@jbrowse/embedded-core 4.3.0 → 5.0.0-beta.10
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/esm/EmbeddedSessionMixin.d.ts +2818 -0
- package/esm/EmbeddedSessionMixin.js +61 -0
- package/esm/EmbeddedSessionThemeMixin.d.ts +1448 -0
- package/esm/EmbeddedSessionThemeMixin.js +113 -0
- package/esm/createEmbeddedRootModel.d.ts +1638 -0
- package/esm/createEmbeddedRootModel.js +126 -0
- package/esm/index.d.ts +4 -1
- package/esm/index.js +4 -2
- package/esm/ui/EmbeddedViewContainer.d.ts +3 -3
- package/esm/ui/EmbeddedViewContainer.js +14 -18
- package/package.json +12 -14
- package/esm/ui/ModalWidget.d.ts +0 -5
- package/esm/ui/ModalWidget.js +0 -32
- package/esm/ui/VersionAboutDialog.d.ts +0 -5
- package/esm/ui/VersionAboutDialog.js +0 -13
- package/esm/ui/ViewMenu.d.ts +0 -8
- package/esm/ui/ViewMenu.js +0 -8
- package/esm/ui/ViewTitle.d.ts +0 -5
- package/esm/ui/ViewTitle.js +0 -47
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@@ -0,0 +1,1638 @@
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import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
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import RpcManager from '@jbrowse/core/rpc/RpcManager';
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import type PluginManager from '@jbrowse/core/PluginManager';
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import type { IAnyModelType, SnapshotIn } from '@jbrowse/mobx-state-tree';
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import type { SessionSnapshot } from '@jbrowse/product-core';
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interface SessionWithSetName {
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setName: (name: string) => void;
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}
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/**
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* #stateModel EmbeddedRootModel
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* #category root
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* Root model shared by the single-view embedded products
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* (react-linear-genome-view, react-circular-genome-view). Each product supplies
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* its own model name, version, and session model, and may `.props()` on extra
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* fields (e.g. the LGV `disableAddTracks`/`drawerViewHeight`). Internet accounts
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* come from the same product-core mixin the web/desktop root models use, so
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* config `internetAccounts` are auto-initialized (no manual wiring needed).
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*/
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export declare function createEmbeddedRootModel<SESSION extends IAnyModelType & {
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Type: SessionWithSetName;
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}>({ name, version, pluginManager, sessionModelType, makeWorkerInstance, }: {
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name: string;
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version: string;
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pluginManager: PluginManager;
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sessionModelType: SESSION;
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makeWorkerInstance?: () => Worker;
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}): import("@jbrowse/mobx-state-tree").IModelType<Omit<import("@jbrowse/mobx-state-tree").ModelPropertiesDeclarationToProperties<{
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/**
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* #property
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*/
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config: import("@jbrowse/mobx-state-tree").IModelType<{
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configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly defaultDriver: {
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type: "string";
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} & {
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defaultValue: string;
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};
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readonly workerCount: {
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type: "number";
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} & {
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defaultValue: number;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly trackNames: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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readonly categories: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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readonly defaultFolderCategories: {
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type: "stringArray";
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} & {
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defaultValue: unknown;
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};
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readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly categoryNames: {
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type: "stringArray";
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} & {
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defaultValue: unknown;
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};
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readonly topLevelCategories: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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readonly subCategories: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly animationMode: {
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type: "stringEnum";
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} & {
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model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
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} & {
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defaultValue: string;
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};
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readonly scrollZoom: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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readonly numberGrouping: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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readonly useWorkspaces: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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readonly developerMode: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly feature: {
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type: "frozen";
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} & {
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defaultValue: unknown;
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};
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readonly subfeatures: {
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type: "frozen";
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} & {
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defaultValue: unknown;
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};
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readonly depth: {
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type: "maybeNumber";
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};
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readonly maxDepth: {
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type: "maybeNumber";
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly config: {
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type: "frozen";
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} & {
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defaultValue: unknown;
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};
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readonly hideUris: {
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type: "boolean";
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} & {
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defaultValue: boolean;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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readonly theme: {
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type: "frozen";
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} & {
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defaultValue: unknown;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
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assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
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tracks: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown>[] | null | undefined, Record<string, unknown>[], Record<string, unknown>[]>;
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internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
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connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
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aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
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plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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}, {
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readonly assemblyNames: string[];
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readonly rpcManager: RpcManager;
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}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
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/**
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* #property
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*/
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session: SESSION;
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/**
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* #property
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*/
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assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
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assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
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configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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}, {
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error: unknown;
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loadingP: Promise<void> | undefined;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
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} & {
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getConf(arg: string): any;
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} & {
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readonly name: string;
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readonly aliases: string[];
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readonly displayName: string;
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readonly refNameColors: string[];
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} & {
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readonly allAliases: string[];
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hasName(name: string): boolean;
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} & {
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setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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} & {
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setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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regions: import("@jbrowse/core/util").Region[];
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cytobands: import("@jbrowse/core/util").Feature[];
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geneticCodes: Record<string, number>;
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}): void;
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setError(e: unknown): void;
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setLoadingP(p?: Promise<void>): void;
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loadPre(): Promise<void>;
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} & {
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load(): Promise<void>;
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} & {
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afterAttach(): void;
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} & {
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readonly initialized: boolean;
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readonly allRefNames: string[] | undefined;
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readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
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readonly rpcManager: RpcManager;
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} & {
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readonly refNames: string[] | undefined;
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} & {
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readonly refNameToIndex: Map<string, number> | undefined;
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} & {
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getCanonicalRefName(refName: string): string | undefined;
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getRefNameColor(refName: string): string | undefined;
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getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
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getGeneticCodeId(refName: string): number;
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getSeqAdapterRefName(canonicalRefName: string): string;
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} & {
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getCanonicalRefName2(refName: string): string;
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isValidRefName(refName: string): boolean;
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} & {
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getRefNamePosition(refName: string): number | undefined;
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getAliasesForRefName(refName: string): string[];
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getRefNameMapForAdapter(adapterConf: {
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[x: string]: unknown;
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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}, {
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unrecognizedReports: {
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report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
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reportFor(session: unknown, name: string): {
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handled: boolean;
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claim?: Promise<void>;
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} | undefined;
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};
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} & {
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readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
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} & {
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getCanonicalAssemblyName(asmName: string): string | undefined;
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getDisplayName(asmName: string): string;
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get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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}> & {
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error: unknown;
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loadingP: Promise<void> | undefined;
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adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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loadedGeneticCodes: Record<string, number> | undefined;
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lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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statusMessage: string | undefined;
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statusProgress: number | undefined;
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statusSource: string | undefined;
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refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
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} & {
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getConf(arg: string): any;
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} & {
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readonly name: string;
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readonly aliases: string[];
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+
readonly displayName: string;
|
|
267
|
+
readonly refNameColors: string[];
|
|
268
|
+
} & {
|
|
269
|
+
readonly allAliases: string[];
|
|
270
|
+
hasName(name: string): boolean;
|
|
271
|
+
} & {
|
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272
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
273
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
274
|
+
} & {
|
|
275
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
276
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
277
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
278
|
+
geneticCodes: Record<string, number>;
|
|
279
|
+
}): void;
|
|
280
|
+
setError(e: unknown): void;
|
|
281
|
+
setLoadingP(p?: Promise<void>): void;
|
|
282
|
+
loadPre(): Promise<void>;
|
|
283
|
+
} & {
|
|
284
|
+
load(): Promise<void>;
|
|
285
|
+
} & {
|
|
286
|
+
afterAttach(): void;
|
|
287
|
+
} & {
|
|
288
|
+
readonly initialized: boolean;
|
|
289
|
+
readonly allRefNames: string[] | undefined;
|
|
290
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
291
|
+
readonly rpcManager: RpcManager;
|
|
292
|
+
} & {
|
|
293
|
+
readonly refNames: string[] | undefined;
|
|
294
|
+
} & {
|
|
295
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
296
|
+
} & {
|
|
297
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
298
|
+
getRefNameColor(refName: string): string | undefined;
|
|
299
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
300
|
+
getGeneticCodeId(refName: string): number;
|
|
301
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
302
|
+
} & {
|
|
303
|
+
getCanonicalRefName2(refName: string): string;
|
|
304
|
+
isValidRefName(refName: string): boolean;
|
|
305
|
+
} & {
|
|
306
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
307
|
+
getAliasesForRefName(refName: string): string[];
|
|
308
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
309
|
+
[x: string]: unknown;
|
|
310
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
311
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
312
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
313
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
314
|
+
}, {
|
|
315
|
+
error: unknown;
|
|
316
|
+
loadingP: Promise<void> | undefined;
|
|
317
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
318
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
319
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
320
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
321
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
322
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
323
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
324
|
+
statusMessage: string | undefined;
|
|
325
|
+
statusProgress: number | undefined;
|
|
326
|
+
statusSource: string | undefined;
|
|
327
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
328
|
+
} & {
|
|
329
|
+
getConf(arg: string): any;
|
|
330
|
+
} & {
|
|
331
|
+
readonly name: string;
|
|
332
|
+
readonly aliases: string[];
|
|
333
|
+
readonly displayName: string;
|
|
334
|
+
readonly refNameColors: string[];
|
|
335
|
+
} & {
|
|
336
|
+
readonly allAliases: string[];
|
|
337
|
+
hasName(name: string): boolean;
|
|
338
|
+
} & {
|
|
339
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
340
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
341
|
+
} & {
|
|
342
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
343
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
344
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
345
|
+
geneticCodes: Record<string, number>;
|
|
346
|
+
}): void;
|
|
347
|
+
setError(e: unknown): void;
|
|
348
|
+
setLoadingP(p?: Promise<void>): void;
|
|
349
|
+
loadPre(): Promise<void>;
|
|
350
|
+
} & {
|
|
351
|
+
load(): Promise<void>;
|
|
352
|
+
} & {
|
|
353
|
+
afterAttach(): void;
|
|
354
|
+
} & {
|
|
355
|
+
readonly initialized: boolean;
|
|
356
|
+
readonly allRefNames: string[] | undefined;
|
|
357
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
358
|
+
readonly rpcManager: RpcManager;
|
|
359
|
+
} & {
|
|
360
|
+
readonly refNames: string[] | undefined;
|
|
361
|
+
} & {
|
|
362
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
363
|
+
} & {
|
|
364
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
365
|
+
getRefNameColor(refName: string): string | undefined;
|
|
366
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
367
|
+
getGeneticCodeId(refName: string): number;
|
|
368
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
369
|
+
} & {
|
|
370
|
+
getCanonicalRefName2(refName: string): string;
|
|
371
|
+
isValidRefName(refName: string): boolean;
|
|
372
|
+
} & {
|
|
373
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
374
|
+
getAliasesForRefName(refName: string): string[];
|
|
375
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
376
|
+
[x: string]: unknown;
|
|
377
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
378
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
379
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
|
|
380
|
+
has(asmName: string): boolean;
|
|
381
|
+
loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
382
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
383
|
+
}> & {
|
|
384
|
+
error: unknown;
|
|
385
|
+
loadingP: Promise<void> | undefined;
|
|
386
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
387
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
388
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
389
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
390
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
391
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
392
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
393
|
+
statusMessage: string | undefined;
|
|
394
|
+
statusProgress: number | undefined;
|
|
395
|
+
statusSource: string | undefined;
|
|
396
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
397
|
+
} & {
|
|
398
|
+
getConf(arg: string): any;
|
|
399
|
+
} & {
|
|
400
|
+
readonly name: string;
|
|
401
|
+
readonly aliases: string[];
|
|
402
|
+
readonly displayName: string;
|
|
403
|
+
readonly refNameColors: string[];
|
|
404
|
+
} & {
|
|
405
|
+
readonly allAliases: string[];
|
|
406
|
+
hasName(name: string): boolean;
|
|
407
|
+
} & {
|
|
408
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
409
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
410
|
+
} & {
|
|
411
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
412
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
413
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
414
|
+
geneticCodes: Record<string, number>;
|
|
415
|
+
}): void;
|
|
416
|
+
setError(e: unknown): void;
|
|
417
|
+
setLoadingP(p?: Promise<void>): void;
|
|
418
|
+
loadPre(): Promise<void>;
|
|
419
|
+
} & {
|
|
420
|
+
load(): Promise<void>;
|
|
421
|
+
} & {
|
|
422
|
+
afterAttach(): void;
|
|
423
|
+
} & {
|
|
424
|
+
readonly initialized: boolean;
|
|
425
|
+
readonly allRefNames: string[] | undefined;
|
|
426
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
427
|
+
readonly rpcManager: RpcManager;
|
|
428
|
+
} & {
|
|
429
|
+
readonly refNames: string[] | undefined;
|
|
430
|
+
} & {
|
|
431
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
432
|
+
} & {
|
|
433
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
434
|
+
getRefNameColor(refName: string): string | undefined;
|
|
435
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
436
|
+
getGeneticCodeId(refName: string): number;
|
|
437
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
438
|
+
} & {
|
|
439
|
+
getCanonicalRefName2(refName: string): string;
|
|
440
|
+
isValidRefName(refName: string): boolean;
|
|
441
|
+
} & {
|
|
442
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
443
|
+
getAliasesForRefName(refName: string): string[];
|
|
444
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
445
|
+
[x: string]: unknown;
|
|
446
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
447
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
448
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
449
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
450
|
+
}, {
|
|
451
|
+
error: unknown;
|
|
452
|
+
loadingP: Promise<void> | undefined;
|
|
453
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
454
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
455
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
456
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
457
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
458
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
459
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
460
|
+
statusMessage: string | undefined;
|
|
461
|
+
statusProgress: number | undefined;
|
|
462
|
+
statusSource: string | undefined;
|
|
463
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
464
|
+
} & {
|
|
465
|
+
getConf(arg: string): any;
|
|
466
|
+
} & {
|
|
467
|
+
readonly name: string;
|
|
468
|
+
readonly aliases: string[];
|
|
469
|
+
readonly displayName: string;
|
|
470
|
+
readonly refNameColors: string[];
|
|
471
|
+
} & {
|
|
472
|
+
readonly allAliases: string[];
|
|
473
|
+
hasName(name: string): boolean;
|
|
474
|
+
} & {
|
|
475
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
476
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
477
|
+
} & {
|
|
478
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
479
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
480
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
481
|
+
geneticCodes: Record<string, number>;
|
|
482
|
+
}): void;
|
|
483
|
+
setError(e: unknown): void;
|
|
484
|
+
setLoadingP(p?: Promise<void>): void;
|
|
485
|
+
loadPre(): Promise<void>;
|
|
486
|
+
} & {
|
|
487
|
+
load(): Promise<void>;
|
|
488
|
+
} & {
|
|
489
|
+
afterAttach(): void;
|
|
490
|
+
} & {
|
|
491
|
+
readonly initialized: boolean;
|
|
492
|
+
readonly allRefNames: string[] | undefined;
|
|
493
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
494
|
+
readonly rpcManager: RpcManager;
|
|
495
|
+
} & {
|
|
496
|
+
readonly refNames: string[] | undefined;
|
|
497
|
+
} & {
|
|
498
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
499
|
+
} & {
|
|
500
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
501
|
+
getRefNameColor(refName: string): string | undefined;
|
|
502
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
503
|
+
getGeneticCodeId(refName: string): number;
|
|
504
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
505
|
+
} & {
|
|
506
|
+
getCanonicalRefName2(refName: string): string;
|
|
507
|
+
isValidRefName(refName: string): boolean;
|
|
508
|
+
} & {
|
|
509
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
510
|
+
getAliasesForRefName(refName: string): string[];
|
|
511
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
512
|
+
[x: string]: unknown;
|
|
513
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
514
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
515
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
|
|
516
|
+
readonly assemblyNamesList: string[];
|
|
517
|
+
readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
|
|
518
|
+
readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
|
|
519
|
+
readonly rpcManager: RpcManager;
|
|
520
|
+
} & {
|
|
521
|
+
settleAssemblyResolution(assemblyName: string): Promise<void>;
|
|
522
|
+
} & {
|
|
523
|
+
waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
524
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
525
|
+
}> & {
|
|
526
|
+
error: unknown;
|
|
527
|
+
loadingP: Promise<void> | undefined;
|
|
528
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
529
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
530
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
531
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
532
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
533
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
534
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
535
|
+
statusMessage: string | undefined;
|
|
536
|
+
statusProgress: number | undefined;
|
|
537
|
+
statusSource: string | undefined;
|
|
538
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
539
|
+
} & {
|
|
540
|
+
getConf(arg: string): any;
|
|
541
|
+
} & {
|
|
542
|
+
readonly name: string;
|
|
543
|
+
readonly aliases: string[];
|
|
544
|
+
readonly displayName: string;
|
|
545
|
+
readonly refNameColors: string[];
|
|
546
|
+
} & {
|
|
547
|
+
readonly allAliases: string[];
|
|
548
|
+
hasName(name: string): boolean;
|
|
549
|
+
} & {
|
|
550
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
551
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
552
|
+
} & {
|
|
553
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
554
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
555
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
556
|
+
geneticCodes: Record<string, number>;
|
|
557
|
+
}): void;
|
|
558
|
+
setError(e: unknown): void;
|
|
559
|
+
setLoadingP(p?: Promise<void>): void;
|
|
560
|
+
loadPre(): Promise<void>;
|
|
561
|
+
} & {
|
|
562
|
+
load(): Promise<void>;
|
|
563
|
+
} & {
|
|
564
|
+
afterAttach(): void;
|
|
565
|
+
} & {
|
|
566
|
+
readonly initialized: boolean;
|
|
567
|
+
readonly allRefNames: string[] | undefined;
|
|
568
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
569
|
+
readonly rpcManager: RpcManager;
|
|
570
|
+
} & {
|
|
571
|
+
readonly refNames: string[] | undefined;
|
|
572
|
+
} & {
|
|
573
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
574
|
+
} & {
|
|
575
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
576
|
+
getRefNameColor(refName: string): string | undefined;
|
|
577
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
578
|
+
getGeneticCodeId(refName: string): number;
|
|
579
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
580
|
+
} & {
|
|
581
|
+
getCanonicalRefName2(refName: string): string;
|
|
582
|
+
isValidRefName(refName: string): boolean;
|
|
583
|
+
} & {
|
|
584
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
585
|
+
getAliasesForRefName(refName: string): string[];
|
|
586
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
587
|
+
[x: string]: unknown;
|
|
588
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
589
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
590
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
591
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
592
|
+
}, {
|
|
593
|
+
error: unknown;
|
|
594
|
+
loadingP: Promise<void> | undefined;
|
|
595
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
596
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
597
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
598
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
599
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
600
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
601
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
602
|
+
statusMessage: string | undefined;
|
|
603
|
+
statusProgress: number | undefined;
|
|
604
|
+
statusSource: string | undefined;
|
|
605
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
606
|
+
} & {
|
|
607
|
+
getConf(arg: string): any;
|
|
608
|
+
} & {
|
|
609
|
+
readonly name: string;
|
|
610
|
+
readonly aliases: string[];
|
|
611
|
+
readonly displayName: string;
|
|
612
|
+
readonly refNameColors: string[];
|
|
613
|
+
} & {
|
|
614
|
+
readonly allAliases: string[];
|
|
615
|
+
hasName(name: string): boolean;
|
|
616
|
+
} & {
|
|
617
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
618
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
619
|
+
} & {
|
|
620
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
621
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
622
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
623
|
+
geneticCodes: Record<string, number>;
|
|
624
|
+
}): void;
|
|
625
|
+
setError(e: unknown): void;
|
|
626
|
+
setLoadingP(p?: Promise<void>): void;
|
|
627
|
+
loadPre(): Promise<void>;
|
|
628
|
+
} & {
|
|
629
|
+
load(): Promise<void>;
|
|
630
|
+
} & {
|
|
631
|
+
afterAttach(): void;
|
|
632
|
+
} & {
|
|
633
|
+
readonly initialized: boolean;
|
|
634
|
+
readonly allRefNames: string[] | undefined;
|
|
635
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
636
|
+
readonly rpcManager: RpcManager;
|
|
637
|
+
} & {
|
|
638
|
+
readonly refNames: string[] | undefined;
|
|
639
|
+
} & {
|
|
640
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
641
|
+
} & {
|
|
642
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
643
|
+
getRefNameColor(refName: string): string | undefined;
|
|
644
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
645
|
+
getGeneticCodeId(refName: string): number;
|
|
646
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
647
|
+
} & {
|
|
648
|
+
getCanonicalRefName2(refName: string): string;
|
|
649
|
+
isValidRefName(refName: string): boolean;
|
|
650
|
+
} & {
|
|
651
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
652
|
+
getAliasesForRefName(refName: string): string[];
|
|
653
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
654
|
+
[x: string]: unknown;
|
|
655
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
656
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
657
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
|
|
658
|
+
requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
659
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
660
|
+
}> & {
|
|
661
|
+
error: unknown;
|
|
662
|
+
loadingP: Promise<void> | undefined;
|
|
663
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
664
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
665
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
666
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
667
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
668
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
669
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
670
|
+
statusMessage: string | undefined;
|
|
671
|
+
statusProgress: number | undefined;
|
|
672
|
+
statusSource: string | undefined;
|
|
673
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
674
|
+
} & {
|
|
675
|
+
getConf(arg: string): any;
|
|
676
|
+
} & {
|
|
677
|
+
readonly name: string;
|
|
678
|
+
readonly aliases: string[];
|
|
679
|
+
readonly displayName: string;
|
|
680
|
+
readonly refNameColors: string[];
|
|
681
|
+
} & {
|
|
682
|
+
readonly allAliases: string[];
|
|
683
|
+
hasName(name: string): boolean;
|
|
684
|
+
} & {
|
|
685
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
686
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
687
|
+
} & {
|
|
688
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
689
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
690
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
691
|
+
geneticCodes: Record<string, number>;
|
|
692
|
+
}): void;
|
|
693
|
+
setError(e: unknown): void;
|
|
694
|
+
setLoadingP(p?: Promise<void>): void;
|
|
695
|
+
loadPre(): Promise<void>;
|
|
696
|
+
} & {
|
|
697
|
+
load(): Promise<void>;
|
|
698
|
+
} & {
|
|
699
|
+
afterAttach(): void;
|
|
700
|
+
} & {
|
|
701
|
+
readonly initialized: boolean;
|
|
702
|
+
readonly allRefNames: string[] | undefined;
|
|
703
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
704
|
+
readonly rpcManager: RpcManager;
|
|
705
|
+
} & {
|
|
706
|
+
readonly refNames: string[] | undefined;
|
|
707
|
+
} & {
|
|
708
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
709
|
+
} & {
|
|
710
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
711
|
+
getRefNameColor(refName: string): string | undefined;
|
|
712
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
713
|
+
getGeneticCodeId(refName: string): number;
|
|
714
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
715
|
+
} & {
|
|
716
|
+
getCanonicalRefName2(refName: string): string;
|
|
717
|
+
isValidRefName(refName: string): boolean;
|
|
718
|
+
} & {
|
|
719
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
720
|
+
getAliasesForRefName(refName: string): string[];
|
|
721
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
722
|
+
[x: string]: unknown;
|
|
723
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
724
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
725
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
726
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
727
|
+
}, {
|
|
728
|
+
error: unknown;
|
|
729
|
+
loadingP: Promise<void> | undefined;
|
|
730
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
731
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
732
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
733
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
734
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
735
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
736
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
737
|
+
statusMessage: string | undefined;
|
|
738
|
+
statusProgress: number | undefined;
|
|
739
|
+
statusSource: string | undefined;
|
|
740
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
741
|
+
} & {
|
|
742
|
+
getConf(arg: string): any;
|
|
743
|
+
} & {
|
|
744
|
+
readonly name: string;
|
|
745
|
+
readonly aliases: string[];
|
|
746
|
+
readonly displayName: string;
|
|
747
|
+
readonly refNameColors: string[];
|
|
748
|
+
} & {
|
|
749
|
+
readonly allAliases: string[];
|
|
750
|
+
hasName(name: string): boolean;
|
|
751
|
+
} & {
|
|
752
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
753
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
754
|
+
} & {
|
|
755
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
756
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
757
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
758
|
+
geneticCodes: Record<string, number>;
|
|
759
|
+
}): void;
|
|
760
|
+
setError(e: unknown): void;
|
|
761
|
+
setLoadingP(p?: Promise<void>): void;
|
|
762
|
+
loadPre(): Promise<void>;
|
|
763
|
+
} & {
|
|
764
|
+
load(): Promise<void>;
|
|
765
|
+
} & {
|
|
766
|
+
afterAttach(): void;
|
|
767
|
+
} & {
|
|
768
|
+
readonly initialized: boolean;
|
|
769
|
+
readonly allRefNames: string[] | undefined;
|
|
770
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
771
|
+
readonly rpcManager: RpcManager;
|
|
772
|
+
} & {
|
|
773
|
+
readonly refNames: string[] | undefined;
|
|
774
|
+
} & {
|
|
775
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
776
|
+
} & {
|
|
777
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
778
|
+
getRefNameColor(refName: string): string | undefined;
|
|
779
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
780
|
+
getGeneticCodeId(refName: string): number;
|
|
781
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
782
|
+
} & {
|
|
783
|
+
getCanonicalRefName2(refName: string): string;
|
|
784
|
+
isValidRefName(refName: string): boolean;
|
|
785
|
+
} & {
|
|
786
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
787
|
+
getAliasesForRefName(refName: string): string[];
|
|
788
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
789
|
+
[x: string]: unknown;
|
|
790
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
791
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
792
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
|
|
793
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
794
|
+
[x: string]: unknown;
|
|
795
|
+
}, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
796
|
+
isValidRefName(refName: string, assemblyName: string): boolean;
|
|
797
|
+
} & {
|
|
798
|
+
afterAttach(): void;
|
|
799
|
+
removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
|
|
800
|
+
addAssembly(configuration: any): void;
|
|
801
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
|
|
802
|
+
}>, "internetAccounts"> & {
|
|
803
|
+
internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
|
|
804
|
+
}, {
|
|
805
|
+
/**
|
|
806
|
+
* #volatile
|
|
807
|
+
*/
|
|
808
|
+
adminMode: boolean;
|
|
809
|
+
/**
|
|
810
|
+
* #volatile
|
|
811
|
+
*/
|
|
812
|
+
version: string;
|
|
813
|
+
/**
|
|
814
|
+
* #volatile
|
|
815
|
+
*/
|
|
816
|
+
rpcManager: RpcManager;
|
|
817
|
+
/**
|
|
818
|
+
* #volatile
|
|
819
|
+
*/
|
|
820
|
+
textSearchManager: TextSearchManager;
|
|
821
|
+
} & {
|
|
822
|
+
/**
|
|
823
|
+
* #action
|
|
824
|
+
* Synchronous: an async caller must
|
|
825
|
+
* `await pluginManager.preloadSessionTypes(snapshot)` first.
|
|
826
|
+
*/
|
|
827
|
+
setSession(sessionSnapshot: SnapshotIn<SESSION>): void;
|
|
828
|
+
/**
|
|
829
|
+
* #action
|
|
830
|
+
* Load a session whose shape is only known at runtime — decoded from a
|
|
831
|
+
* URL, read back from storage, handed over by a non-TypeScript host.
|
|
832
|
+
*
|
|
833
|
+
* Separate from `setSession` because that one takes the compiler-checked
|
|
834
|
+
* snapshot type, which a value parsed out of JSON can never satisfy.
|
|
835
|
+
* The assertion below is the whole reason this exists: it is the single
|
|
836
|
+
* place the conversion happens, instead of every caller asserting at its
|
|
837
|
+
* own site. Nothing is unchecked at runtime — MST validates the snapshot
|
|
838
|
+
* as it applies it and throws on a mismatch, which is the check that
|
|
839
|
+
* actually matters for a value this app did not author.
|
|
840
|
+
*/
|
|
841
|
+
restoreSession(sessionSnapshot: SessionSnapshot): void;
|
|
842
|
+
/**
|
|
843
|
+
* #action
|
|
844
|
+
*/
|
|
845
|
+
renameCurrentSession(sessionName: string): void;
|
|
846
|
+
} & {
|
|
847
|
+
/**
|
|
848
|
+
* #getter
|
|
849
|
+
*/
|
|
850
|
+
readonly jbrowse: import("@jbrowse/mobx-state-tree").ModelPropertiesDeclarationToProperties<{
|
|
851
|
+
/**
|
|
852
|
+
* #property
|
|
853
|
+
*/
|
|
854
|
+
config: import("@jbrowse/mobx-state-tree").IModelType<{
|
|
855
|
+
configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
856
|
+
readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
857
|
+
readonly defaultDriver: {
|
|
858
|
+
type: "string";
|
|
859
|
+
} & {
|
|
860
|
+
defaultValue: string;
|
|
861
|
+
};
|
|
862
|
+
readonly workerCount: {
|
|
863
|
+
type: "number";
|
|
864
|
+
} & {
|
|
865
|
+
defaultValue: number;
|
|
866
|
+
};
|
|
867
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
868
|
+
readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
869
|
+
readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
870
|
+
readonly trackNames: {
|
|
871
|
+
type: "boolean";
|
|
872
|
+
} & {
|
|
873
|
+
defaultValue: boolean;
|
|
874
|
+
};
|
|
875
|
+
readonly categories: {
|
|
876
|
+
type: "boolean";
|
|
877
|
+
} & {
|
|
878
|
+
defaultValue: boolean;
|
|
879
|
+
};
|
|
880
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
881
|
+
readonly defaultFolderCategories: {
|
|
882
|
+
type: "stringArray";
|
|
883
|
+
} & {
|
|
884
|
+
defaultValue: unknown;
|
|
885
|
+
};
|
|
886
|
+
readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
887
|
+
readonly categoryNames: {
|
|
888
|
+
type: "stringArray";
|
|
889
|
+
} & {
|
|
890
|
+
defaultValue: unknown;
|
|
891
|
+
};
|
|
892
|
+
readonly topLevelCategories: {
|
|
893
|
+
type: "boolean";
|
|
894
|
+
} & {
|
|
895
|
+
defaultValue: boolean;
|
|
896
|
+
};
|
|
897
|
+
readonly subCategories: {
|
|
898
|
+
type: "boolean";
|
|
899
|
+
} & {
|
|
900
|
+
defaultValue: boolean;
|
|
901
|
+
};
|
|
902
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
903
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
904
|
+
readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
905
|
+
readonly animationMode: {
|
|
906
|
+
type: "stringEnum";
|
|
907
|
+
} & {
|
|
908
|
+
model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
|
|
909
|
+
} & {
|
|
910
|
+
defaultValue: string;
|
|
911
|
+
};
|
|
912
|
+
readonly scrollZoom: {
|
|
913
|
+
type: "boolean";
|
|
914
|
+
} & {
|
|
915
|
+
defaultValue: boolean;
|
|
916
|
+
};
|
|
917
|
+
readonly numberGrouping: {
|
|
918
|
+
type: "boolean";
|
|
919
|
+
} & {
|
|
920
|
+
defaultValue: boolean;
|
|
921
|
+
};
|
|
922
|
+
readonly useWorkspaces: {
|
|
923
|
+
type: "boolean";
|
|
924
|
+
} & {
|
|
925
|
+
defaultValue: boolean;
|
|
926
|
+
};
|
|
927
|
+
readonly developerMode: {
|
|
928
|
+
type: "boolean";
|
|
929
|
+
} & {
|
|
930
|
+
defaultValue: boolean;
|
|
931
|
+
};
|
|
932
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
933
|
+
readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
934
|
+
readonly feature: {
|
|
935
|
+
type: "frozen";
|
|
936
|
+
} & {
|
|
937
|
+
defaultValue: unknown;
|
|
938
|
+
};
|
|
939
|
+
readonly subfeatures: {
|
|
940
|
+
type: "frozen";
|
|
941
|
+
} & {
|
|
942
|
+
defaultValue: unknown;
|
|
943
|
+
};
|
|
944
|
+
readonly depth: {
|
|
945
|
+
type: "maybeNumber";
|
|
946
|
+
};
|
|
947
|
+
readonly maxDepth: {
|
|
948
|
+
type: "maybeNumber";
|
|
949
|
+
};
|
|
950
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
951
|
+
readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
952
|
+
readonly config: {
|
|
953
|
+
type: "frozen";
|
|
954
|
+
} & {
|
|
955
|
+
defaultValue: unknown;
|
|
956
|
+
};
|
|
957
|
+
readonly hideUris: {
|
|
958
|
+
type: "boolean";
|
|
959
|
+
} & {
|
|
960
|
+
defaultValue: boolean;
|
|
961
|
+
};
|
|
962
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
963
|
+
readonly theme: {
|
|
964
|
+
type: "frozen";
|
|
965
|
+
} & {
|
|
966
|
+
defaultValue: unknown;
|
|
967
|
+
};
|
|
968
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
|
|
969
|
+
assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
|
|
970
|
+
tracks: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown>[] | null | undefined, Record<string, unknown>[], Record<string, unknown>[]>;
|
|
971
|
+
internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
|
|
972
|
+
connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
|
|
973
|
+
aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
|
|
974
|
+
plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
|
|
975
|
+
}, {
|
|
976
|
+
readonly assemblyNames: string[];
|
|
977
|
+
readonly rpcManager: RpcManager;
|
|
978
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
|
|
979
|
+
/**
|
|
980
|
+
* #property
|
|
981
|
+
*/
|
|
982
|
+
session: SESSION;
|
|
983
|
+
/**
|
|
984
|
+
* #property
|
|
985
|
+
*/
|
|
986
|
+
assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
987
|
+
assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
988
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
989
|
+
}, {
|
|
990
|
+
error: unknown;
|
|
991
|
+
loadingP: Promise<void> | undefined;
|
|
992
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
993
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
994
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
995
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
996
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
997
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
998
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
999
|
+
statusMessage: string | undefined;
|
|
1000
|
+
statusProgress: number | undefined;
|
|
1001
|
+
statusSource: string | undefined;
|
|
1002
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1003
|
+
} & {
|
|
1004
|
+
getConf(arg: string): any;
|
|
1005
|
+
} & {
|
|
1006
|
+
readonly name: string;
|
|
1007
|
+
readonly aliases: string[];
|
|
1008
|
+
readonly displayName: string;
|
|
1009
|
+
readonly refNameColors: string[];
|
|
1010
|
+
} & {
|
|
1011
|
+
readonly allAliases: string[];
|
|
1012
|
+
hasName(name: string): boolean;
|
|
1013
|
+
} & {
|
|
1014
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1015
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1016
|
+
} & {
|
|
1017
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1018
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1019
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1020
|
+
geneticCodes: Record<string, number>;
|
|
1021
|
+
}): void;
|
|
1022
|
+
setError(e: unknown): void;
|
|
1023
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1024
|
+
loadPre(): Promise<void>;
|
|
1025
|
+
} & {
|
|
1026
|
+
load(): Promise<void>;
|
|
1027
|
+
} & {
|
|
1028
|
+
afterAttach(): void;
|
|
1029
|
+
} & {
|
|
1030
|
+
readonly initialized: boolean;
|
|
1031
|
+
readonly allRefNames: string[] | undefined;
|
|
1032
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1033
|
+
readonly rpcManager: RpcManager;
|
|
1034
|
+
} & {
|
|
1035
|
+
readonly refNames: string[] | undefined;
|
|
1036
|
+
} & {
|
|
1037
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1038
|
+
} & {
|
|
1039
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1040
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1041
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1042
|
+
getGeneticCodeId(refName: string): number;
|
|
1043
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1044
|
+
} & {
|
|
1045
|
+
getCanonicalRefName2(refName: string): string;
|
|
1046
|
+
isValidRefName(refName: string): boolean;
|
|
1047
|
+
} & {
|
|
1048
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1049
|
+
getAliasesForRefName(refName: string): string[];
|
|
1050
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1051
|
+
[x: string]: unknown;
|
|
1052
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1053
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1054
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
1055
|
+
}, {
|
|
1056
|
+
unrecognizedReports: {
|
|
1057
|
+
report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
|
|
1058
|
+
reportFor(session: unknown, name: string): {
|
|
1059
|
+
handled: boolean;
|
|
1060
|
+
claim?: Promise<void>;
|
|
1061
|
+
} | undefined;
|
|
1062
|
+
};
|
|
1063
|
+
} & {
|
|
1064
|
+
readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
|
|
1065
|
+
} & {
|
|
1066
|
+
getCanonicalAssemblyName(asmName: string): string | undefined;
|
|
1067
|
+
getDisplayName(asmName: string): string;
|
|
1068
|
+
get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
1069
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1070
|
+
}> & {
|
|
1071
|
+
error: unknown;
|
|
1072
|
+
loadingP: Promise<void> | undefined;
|
|
1073
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1074
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1075
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1076
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1077
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1078
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1079
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1080
|
+
statusMessage: string | undefined;
|
|
1081
|
+
statusProgress: number | undefined;
|
|
1082
|
+
statusSource: string | undefined;
|
|
1083
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1084
|
+
} & {
|
|
1085
|
+
getConf(arg: string): any;
|
|
1086
|
+
} & {
|
|
1087
|
+
readonly name: string;
|
|
1088
|
+
readonly aliases: string[];
|
|
1089
|
+
readonly displayName: string;
|
|
1090
|
+
readonly refNameColors: string[];
|
|
1091
|
+
} & {
|
|
1092
|
+
readonly allAliases: string[];
|
|
1093
|
+
hasName(name: string): boolean;
|
|
1094
|
+
} & {
|
|
1095
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1096
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1097
|
+
} & {
|
|
1098
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1099
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1100
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1101
|
+
geneticCodes: Record<string, number>;
|
|
1102
|
+
}): void;
|
|
1103
|
+
setError(e: unknown): void;
|
|
1104
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1105
|
+
loadPre(): Promise<void>;
|
|
1106
|
+
} & {
|
|
1107
|
+
load(): Promise<void>;
|
|
1108
|
+
} & {
|
|
1109
|
+
afterAttach(): void;
|
|
1110
|
+
} & {
|
|
1111
|
+
readonly initialized: boolean;
|
|
1112
|
+
readonly allRefNames: string[] | undefined;
|
|
1113
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1114
|
+
readonly rpcManager: RpcManager;
|
|
1115
|
+
} & {
|
|
1116
|
+
readonly refNames: string[] | undefined;
|
|
1117
|
+
} & {
|
|
1118
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1119
|
+
} & {
|
|
1120
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1121
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1122
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1123
|
+
getGeneticCodeId(refName: string): number;
|
|
1124
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1125
|
+
} & {
|
|
1126
|
+
getCanonicalRefName2(refName: string): string;
|
|
1127
|
+
isValidRefName(refName: string): boolean;
|
|
1128
|
+
} & {
|
|
1129
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1130
|
+
getAliasesForRefName(refName: string): string[];
|
|
1131
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1132
|
+
[x: string]: unknown;
|
|
1133
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1134
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1135
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
1136
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1137
|
+
}, {
|
|
1138
|
+
error: unknown;
|
|
1139
|
+
loadingP: Promise<void> | undefined;
|
|
1140
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1141
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1142
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1143
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1144
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1145
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1146
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1147
|
+
statusMessage: string | undefined;
|
|
1148
|
+
statusProgress: number | undefined;
|
|
1149
|
+
statusSource: string | undefined;
|
|
1150
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1151
|
+
} & {
|
|
1152
|
+
getConf(arg: string): any;
|
|
1153
|
+
} & {
|
|
1154
|
+
readonly name: string;
|
|
1155
|
+
readonly aliases: string[];
|
|
1156
|
+
readonly displayName: string;
|
|
1157
|
+
readonly refNameColors: string[];
|
|
1158
|
+
} & {
|
|
1159
|
+
readonly allAliases: string[];
|
|
1160
|
+
hasName(name: string): boolean;
|
|
1161
|
+
} & {
|
|
1162
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1163
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1164
|
+
} & {
|
|
1165
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1166
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1167
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1168
|
+
geneticCodes: Record<string, number>;
|
|
1169
|
+
}): void;
|
|
1170
|
+
setError(e: unknown): void;
|
|
1171
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1172
|
+
loadPre(): Promise<void>;
|
|
1173
|
+
} & {
|
|
1174
|
+
load(): Promise<void>;
|
|
1175
|
+
} & {
|
|
1176
|
+
afterAttach(): void;
|
|
1177
|
+
} & {
|
|
1178
|
+
readonly initialized: boolean;
|
|
1179
|
+
readonly allRefNames: string[] | undefined;
|
|
1180
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1181
|
+
readonly rpcManager: RpcManager;
|
|
1182
|
+
} & {
|
|
1183
|
+
readonly refNames: string[] | undefined;
|
|
1184
|
+
} & {
|
|
1185
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1186
|
+
} & {
|
|
1187
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1188
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1189
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1190
|
+
getGeneticCodeId(refName: string): number;
|
|
1191
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1192
|
+
} & {
|
|
1193
|
+
getCanonicalRefName2(refName: string): string;
|
|
1194
|
+
isValidRefName(refName: string): boolean;
|
|
1195
|
+
} & {
|
|
1196
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1197
|
+
getAliasesForRefName(refName: string): string[];
|
|
1198
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1199
|
+
[x: string]: unknown;
|
|
1200
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1201
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1202
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
|
|
1203
|
+
has(asmName: string): boolean;
|
|
1204
|
+
loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
1205
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1206
|
+
}> & {
|
|
1207
|
+
error: unknown;
|
|
1208
|
+
loadingP: Promise<void> | undefined;
|
|
1209
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1210
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1211
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1212
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1213
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1214
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1215
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1216
|
+
statusMessage: string | undefined;
|
|
1217
|
+
statusProgress: number | undefined;
|
|
1218
|
+
statusSource: string | undefined;
|
|
1219
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1220
|
+
} & {
|
|
1221
|
+
getConf(arg: string): any;
|
|
1222
|
+
} & {
|
|
1223
|
+
readonly name: string;
|
|
1224
|
+
readonly aliases: string[];
|
|
1225
|
+
readonly displayName: string;
|
|
1226
|
+
readonly refNameColors: string[];
|
|
1227
|
+
} & {
|
|
1228
|
+
readonly allAliases: string[];
|
|
1229
|
+
hasName(name: string): boolean;
|
|
1230
|
+
} & {
|
|
1231
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1232
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1233
|
+
} & {
|
|
1234
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1235
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1236
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1237
|
+
geneticCodes: Record<string, number>;
|
|
1238
|
+
}): void;
|
|
1239
|
+
setError(e: unknown): void;
|
|
1240
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1241
|
+
loadPre(): Promise<void>;
|
|
1242
|
+
} & {
|
|
1243
|
+
load(): Promise<void>;
|
|
1244
|
+
} & {
|
|
1245
|
+
afterAttach(): void;
|
|
1246
|
+
} & {
|
|
1247
|
+
readonly initialized: boolean;
|
|
1248
|
+
readonly allRefNames: string[] | undefined;
|
|
1249
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1250
|
+
readonly rpcManager: RpcManager;
|
|
1251
|
+
} & {
|
|
1252
|
+
readonly refNames: string[] | undefined;
|
|
1253
|
+
} & {
|
|
1254
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1255
|
+
} & {
|
|
1256
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1257
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1258
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1259
|
+
getGeneticCodeId(refName: string): number;
|
|
1260
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1261
|
+
} & {
|
|
1262
|
+
getCanonicalRefName2(refName: string): string;
|
|
1263
|
+
isValidRefName(refName: string): boolean;
|
|
1264
|
+
} & {
|
|
1265
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1266
|
+
getAliasesForRefName(refName: string): string[];
|
|
1267
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1268
|
+
[x: string]: unknown;
|
|
1269
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1270
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1271
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
1272
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1273
|
+
}, {
|
|
1274
|
+
error: unknown;
|
|
1275
|
+
loadingP: Promise<void> | undefined;
|
|
1276
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1277
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1278
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1279
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1280
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1281
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1282
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1283
|
+
statusMessage: string | undefined;
|
|
1284
|
+
statusProgress: number | undefined;
|
|
1285
|
+
statusSource: string | undefined;
|
|
1286
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1287
|
+
} & {
|
|
1288
|
+
getConf(arg: string): any;
|
|
1289
|
+
} & {
|
|
1290
|
+
readonly name: string;
|
|
1291
|
+
readonly aliases: string[];
|
|
1292
|
+
readonly displayName: string;
|
|
1293
|
+
readonly refNameColors: string[];
|
|
1294
|
+
} & {
|
|
1295
|
+
readonly allAliases: string[];
|
|
1296
|
+
hasName(name: string): boolean;
|
|
1297
|
+
} & {
|
|
1298
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1299
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1300
|
+
} & {
|
|
1301
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1302
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1303
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1304
|
+
geneticCodes: Record<string, number>;
|
|
1305
|
+
}): void;
|
|
1306
|
+
setError(e: unknown): void;
|
|
1307
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1308
|
+
loadPre(): Promise<void>;
|
|
1309
|
+
} & {
|
|
1310
|
+
load(): Promise<void>;
|
|
1311
|
+
} & {
|
|
1312
|
+
afterAttach(): void;
|
|
1313
|
+
} & {
|
|
1314
|
+
readonly initialized: boolean;
|
|
1315
|
+
readonly allRefNames: string[] | undefined;
|
|
1316
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1317
|
+
readonly rpcManager: RpcManager;
|
|
1318
|
+
} & {
|
|
1319
|
+
readonly refNames: string[] | undefined;
|
|
1320
|
+
} & {
|
|
1321
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1322
|
+
} & {
|
|
1323
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1324
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1325
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1326
|
+
getGeneticCodeId(refName: string): number;
|
|
1327
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1328
|
+
} & {
|
|
1329
|
+
getCanonicalRefName2(refName: string): string;
|
|
1330
|
+
isValidRefName(refName: string): boolean;
|
|
1331
|
+
} & {
|
|
1332
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1333
|
+
getAliasesForRefName(refName: string): string[];
|
|
1334
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1335
|
+
[x: string]: unknown;
|
|
1336
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1337
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1338
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
|
|
1339
|
+
readonly assemblyNamesList: string[];
|
|
1340
|
+
readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
|
|
1341
|
+
readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
|
|
1342
|
+
readonly rpcManager: RpcManager;
|
|
1343
|
+
} & {
|
|
1344
|
+
settleAssemblyResolution(assemblyName: string): Promise<void>;
|
|
1345
|
+
} & {
|
|
1346
|
+
waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
1347
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1348
|
+
}> & {
|
|
1349
|
+
error: unknown;
|
|
1350
|
+
loadingP: Promise<void> | undefined;
|
|
1351
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1352
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1353
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1354
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1355
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1356
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1357
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1358
|
+
statusMessage: string | undefined;
|
|
1359
|
+
statusProgress: number | undefined;
|
|
1360
|
+
statusSource: string | undefined;
|
|
1361
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1362
|
+
} & {
|
|
1363
|
+
getConf(arg: string): any;
|
|
1364
|
+
} & {
|
|
1365
|
+
readonly name: string;
|
|
1366
|
+
readonly aliases: string[];
|
|
1367
|
+
readonly displayName: string;
|
|
1368
|
+
readonly refNameColors: string[];
|
|
1369
|
+
} & {
|
|
1370
|
+
readonly allAliases: string[];
|
|
1371
|
+
hasName(name: string): boolean;
|
|
1372
|
+
} & {
|
|
1373
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1374
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1375
|
+
} & {
|
|
1376
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1377
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1378
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1379
|
+
geneticCodes: Record<string, number>;
|
|
1380
|
+
}): void;
|
|
1381
|
+
setError(e: unknown): void;
|
|
1382
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1383
|
+
loadPre(): Promise<void>;
|
|
1384
|
+
} & {
|
|
1385
|
+
load(): Promise<void>;
|
|
1386
|
+
} & {
|
|
1387
|
+
afterAttach(): void;
|
|
1388
|
+
} & {
|
|
1389
|
+
readonly initialized: boolean;
|
|
1390
|
+
readonly allRefNames: string[] | undefined;
|
|
1391
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1392
|
+
readonly rpcManager: RpcManager;
|
|
1393
|
+
} & {
|
|
1394
|
+
readonly refNames: string[] | undefined;
|
|
1395
|
+
} & {
|
|
1396
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1397
|
+
} & {
|
|
1398
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1399
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1400
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1401
|
+
getGeneticCodeId(refName: string): number;
|
|
1402
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1403
|
+
} & {
|
|
1404
|
+
getCanonicalRefName2(refName: string): string;
|
|
1405
|
+
isValidRefName(refName: string): boolean;
|
|
1406
|
+
} & {
|
|
1407
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1408
|
+
getAliasesForRefName(refName: string): string[];
|
|
1409
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1410
|
+
[x: string]: unknown;
|
|
1411
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1412
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1413
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
1414
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1415
|
+
}, {
|
|
1416
|
+
error: unknown;
|
|
1417
|
+
loadingP: Promise<void> | undefined;
|
|
1418
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1419
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1420
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1421
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1422
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1423
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1424
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1425
|
+
statusMessage: string | undefined;
|
|
1426
|
+
statusProgress: number | undefined;
|
|
1427
|
+
statusSource: string | undefined;
|
|
1428
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1429
|
+
} & {
|
|
1430
|
+
getConf(arg: string): any;
|
|
1431
|
+
} & {
|
|
1432
|
+
readonly name: string;
|
|
1433
|
+
readonly aliases: string[];
|
|
1434
|
+
readonly displayName: string;
|
|
1435
|
+
readonly refNameColors: string[];
|
|
1436
|
+
} & {
|
|
1437
|
+
readonly allAliases: string[];
|
|
1438
|
+
hasName(name: string): boolean;
|
|
1439
|
+
} & {
|
|
1440
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1441
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1442
|
+
} & {
|
|
1443
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1444
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1445
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1446
|
+
geneticCodes: Record<string, number>;
|
|
1447
|
+
}): void;
|
|
1448
|
+
setError(e: unknown): void;
|
|
1449
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1450
|
+
loadPre(): Promise<void>;
|
|
1451
|
+
} & {
|
|
1452
|
+
load(): Promise<void>;
|
|
1453
|
+
} & {
|
|
1454
|
+
afterAttach(): void;
|
|
1455
|
+
} & {
|
|
1456
|
+
readonly initialized: boolean;
|
|
1457
|
+
readonly allRefNames: string[] | undefined;
|
|
1458
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1459
|
+
readonly rpcManager: RpcManager;
|
|
1460
|
+
} & {
|
|
1461
|
+
readonly refNames: string[] | undefined;
|
|
1462
|
+
} & {
|
|
1463
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1464
|
+
} & {
|
|
1465
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1466
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1467
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1468
|
+
getGeneticCodeId(refName: string): number;
|
|
1469
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1470
|
+
} & {
|
|
1471
|
+
getCanonicalRefName2(refName: string): string;
|
|
1472
|
+
isValidRefName(refName: string): boolean;
|
|
1473
|
+
} & {
|
|
1474
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1475
|
+
getAliasesForRefName(refName: string): string[];
|
|
1476
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1477
|
+
[x: string]: unknown;
|
|
1478
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1479
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1480
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
|
|
1481
|
+
requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
1482
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1483
|
+
}> & {
|
|
1484
|
+
error: unknown;
|
|
1485
|
+
loadingP: Promise<void> | undefined;
|
|
1486
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1487
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1488
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1489
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1490
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1491
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1492
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1493
|
+
statusMessage: string | undefined;
|
|
1494
|
+
statusProgress: number | undefined;
|
|
1495
|
+
statusSource: string | undefined;
|
|
1496
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1497
|
+
} & {
|
|
1498
|
+
getConf(arg: string): any;
|
|
1499
|
+
} & {
|
|
1500
|
+
readonly name: string;
|
|
1501
|
+
readonly aliases: string[];
|
|
1502
|
+
readonly displayName: string;
|
|
1503
|
+
readonly refNameColors: string[];
|
|
1504
|
+
} & {
|
|
1505
|
+
readonly allAliases: string[];
|
|
1506
|
+
hasName(name: string): boolean;
|
|
1507
|
+
} & {
|
|
1508
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1509
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1510
|
+
} & {
|
|
1511
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1512
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1513
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1514
|
+
geneticCodes: Record<string, number>;
|
|
1515
|
+
}): void;
|
|
1516
|
+
setError(e: unknown): void;
|
|
1517
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1518
|
+
loadPre(): Promise<void>;
|
|
1519
|
+
} & {
|
|
1520
|
+
load(): Promise<void>;
|
|
1521
|
+
} & {
|
|
1522
|
+
afterAttach(): void;
|
|
1523
|
+
} & {
|
|
1524
|
+
readonly initialized: boolean;
|
|
1525
|
+
readonly allRefNames: string[] | undefined;
|
|
1526
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1527
|
+
readonly rpcManager: RpcManager;
|
|
1528
|
+
} & {
|
|
1529
|
+
readonly refNames: string[] | undefined;
|
|
1530
|
+
} & {
|
|
1531
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1532
|
+
} & {
|
|
1533
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1534
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1535
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1536
|
+
getGeneticCodeId(refName: string): number;
|
|
1537
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1538
|
+
} & {
|
|
1539
|
+
getCanonicalRefName2(refName: string): string;
|
|
1540
|
+
isValidRefName(refName: string): boolean;
|
|
1541
|
+
} & {
|
|
1542
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1543
|
+
getAliasesForRefName(refName: string): string[];
|
|
1544
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1545
|
+
[x: string]: unknown;
|
|
1546
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1547
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1548
|
+
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
1549
|
+
configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
|
|
1550
|
+
}, {
|
|
1551
|
+
error: unknown;
|
|
1552
|
+
loadingP: Promise<void> | undefined;
|
|
1553
|
+
adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
|
|
1554
|
+
regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
1555
|
+
refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1556
|
+
canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
|
|
1557
|
+
cytobands: import("@jbrowse/core/util").Feature[] | undefined;
|
|
1558
|
+
loadedGeneticCodes: Record<string, number> | undefined;
|
|
1559
|
+
lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
|
|
1560
|
+
statusMessage: string | undefined;
|
|
1561
|
+
statusProgress: number | undefined;
|
|
1562
|
+
statusSource: string | undefined;
|
|
1563
|
+
refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
|
|
1564
|
+
} & {
|
|
1565
|
+
getConf(arg: string): any;
|
|
1566
|
+
} & {
|
|
1567
|
+
readonly name: string;
|
|
1568
|
+
readonly aliases: string[];
|
|
1569
|
+
readonly displayName: string;
|
|
1570
|
+
readonly refNameColors: string[];
|
|
1571
|
+
} & {
|
|
1572
|
+
readonly allAliases: string[];
|
|
1573
|
+
hasName(name: string): boolean;
|
|
1574
|
+
} & {
|
|
1575
|
+
setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
|
|
1576
|
+
setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
|
|
1577
|
+
} & {
|
|
1578
|
+
setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
|
|
1579
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
1580
|
+
cytobands: import("@jbrowse/core/util").Feature[];
|
|
1581
|
+
geneticCodes: Record<string, number>;
|
|
1582
|
+
}): void;
|
|
1583
|
+
setError(e: unknown): void;
|
|
1584
|
+
setLoadingP(p?: Promise<void>): void;
|
|
1585
|
+
loadPre(): Promise<void>;
|
|
1586
|
+
} & {
|
|
1587
|
+
load(): Promise<void>;
|
|
1588
|
+
} & {
|
|
1589
|
+
afterAttach(): void;
|
|
1590
|
+
} & {
|
|
1591
|
+
readonly initialized: boolean;
|
|
1592
|
+
readonly allRefNames: string[] | undefined;
|
|
1593
|
+
readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
|
|
1594
|
+
readonly rpcManager: RpcManager;
|
|
1595
|
+
} & {
|
|
1596
|
+
readonly refNames: string[] | undefined;
|
|
1597
|
+
} & {
|
|
1598
|
+
readonly refNameToIndex: Map<string, number> | undefined;
|
|
1599
|
+
} & {
|
|
1600
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
1601
|
+
getRefNameColor(refName: string): string | undefined;
|
|
1602
|
+
getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
|
|
1603
|
+
getGeneticCodeId(refName: string): number;
|
|
1604
|
+
getSeqAdapterRefName(canonicalRefName: string): string;
|
|
1605
|
+
} & {
|
|
1606
|
+
getCanonicalRefName2(refName: string): string;
|
|
1607
|
+
isValidRefName(refName: string): boolean;
|
|
1608
|
+
} & {
|
|
1609
|
+
getRefNamePosition(refName: string): number | undefined;
|
|
1610
|
+
getAliasesForRefName(refName: string): string[];
|
|
1611
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1612
|
+
[x: string]: unknown;
|
|
1613
|
+
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1614
|
+
getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
|
|
1615
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
|
|
1616
|
+
getRefNameMapForAdapter(adapterConf: {
|
|
1617
|
+
[x: string]: unknown;
|
|
1618
|
+
}, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
|
|
1619
|
+
isValidRefName(refName: string, assemblyName: string): boolean;
|
|
1620
|
+
} & {
|
|
1621
|
+
afterAttach(): void;
|
|
1622
|
+
removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
|
|
1623
|
+
addAssembly(configuration: any): void;
|
|
1624
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
|
|
1625
|
+
}>["config"]["Type"];
|
|
1626
|
+
/**
|
|
1627
|
+
* #getter
|
|
1628
|
+
*/
|
|
1629
|
+
readonly pluginManager: PluginManager;
|
|
1630
|
+
} & {
|
|
1631
|
+
initializeInternetAccount(internetAccountConfig: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: object): any;
|
|
1632
|
+
createEphemeralInternetAccount(internetAccountId: string, initialSnapshot: Record<string, unknown>, url: string): any;
|
|
1633
|
+
} & {
|
|
1634
|
+
findAppropriateInternetAccount(location: import("@jbrowse/core/util").UriLocation): any;
|
|
1635
|
+
} & {
|
|
1636
|
+
afterCreate(): void;
|
|
1637
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
|
|
1638
|
+
export {};
|