@apollo-annotation/jbrowse-plugin-apollo 0.3.10 → 0.3.12

package/dist/ApolloInternetAccount/components/AuthTypeSelector.d.ts

@@ -0,0 +1,6 @@
+export declare const AuthTypeSelector: ({ baseURL, handleClose, name, }: {
+    baseURL: string;
+    name: string;
+    handleClose: (type?: "google" | "microsoft" | "guest" | Error) => void;
+}) => import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=AuthTypeSelector.d.ts.map

package/dist/ApolloInternetAccount/components/AuthTypeSelector.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AuthTypeSelector.d.ts","sourceRoot":"","sources":["../../../src/ApolloInternetAccount/components/AuthTypeSelector.tsx"],"names":[],"mappings":"AAwBA,eAAO,MAAM,gBAAgB,oCAI1B;IACD,OAAO,EAAE,MAAM,CAAA;IACf,IAAI,EAAE,MAAM,CAAA;IACZ,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,QAAQ,GAAG,WAAW,GAAG,OAAO,GAAG,KAAK,KAAK,IAAI,CAAA;CACvE,4CAyGA,CAAA"}

package/dist/ApolloInternetAccount/components/LoginButtons.d.ts

@@ -0,0 +1,5 @@
+import { type ButtonProps } from '@mui/material';
+export declare function GoogleButton(props: ButtonProps): import("react/jsx-runtime").JSX.Element;
+export declare function MicrosoftButton(props: ButtonProps): import("react/jsx-runtime").JSX.Element;
+export declare function GuestButton(props: ButtonProps): import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=LoginButtons.d.ts.map

package/dist/ApolloInternetAccount/components/LoginButtons.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoginButtons.d.ts","sourceRoot":"","sources":["../../../src/ApolloInternetAccount/components/LoginButtons.tsx"],"names":[],"mappings":"AAEA,OAAO,EAAU,KAAK,WAAW,EAAE,MAAM,eAAe,CAAA;AAiBxD,wBAAgB,YAAY,CAAC,KAAK,EAAE,WAAW,2CAa9C;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,WAAW,2CAajD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,WAAW,2CAY7C"}

package/dist/ApolloInternetAccount/components/LoginIcons.d.ts

@@ -0,0 +1,4 @@
+import { type SvgIconProps } from '@mui/material';
+export declare function Google(props: SvgIconProps): import("react/jsx-runtime").JSX.Element;
+export declare function Microsoft(props: SvgIconProps): import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=LoginIcons.d.ts.map

package/dist/ApolloInternetAccount/components/LoginIcons.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoginIcons.d.ts","sourceRoot":"","sources":["../../../src/ApolloInternetAccount/components/LoginIcons.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAW,KAAK,YAAY,EAAE,MAAM,eAAe,CAAA;AAI1D,wBAAgB,MAAM,CAAC,KAAK,EAAE,YAAY,2CAgCzC;AAGD,wBAAgB,SAAS,CAAC,KAAK,EAAE,YAAY,2CAkC5C"}

package/dist/ApolloInternetAccount/index.d.ts

@@ -0,0 +1,3 @@
+export { default as configSchema } from './configSchema';
+export { default as modelFactory } from './model';
+//# sourceMappingURL=index.d.ts.map

package/dist/ApolloInternetAccount/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/ApolloInternetAccount/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACxD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,SAAS,CAAA"}

package/dist/ApolloJobModel.d.ts

@@ -0,0 +1,53 @@
+export interface JobsEntry {
+    name: string;
+    cancelCallback?: () => void;
+    progressPct?: number;
+    statusMessage?: string;
+}
+export interface JobsListModel {
+    id: number;
+    type: 'JobsListWidget';
+    jobs: JobsEntry[];
+    finished: JobsEntry[];
+    queued: JobsEntry[];
+    aborted: JobsEntry[];
+    addJob(job: JobsEntry): void;
+    removeJob(jobName: string): void;
+    addFinishedJob(job: JobsEntry): void;
+    addQueuedJob(job: JobsEntry): void;
+    addAbortedJob(job: JobsEntry): void;
+    removeQueuedJob(jobName: string): void;
+    updateJobStatusMessage(jobName: string, message?: string): void;
+    updateJobProgressPct(jobName: string, pct: number): void;
+}
+export declare const ApolloJobModel: import("@jbrowse/mobx-state-tree").IModelType<{}, {
+    readonly jobStatusWidget: JobsListModel;
+} & {
+    /**
+     * updates the status message and the progress percent of the provided job
+     * @param jobName - the name of the job to be updated
+     * @param statusMessage - the message to be communicated to the user
+     * @param progressPct - the percent through the run the job is
+     */
+    update(jobName: string, statusMessage: string, progressPct?: number): void;
+    /**
+     * aborts the provided job with a message to the user
+     * @param jobName - the name of the job to be aborted
+     * @param msg - a message to communicate to the user about the abort operation
+     */
+    abortJob(jobName: string, msg?: string): void;
+    /**
+     * opens the job status widget and adds the job to the running jobs
+     * @param job - the job to be run within the JobsManager
+     */
+    runJob(job: JobsEntry): void;
+    /**
+     * sets the progress and status message of the provided job
+     * adds the finished jobs to the list of finished jobs
+     * clears the jobs manager of the now done job
+     * begins to run the next job if one is queued
+     * @param job - the job to be completed
+     */
+    done(job: JobsEntry): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
+//# sourceMappingURL=ApolloJobModel.d.ts.map

package/dist/ApolloJobModel.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ApolloJobModel.d.ts","sourceRoot":"","sources":["../src/ApolloJobModel.ts"],"names":[],"mappings":"AASA,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAA;IACZ,cAAc,CAAC,EAAE,MAAM,IAAI,CAAA;IAC3B,WAAW,CAAC,EAAE,MAAM,CAAA;IACpB,aAAa,CAAC,EAAE,MAAM,CAAA;CACvB;AACD,MAAM,WAAW,aAAa;IAC5B,EAAE,EAAE,MAAM,CAAA;IACV,IAAI,EAAE,gBAAgB,CAAA;IACtB,IAAI,EAAE,SAAS,EAAE,CAAA;IACjB,QAAQ,EAAE,SAAS,EAAE,CAAA;IACrB,MAAM,EAAE,SAAS,EAAE,CAAA;IACnB,OAAO,EAAE,SAAS,EAAE,CAAA;IACpB,MAAM,CAAC,GAAG,EAAE,SAAS,GAAG,IAAI,CAAA;IAC5B,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAA;IAChC,cAAc,CAAC,GAAG,EAAE,SAAS,GAAG,IAAI,CAAA;IACpC,YAAY,CAAC,GAAG,EAAE,SAAS,GAAG,IAAI,CAAA;IAClC,aAAa,CAAC,GAAG,EAAE,SAAS,GAAG,IAAI,CAAA;IACnC,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAA;IACtC,sBAAsB,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,CAAA;IAC/D,oBAAoB,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,IAAI,CAAA;CACzD;AAED,eAAO,MAAM,cAAc;8BAagB,aAAa;;IAIpD;;;;;OAKG;oBACa,MAAM,iBAAiB,MAAM,gBAAgB,MAAM;IAMnE;;;;OAIG;sBACe,MAAM,QAAQ,MAAM;IAoBtC;;;OAGG;gBACS,SAAS;IAOrB;;;;;;OAMG;cACO,SAAS;wGAclB,CAAA"}

package/dist/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.d.ts

@@ -0,0 +1,12 @@
+import { BaseAdapter, type BaseRefNameAliasAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type RpcServer from 'librpc-web-mod/dist/server';
+import type { RefNameAliases } from './../BackendDrivers/BackendDriver';
+declare global {
+    const rpcServer: RpcServer;
+}
+export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
+    private refNameAliases;
+    getRefNameAliases(): Promise<RefNameAliases[]>;
+    freeResources(): void;
+}
+//# sourceMappingURL=ApolloRefNameAliasAdapter.d.ts.map

package/dist/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ApolloRefNameAliasAdapter.d.ts","sourceRoot":"","sources":["../../src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts"],"names":[],"mappings":"AACA,OAAO,EACL,WAAW,EACX,KAAK,uBAAuB,EAC7B,MAAM,yCAAyC,CAAA;AAChD,OAAO,KAAK,SAAS,MAAM,4BAA4B,CAAA;AAKvD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,mCAAmC,CAAA;AAEvE,OAAO,CAAC,MAAM,CAAC;IACb,MAAM,SAAS,EAAE,SAAS,CAAA;CAC3B;AAsBD,MAAM,CAAC,OAAO,OAAO,mBACnB,SAAQ,WACR,YAAW,uBAAuB;IAElC,OAAO,CAAC,cAAc,CAA8B;IAE9C,iBAAiB;IAkDvB,aAAa;CAGd"}

package/dist/ApolloRefNameAliasAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function installApolloRefNameAliasAdapter(pluginManager: PluginManager): void;
+//# sourceMappingURL=index.d.ts.map

package/dist/ApolloRefNameAliasAdapter/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/ApolloRefNameAliasAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,aAAa,MAAM,6BAA6B,CAAA;AAM5D,wBAAgB,gCAAgC,CAAC,aAAa,EAAE,aAAa,QAc5E"}

package/dist/ApolloSequenceAdapter/ApolloSequenceAdapter.d.ts

@@ -0,0 +1,27 @@
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { type Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
+export interface RefSeq {
+    _id: string;
+    name: string;
+    description: string;
+    length: number;
+}
+export declare class ApolloSequenceAdapter extends BaseSequenceAdapter {
+    private regions;
+    getRefNames(): Promise<string[]>;
+    getRegions(): Promise<NoAssemblyRegion[]>;
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region: Region): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the foreseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}
+//# sourceMappingURL=ApolloSequenceAdapter.d.ts.map

package/dist/ApolloSequenceAdapter/ApolloSequenceAdapter.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ApolloSequenceAdapter.d.ts","sourceRoot":"","sources":["../../src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAA;AAE7E,OAAsB,EAAE,KAAK,OAAO,EAAE,MAAM,kCAAkC,CAAA;AAC9E,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,EAAE,MAAM,0BAA0B,CAAA;AASxE,MAAM,WAAW,MAAM;IACrB,GAAG,EAAE,MAAM,CAAA;IACX,IAAI,EAAE,MAAM,CAAA;IACZ,WAAW,EAAE,MAAM,CAAA;IACnB,MAAM,EAAE,MAAM,CAAA;CACf;AAoBD,qBAAa,qBAAsB,SAAQ,mBAAmB;IAC5D,OAAO,CAAC,OAAO,CAAgC;IAElC,WAAW;IAKX,UAAU,IAAI,OAAO,CAAC,gBAAgB,EAAE,CAAC;IAuDtD;;;;OAIG;IACI,WAAW,CAAC,MAAM,EAAE,MAAM;IAoFjC;;;;OAIG;IAEI,aAAa,IAAoB,IAAI;CAC7C"}

package/dist/ApolloSequenceAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function installApolloSequenceAdapter(pluginManager: PluginManager): void;
+//# sourceMappingURL=index.d.ts.map

package/dist/ApolloSequenceAdapter/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/ApolloSequenceAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,aAAa,MAAM,6BAA6B,CAAA;AAM5D,wBAAgB,4BAA4B,CAAC,aAAa,EAAE,aAAa,QAcxE"}

package/dist/ApolloTextSearchAdapter/ApolloTextSearchAdapter.d.ts

@@ -0,0 +1,13 @@
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { BaseAdapter, type BaseTextSearchAdapter, type BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
+export declare class ApolloTextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
+    get baseURL(): string;
+    get trackId(): string;
+    get assemblyNames(): string[];
+    mapBaseResult(features: AnnotationFeatureSnapshot[], assembly: Assembly, query: string): BaseResult[];
+    searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
+    freeResources(): void;
+}
+//# sourceMappingURL=ApolloTextSearchAdapter.d.ts.map

package/dist/ApolloTextSearchAdapter/ApolloTextSearchAdapter.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ApolloTextSearchAdapter.d.ts","sourceRoot":"","sources":["../../src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAA;AACvE,OAAO,UAAU,MAAM,sCAAsC,CAAA;AAC7D,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,wCAAwC,CAAA;AAEtE,OAAO,EACL,WAAW,EACX,KAAK,qBAAqB,EAC1B,KAAK,kBAAkB,EACxB,MAAM,yCAAyC,CAAA;AA0BhD,qBAAa,uBACX,SAAQ,WACR,YAAW,qBAAqB;IAEhC,IAAI,OAAO,WAEV;IAED,IAAI,OAAO,IACwC,MAAM,CACxD;IAED,IAAI,aAAa,IACwC,MAAM,EAAE,CAChE;IAED,aAAa,CACX,QAAQ,EAAE,yBAAyB,EAAE,EACrC,QAAQ,EAAE,QAAQ,EAClB,KAAK,EAAE,MAAM;IAcT,WAAW,CAAC,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,UAAU,EAAE,CAAC;IA2BlE,aAAa;CACd"}

package/dist/ApolloTextSearchAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function installApolloTextSearchAdapter(pluginManager: PluginManager): void;
+//# sourceMappingURL=index.d.ts.map

package/dist/ApolloTextSearchAdapter/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/ApolloTextSearchAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,aAAa,MAAM,6BAA6B,CAAA;AAM5D,wBAAgB,8BAA8B,CAAC,aAAa,EAAE,aAAa,QAW1E"}

package/dist/BackendDrivers/BackendDriver.d.ts

@@ -0,0 +1,26 @@
+import type { Change, ClientDataStore } from '@apollo-annotation/common';
+import type { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
+import type { ValidationResultSet } from '@apollo-annotation/shared';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { Region } from '@jbrowse/core/util';
+import type { SubmitOpts } from '../ChangeManager';
+export interface RefNameAliases {
+    refName: string;
+    aliases: string[];
+    uniqueId: string;
+}
+export declare abstract class BackendDriver {
+    protected clientStore: ClientDataStore;
+    constructor(clientStore: ClientDataStore);
+    abstract getFeatures(region: Region): Promise<[AnnotationFeatureSnapshot[], CheckResultSnapshot[]]>;
+    abstract getSequence(region: Region): Promise<{
+        seq: string;
+        refSeq: string;
+    }>;
+    abstract getRegions(assemblyName: string): Promise<Region[]>;
+    abstract getAssemblies(internetAccountConfigId?: string): Assembly[];
+    abstract getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]>;
+    abstract submitChange(change: Change, opts: SubmitOpts): Promise<ValidationResultSet>;
+    abstract searchFeatures(term: string, assemblies: string[]): Promise<AnnotationFeatureSnapshot[]>;
+}
+//# sourceMappingURL=BackendDriver.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"BackendDriver.d.ts","sourceRoot":"","sources":["../../src/BackendDrivers/BackendDriver.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AACxE,OAAO,KAAK,EACV,yBAAyB,EACzB,mBAAmB,EACpB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAA;AACpE,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,wCAAwC,CAAA;AACtE,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAEhD,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAA;AAElD,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,MAAM,CAAA;IACf,OAAO,EAAE,MAAM,EAAE,CAAA;IACjB,QAAQ,EAAE,MAAM,CAAA;CACjB;AAED,8BAAsB,aAAa;IACrB,SAAS,CAAC,WAAW,EAAE,eAAe;gBAA5B,WAAW,EAAE,eAAe;IAElD,QAAQ,CAAC,WAAW,CAClB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,CAAC,yBAAyB,EAAE,EAAE,mBAAmB,EAAE,CAAC,CAAC;IAEhE,QAAQ,CAAC,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;QAAE,GAAG,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;IAE9E,QAAQ,CAAC,UAAU,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAE5D,QAAQ,CAAC,aAAa,CAAC,uBAAuB,CAAC,EAAE,MAAM,GAAG,QAAQ,EAAE;IAEpE,QAAQ,CAAC,iBAAiB,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAE3E,QAAQ,CAAC,YAAY,CACnB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,UAAU,GACf,OAAO,CAAC,mBAAmB,CAAC;IAE/B,QAAQ,CAAC,cAAc,CACrB,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,yBAAyB,EAAE,CAAC;CACxC"}

package/dist/BackendDrivers/CollaborationServerDriver.d.ts

@@ -0,0 +1,206 @@
+import { type AssemblySpecificChange, Change } from '@apollo-annotation/common';
+import type { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
+import { ValidationResultSet } from '@apollo-annotation/shared';
+import type { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes';
+import { type Region } from '@jbrowse/core/util';
+import type { Socket } from 'socket.io-client';
+import { type SubmitOpts } from '../ChangeManager';
+import { BackendDriver, type RefNameAliases } from './BackendDriver';
+export interface ApolloRefSeqResponse {
+    _id: string;
+    name: string;
+    description?: string;
+    aliases: string[];
+    length: string;
+    assembly: string;
+}
+interface RefSeq {
+    refName: string;
+    id: string;
+    aliases: string[];
+}
+type RefSeqMap = Map<string, RefSeq>;
+export interface ApolloInternetAccount extends BaseInternetAccountModel {
+    baseURL: string;
+    socket: Socket;
+    setLastChangeSequenceNumber(sequenceNumber: number): void;
+    getMissingChanges(): void;
+}
+export declare class CollaborationServerDriver extends BackendDriver {
+    private inFlight;
+    private refSeqMaps;
+    private fetch;
+    searchFeatures(term: string, assemblies: string[]): Promise<AnnotationFeatureSnapshot[]>;
+    /**
+     * Call backend endpoint to get features by criteria
+     * @param region -  Searchable region containing refSeq, start and end
+     * @returns
+     */
+    getFeatures(region: Region): Promise<[AnnotationFeatureSnapshot[], CheckResultSnapshot[]]>;
+    /**
+     * Checks if there is assembly-refSeq specific socket. If not, it opens one
+     * @param assembly - assemblyId
+     * @param refSeq - refSeqName
+     * @param internetAccount - internet account
+     */
+    checkSocket(assembly: string, refSeq: string, internetAccount: ApolloInternetAccount): void;
+    private haveDataForChange;
+    /**
+     * Call backend endpoint to get sequence by criteria
+     * @param region -  Searchable region containing refSeq, start and end
+     * @returns
+     */
+    getSequence(region: Region): Promise<{
+        seq: string;
+        refSeq: string;
+    }>;
+    private getSeqFromServer;
+    getRefSeqMapping(assemblyName: string): Promise<RefSeqMap>;
+    getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]>;
+    getRefSeqId(assemblyName: string, refName: string): Promise<string | undefined>;
+    getRegions(assemblyName: string): Promise<Region[]>;
+    getAssemblies(internetAccountId?: string): ({
+        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, opts?: SubmitOpts): Promise<ValidationResultSet>;
+}
+export {};
+//# sourceMappingURL=CollaborationServerDriver.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/BackendDrivers/DesktopFileDriver.d.ts

@@ -0,0 +1,160 @@
+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

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