@@ -110,31 +117,22 @@ export function extendSession(
       apolloSetHoveredFeature(feature?: HoveredFeature) {
         self.apolloHoveredFeature = feature
       },
-      addApolloTrackConfig(assembly: AssemblyModel, baseURL?: string) {
+      addApolloLocalTrackConfig(assembly: Assembly) {
         const trackId = `apollo_track_${assembly.name}`
         const hasTrack = (self as unknown as AbstractSessionModel).tracks.some(
           (track) => track.trackId === trackId,
         )
         if (!hasTrack) {
-          ;(self as unknown as SessionWithAddTracks).addTrackConf({
+          ;(
+            getRoot<ApolloRootModel>(self).jbrowse as {
+              addTrackConf: SessionWithAddTracks['addTrackConf']
+            }
+          ).addTrackConf({
             type: 'ApolloTrack',
             trackId,
-            name: `Annotations (${
-              // @ts-expect-error getConf types don't quite work here for some reason
-              getConf(assembly, 'displayName') || assembly.name
-            })`,
+            name: `Annotations (${assembly.displayName})`,
             assemblyNames: [assembly.name],
-            textSearching: {
-              textSearchAdapter: {
-                type: 'ApolloTextSearchAdapter',
-                trackId,
-                assemblyNames: [assembly.name],
-                textSearchAdapterId: `apollo_search_${assembly.name}`,
-                ...(baseURL
-                  ? { baseURL: { uri: baseURL, locationType: 'UriLocation' } }
-                  : {}),
-              },
-            },
+            category: ['Apollo'],
           })
         }
       },
@@ -182,7 +180,7 @@ export function extendSession(
         }
         if (locations.length === 0) {
           for (const internetAccount of internetAccounts) {
-            if ('baseURL' in internetAccount) {
+            if (isApolloInternetAccount(internetAccount)) {
               internetAccount.postUserLocation([])
             }
           }
@@ -191,7 +189,7 @@ export function extendSession(
 
         const allLocations: UserLocation[] = []
         for (const internetAccount of internetAccounts) {
-          if ('baseURL' in internetAccount) {
+          if (isApolloInternetAccount(internetAccount)) {
             for (const location of locations) {
               const tmpLoc: UserLocation = {
                 assemblyId: location.assemblyName,
@@ -257,7 +255,7 @@ export function extendSession(
               }
               if (locations.length === 0) {
                 for (const internetAccount of internetAccounts) {
-                  if ('baseURL' in internetAccount) {
+                  if (isApolloInternetAccount(internetAccount)) {
                     internetAccount.postUserLocation([])
                   }
                 }
@@ -266,7 +264,7 @@ export function extendSession(
 
               const allLocations: UserLocation[] = []
               for (const internetAccount of internetAccounts) {
-                if ('baseURL' in internetAccount) {
+                if (isApolloInternetAccount(internetAccount)) {
                   for (const location of locations) {
                     const tmpLoc: UserLocation = {
                       assemblyId: location.assemblyName,
@@ -301,7 +299,51 @@ export function extendSession(
                 pluginConfiguration,
                 'hasRole',
               ) as boolean
-              if (hasRole) {
+              const featureTypeOntologyName = readConfObject(
+                pluginConfiguration,
+                'featureTypeOntologyName',
+              ) as string
+              const hasApolloInternetAccount = internetAccounts.some((ia) =>
+                isApolloInternetAccount(ia),
+              )
+              const nonApolloAssemblies = (
+                self as unknown as AbstractSessionModel
+              ).assemblyManager.assemblies.filter(
+                (a) =>
+                  !(
+                    getConf(a, ['sequence', 'metadata']) as {
+                      apollo?: boolean
+                    }
+                  ).apollo,
+              )
+              if (!hasApolloInternetAccount || hasRole) {
+                // Wait for assemblyManager to load before we do this part
+                const { assemblies } = (self as unknown as AbstractSessionModel)
+                  .assemblyManager
+                if (assemblies.length === 0) {
+                  return
+                }
+                const { pluginConfiguration } = self.apolloDataStore
+                const configuredOntologies =
+                  pluginConfiguration.ontologies as AnyConfigurationModel[]
+                const featureTypeOntology = configuredOntologies.find(
+                  (ont) =>
+                    readConfObject(ont, 'name') === featureTypeOntologyName,
+                )
+                if (!featureTypeOntology) {
+                  // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                  pluginConfiguration.addOntology({
+                    name: 'Sequence Ontology',
+                    version: '01c33c6d9b6c8dca12e7d3e37b49ee113093c2fa',
+                    source: {
+                      uri: 'https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/01c33c6d9b6c8dca12e7d3e37b49ee113093c2fa/Ontology_Files/so.json',
+                      locationType: 'UriLocation',
+                    },
+                  })
+                }
+                for (const a of nonApolloAssemblies) {
+                  self.addApolloLocalTrackConfig(a)
+                }
                 // @ts-expect-error not sure why snapshot type is wrong for snapshot
                 applySnapshot(self, self.previousSnapshot)
                 reaction.dispose()
@@ -369,23 +411,22 @@ export function extendSession(
     }))
 
     .views((self) => {
-      const superTrackActionMenuItems = (
-        self as unknown as AbstractSessionModel
-      ).getTrackActionMenuItems
+      const superTrackActions = (self as unknown as AbstractSessionModel)
+        .getTrackActions
       return {
-        getTrackActionMenuItems(conf: BaseTrackConfig) {
+        getTrackActions(conf: BaseTrackConfig) {
           if (
             conf.type === 'ApolloTrack' ||
             conf.type === 'ReferenceSequenceTrack'
           ) {
-            return superTrackActionMenuItems?.(conf)
+            return superTrackActions?.(conf)
           }
           const trackId = readConfObject(conf, 'trackId') as string
           const sessionTrackIdentifier = '-sessionTrack'
           const isSessionTrack = trackId.endsWith(sessionTrackIdentifier)
           return isSessionTrack
             ? [
-                ...(superTrackActionMenuItems?.(conf) ?? []),
+                ...(superTrackActions?.(conf) ?? []),
                 {
                   label: 'Save track to Apollo',
                   onClick: async () => {
@@ -438,7 +479,7 @@ export function extendSession(
                 },
               ]
             : [
-                ...(superTrackActionMenuItems?.(conf) ?? []),
+                ...(superTrackActions?.(conf) ?? []),
                 {
                   label: 'Remove track from Apollo',
                   onClick: async () => {
@@ -486,15 +527,9 @@ export function extendSession(
   return types.snapshotProcessor(sm, {
     postProcessor(snap: SnapshotOut<typeof sm>, node) {
       snap.apolloSelectedFeature = undefined
-      const assemblies = Object.fromEntries(
-        Object.entries(snap.apolloDataStore.assemblies).filter(
-          ([, assembly]) => assembly.backendDriverType === 'InMemoryFileDriver',
-        ),
-      )
       // @ts-expect-error ontologyManager isn't actually required
       snap.apolloDataStore = {
         typeName: 'Client',
-        assemblies,
         checkResults: {},
       }
       if (!node) {
@@ -507,10 +542,6 @@ export function extendSession(
         if (!feature) {
           continue
         }
-        const assembly = apolloDataStore.assemblies.get(feature.assemblyId)
-        if (assembly && assembly.backendDriverType === 'InMemoryFileDriver') {
-          snap.apolloDataStore.checkResults[cr._id] = getSnapshot(cr)
-        }
       }
       return snap
     },

package/src/util/annotationFeatureUtils.ts

@@ -1,4 +1,7 @@
-import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
+} from '@apollo-annotation/mst'
 
 export function getFeatureName(feature: AnnotationFeature) {
   const { attributes } = feature
@@ -110,3 +113,28 @@ export function getRelatedFeatures(
   }
   return relatedFeatures
 }
+
+export function removeSkippedAttributes(
+  feature: AnnotationFeatureSnapshot,
+  skippedAttributes: Set<string>,
+) {
+  if (feature.attributes) {
+    const newAttributes: Record<string, readonly string[] | undefined> = {}
+    for (const [attribute, values] of Object.entries(feature.attributes)) {
+      if (!skippedAttributes.has(attribute)) {
+        newAttributes[attribute] = values
+      }
+    }
+    feature.attributes =
+      Object.keys(newAttributes).length === 0 ? undefined : newAttributes
+  }
+  if (feature.children) {
+    const newChildren: Record<string, AnnotationFeatureSnapshot> = {}
+    for (const [childId, child] of Object.entries(feature.children)) {
+      const newChild = { ...child } as AnnotationFeatureSnapshot
+      removeSkippedAttributes(newChild, skippedAttributes)
+      newChildren[childId] = newChild
+    }
+    feature.children = newChildren
+  }
+}

package/src/util/glyphUtils.ts

@@ -1,12 +1,11 @@
 import type {
   AnnotationFeature,
+  Children,
   TranscriptPartCoding,
 } from '@apollo-annotation/mst'
-import type { BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
 import type { MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
-  getContainingView,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -15,11 +14,12 @@ import SkipPreviousRoundedIcon from '@mui/icons-material/SkipPreviousRounded'
 
 import type { LinearApolloDisplayMouseEvents } from '../LinearApolloDisplay/stateModel/mouseEvents'
 import type { LinearApolloSixFrameDisplayMouseEvents } from '../LinearApolloSixFrameDisplay/stateModel/mouseEvents'
-import { AddChildFeature, CopyFeature, DeleteFeature } from '../components'
+import { AddChildFeature } from '../components/AddChildFeature'
+import { ColorFeature } from '../components/ColorFeature'
+import { CopyFeature } from '../components/CopyFeature'
+import { DeleteFeature } from '../components/DeleteFeature'
 import type { ApolloSessionModel } from '../session'
 
-import type { MousePositionWithFeature } from '.'
-
 type NavLocation = Parameters<LinearGenomeViewModel['navTo']>[0]
 
 export function selectFeatureAndOpenWidget(
@@ -63,6 +63,20 @@ export function selectFeatureAndOpenWidget(
   }
 }
 
+export function isGeneFeature(
+  feature: AnnotationFeature,
+  session: ApolloSessionModel,
+): boolean {
+  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
+  if (!featureTypeOntology) {
+    throw new Error('featureTypeOntology is undefined')
+  }
+  return (
+    featureTypeOntology.isTypeOf(feature.type, 'gene') ||
+    featureTypeOntology.isTypeOf(feature.type, 'pseudogene')
+  )
+}
+
 export function isTranscriptFeature(
   feature: AnnotationFeature,
   session: ApolloSessionModel,
@@ -99,6 +113,36 @@ export function isCDSFeature(
   return featureTypeOntology.isTypeOf(feature.type, 'CDS')
 }
 
+export function looksLikeGene(
+  feature: AnnotationFeature,
+  session: ApolloSessionModel,
+) {
+  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
+  if (!featureTypeOntology) {
+    throw new Error('featureTypeOntology is undefined')
+  }
+  const children = feature.children as Children
+  if (!children?.size) {
+    return false
+  }
+  const isGene = isGeneFeature(feature, session)
+  if (!isGene) {
+    return false
+  }
+  for (const [, child] of children) {
+    if (isTranscriptFeature(child, session)) {
+      const { children: grandChildren } = child as { children?: Children }
+      if (!grandChildren?.size) {
+        return false
+      }
+      return [...grandChildren.values()].some((grandchild) =>
+        isExonFeature(grandchild, session),
+      )
+    }
+  }
+  return false
+}
+
 export interface AdjacentExons {
   upstream: AnnotationFeature | undefined
   downstream: AnnotationFeature | undefined
@@ -109,16 +153,8 @@ export function getAdjacentExons(
   display:
     | LinearApolloDisplayMouseEvents
     | LinearApolloSixFrameDisplayMouseEvents,
-  mousePosition: MousePositionWithFeature,
-  session: ApolloSessionModel,
 ): AdjacentExons {
-  const lgv = getContainingView(
-    display as BaseDisplayModel,
-  ) as unknown as LinearGenomeViewModel
-
   // Genomic coords of current view
-  const viewGenomicLeft = mousePosition.bp - lgv.bpPerPx * mousePosition.x
-  const viewGenomicRight = viewGenomicLeft + lgv.coarseTotalBp
   if (!currentExon.parent) {
     return { upstream: undefined, downstream: undefined }
   }
@@ -126,7 +162,8 @@ export function getAdjacentExons(
   if (!transcript.children) {
     throw new Error(`Error getting children of ${transcript._id}`)
   }
-  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
+  const { featureTypeOntology } =
+    display.session.apolloDataStore.ontologyManager
   if (!featureTypeOntology) {
     throw new Error('featureTypeOntology is undefined')
   }
@@ -143,14 +180,14 @@ export function getAdjacentExons(
   }
   exons = exons.sort((a, b) => (a.min < b.min ? -1 : 1))
   for (const exon of exons) {
-    if (exon.min > viewGenomicRight) {
+    if (exon.min > currentExon.max) {
       adjacentExons.downstream = exon
       break
     }
   }
   exons = exons.sort((a, b) => (a.min > b.min ? -1 : 1))
   for (const exon of exons) {
-    if (exon.max < viewGenomicLeft) {
+    if (exon.max < currentExon.min) {
       adjacentExons.upstream = exon
       break
     }
@@ -241,19 +278,6 @@ export function isSelectedFeature(
   return Boolean(selectedFeature && feature._id === selectedFeature._id)
 }
 
-export function containsSelectedFeature(
-  feature: AnnotationFeature,
-  selectedFeature: AnnotationFeature | undefined,
-): boolean {
-  if (!selectedFeature) {
-    return false
-  }
-  if (feature._id === selectedFeature._id) {
-    return true
-  }
-  return feature.hasDescendant(selectedFeature._id)
-}
-
 function makeFeatureLabel(feature: AnnotationFeature) {
   let name: string | undefined
   if (feature.attributes.get('gff_name')) {
@@ -288,7 +312,6 @@ export function getContextMenuItemsForFeature(
   } = display
   const menuItems: MenuItem[] = []
   const role = internetAccount ? internetAccount.role : 'admin'
-  const admin = role === 'admin'
   const readOnly = !(role && ['admin', 'user'].includes(role))
   const [region] = regions
   const sourceAssemblyId = display.getAssemblyId(region.assemblyName)
@@ -341,7 +364,7 @@ export function getContextMenuItemsForFeature(
     },
     {
       label: 'Delete feature',
-      disabled: !admin,
+      disabled: readOnly,
       onClick: () => {
         ;(session as unknown as AbstractSessionModel).queueDialog(
           (doneCallback) => [
@@ -363,6 +386,26 @@ export function getContextMenuItemsForFeature(
         )
       },
     },
+    {
+      label: 'Color feature',
+      disabled: readOnly,
+      onClick: () => {
+        ;(session as unknown as AbstractSessionModel).queueDialog(
+          (doneCallback) => [
+            ColorFeature,
+            {
+              session,
+              handleClose: () => {
+                doneCallback()
+              },
+              changeManager,
+              sourceFeature,
+              sourceAssemblyId: currentAssemblyId,
+            },
+          ],
+        )
+      },
+    },
   )
   if (isSessionModelWithWidgets(session)) {
     menuItems.push({

package/src/util/index.ts

@@ -28,7 +28,6 @@ export function getApolloInternetAccount(session: ApolloSessionModel) {
     | undefined
 }
 
-export * from './loadAssemblyIntoClient'
 export * from './annotationFeatureUtils'
 export * from './glyphUtils'
 export * from './mouseEventsUtils'

package/dist/BackendDrivers/DesktopFileDriver.d.ts

@@ -1,160 +0,0 @@
-import { type AssemblySpecificChange, type Change } from '@apollo-annotation/common';
-import type { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
-import { ValidationResultSet } from '@apollo-annotation/shared';
-import { type Region } from '@jbrowse/core/util';
-import { BackendDriver, type RefNameAliases } from './BackendDriver';
-export declare class DesktopFileDriver extends BackendDriver {
-    loadAssembly(assemblyName: string): Promise<import("@apollo-annotation/mst").ApolloAssemblyI>;
-    getAssembly(assemblyName: string): Promise<import("@apollo-annotation/mst").ApolloAssemblyI>;
-    getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]>;
-    getFeatures(region: Region): Promise<[AnnotationFeatureSnapshot[], CheckResultSnapshot[]]>;
-    getSequence(region: Region): Promise<{
-        seq: string;
-        refSeq: string;
-    }>;
-    getRegions(assemblyName: string): Promise<Region[]>;
-    getAssemblies(): ({
-        configuration: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
-    } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
-            regions: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-    }, {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
-    } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
-            regions: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>)[];
-    submitChange(change: Change | AssemblySpecificChange): Promise<ValidationResultSet>;
-    searchFeatures(_term: string, _assemblies: string[]): Promise<AnnotationFeatureSnapshot[]>;
-}
-//# sourceMappingURL=DesktopFileDriver.d.ts.map

package/dist/BackendDrivers/DesktopFileDriver.d.ts.map

@@ -1 +0,0 @@
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