@jbrowse/embedded-core 4.3.0 → 5.0.0-beta.2

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.
Files changed (19) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +3329 -0
  2. package/esm/EmbeddedSessionMixin.js +54 -0
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +1725 -0
  4. package/esm/EmbeddedSessionThemeMixin.js +104 -0
  5. package/esm/createEmbeddedRootModel.d.ts +1910 -0
  6. package/esm/createEmbeddedRootModel.js +117 -0
  7. package/esm/index.d.ts +4 -1
  8. package/esm/index.js +4 -2
  9. package/esm/ui/EmbeddedViewContainer.d.ts +3 -3
  10. package/esm/ui/EmbeddedViewContainer.js +10 -14
  11. package/esm/ui/VersionAboutDialog.d.ts +1 -1
  12. package/esm/ui/VersionAboutDialog.js +3 -3
  13. package/esm/ui/ViewTitle.d.ts +1 -1
  14. package/esm/ui/ViewTitle.js +26 -8
  15. package/package.json +12 -14
  16. package/esm/ui/ModalWidget.d.ts +0 -5
  17. package/esm/ui/ModalWidget.js +0 -32
  18. package/esm/ui/ViewMenu.d.ts +0 -8
  19. package/esm/ui/ViewMenu.js +0 -8
package/esm/EmbeddedSessionMixin.d.ts ADDED
@@ -0,0 +1,3329 @@
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+ import type PluginManager from '@jbrowse/core/PluginManager';
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+ import type { AssemblyManager } from '@jbrowse/core/util/types';
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+ export interface EmbeddedSessionParent {
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+ version: string;
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+ assemblyManager: AssemblyManager;
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+ config: {
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+ assemblyName: string;
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+ };
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+ }
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+ /**
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+ * #stateModel EmbeddedSessionMixin
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+ * Everything the two single-view embedded products' sessions
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+ * (react-linear-genome-view, react-circular-genome-view) share: the mixin set
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+ * they compose and the three getters that read the root model. The twin of
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+ * {@link createEmbeddedRootModel} one level down.
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+ *
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+ * A mixin the product composes, deliberately, rather than a factory taking the
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+ * product's view type and tracks mixin as parameters. That factory is the
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+ * obvious shape and it does not work: `types.compose`'s overloads are declared
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+ * over `IModelType<P, O, FC, FS>`, so a model handed in as a naked type
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+ * parameter has nothing to infer those four from and the composed result
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+ * degrades — `session.view` becomes `any`, which typechecks at every embedder
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+ * call site and is caught by nothing. Keeping every argument to `compose`
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+ * concrete is what keeps the products' views typed.
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+ *
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+ * So each product still spells out its own tracks mixin, `view` prop, and the
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+ * `views`/`addView`/`removeView` members that read `self.view` — those are the
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+ * ones that need its concrete view type.
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+ */
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+ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<Omit<Omit<Omit<{
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+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/product-core").HeldNode[] | undefined, import("@jbrowse/product-core").HeldNode[] | undefined, import("@jbrowse/product-core").HeldNode[] | undefined>, [undefined]>;
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+ }, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
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+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
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+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
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+ activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
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+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ }, "connectionInstances" | "connectionTrackConfigs"> & {
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+ connectionInstances: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
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+ connectionTrackConfigs: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Record<string, import("@jbrowse/product-core").ConnectionTrackConfigEntry>, Record<string, import("@jbrowse/product-core").ConnectionTrackConfigEntry>, Record<string, import("@jbrowse/product-core").ConnectionTrackConfigEntry>>, [undefined]>;
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+ }, never>, never>, "focusedViewId" | "heldForMissingPlugins" | "highlightsVisible" | "id" | "name"> & Omit<{
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+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/product-core").HeldNode[] | undefined, import("@jbrowse/product-core").HeldNode[] | undefined, import("@jbrowse/product-core").HeldNode[] | undefined>, [undefined]>;
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+ }, never>, {
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+ selection: unknown;
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+ hovered: unknown;
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+ queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>][];
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+ preferencesOverrides: import("mobx").ObservableMap<string, unknown>;
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+ } & {
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+ readonly root: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
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+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
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+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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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>>;
68
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
69
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
71
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
72
+ 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;
80
+ } & {
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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>;
100
+ } & {
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+ load(): Promise<void>;
102
+ } & {
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+ afterAttach(): void;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly allRefNames: string[] | undefined;
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+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
110
+ } & {
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+ readonly refNames: string[] | undefined;
112
+ } & {
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+ readonly refNameToIndex: Map<string, number> | undefined;
114
+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
116
+ 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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+ 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>>;
130
+ }, {
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+ unrecognizedReports: {
132
+ 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;
137
+ };
138
+ } & {
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+ readonly assemblyNameMap: Record<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>>;
141
+ }> & {
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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>>;
145
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
146
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
147
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
148
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
149
+ loadedGeneticCodes: Record<string, number> | undefined;
150
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
151
+ statusMessage: string | undefined;
152
+ statusProgress: number | undefined;
153
+ statusSource: string | undefined;
154
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
155
+ } & {
156
+ getConf(arg: string): any;
157
+ } & {
158
+ readonly name: string;
159
+ readonly aliases: string[];
160
+ readonly displayName: string;
161
+ readonly refNameColors: string[];
162
+ } & {
163
+ readonly allAliases: string[];
164
+ hasName(name: string): boolean;
165
+ } & {
166
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
167
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
168
+ } & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
170
+ regions: import("@jbrowse/core/util").Region[];
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+ cytobands: import("@jbrowse/core/util").Feature[];
172
+ geneticCodes: Record<string, number>;
173
+ }): void;
174
+ setError(e: unknown): void;
175
+ setLoadingP(p?: Promise<void>): void;
176
+ loadPre(): Promise<void>;
177
+ } & {
178
+ load(): Promise<void>;
179
+ } & {
180
+ afterAttach(): void;
181
+ } & {
182
+ readonly initialized: boolean;
183
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
184
+ readonly allRefNames: string[] | undefined;
185
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
186
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
187
+ } & {
188
+ readonly refNames: string[] | undefined;
189
+ } & {
190
+ readonly refNameToIndex: Map<string, number> | undefined;
191
+ } & {
192
+ getCanonicalRefName(refName: string): string | undefined;
193
+ getRefNameColor(refName: string): string | undefined;
194
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
195
+ getGeneticCodeId(refName: string): number;
196
+ getSeqAdapterRefName(canonicalRefName: string): string;
197
+ } & {
198
+ getCanonicalRefName2(refName: string): string;
199
+ isValidRefName(refName: string): boolean;
200
+ } & {
201
+ getAliasesForRefName(refName: string): string[];
202
+ getRefNameMapForAdapter(adapterConf: {
203
+ [x: string]: unknown;
204
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
205
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
206
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
207
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
208
+ }, {
209
+ error: unknown;
210
+ loadingP: Promise<void> | undefined;
211
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
212
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
213
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
214
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
215
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
216
+ loadedGeneticCodes: Record<string, number> | undefined;
217
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
218
+ statusMessage: string | undefined;
219
+ statusProgress: number | undefined;
220
+ statusSource: string | undefined;
221
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
222
+ } & {
223
+ getConf(arg: string): any;
224
+ } & {
225
+ readonly name: string;
226
+ readonly aliases: string[];
227
+ readonly displayName: string;
228
+ readonly refNameColors: string[];
229
+ } & {
230
+ readonly allAliases: string[];
231
+ hasName(name: string): boolean;
232
+ } & {
233
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
234
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
235
+ } & {
236
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
237
+ regions: import("@jbrowse/core/util").Region[];
238
+ cytobands: import("@jbrowse/core/util").Feature[];
239
+ geneticCodes: Record<string, number>;
240
+ }): void;
241
+ setError(e: unknown): void;
242
+ setLoadingP(p?: Promise<void>): void;
243
+ loadPre(): Promise<void>;
244
+ } & {
245
+ load(): Promise<void>;
246
+ } & {
247
+ afterAttach(): void;
248
+ } & {
249
+ readonly initialized: boolean;
250
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
251
+ readonly allRefNames: string[] | undefined;
252
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
253
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
254
+ } & {
255
+ readonly refNames: string[] | undefined;
256
+ } & {
257
+ readonly refNameToIndex: Map<string, number> | undefined;
258
+ } & {
259
+ getCanonicalRefName(refName: string): string | undefined;
260
+ getRefNameColor(refName: string): string | undefined;
261
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
262
+ getGeneticCodeId(refName: string): number;
263
+ getSeqAdapterRefName(canonicalRefName: string): string;
264
+ } & {
265
+ getCanonicalRefName2(refName: string): string;
266
+ isValidRefName(refName: string): boolean;
267
+ } & {
268
+ getAliasesForRefName(refName: string): string[];
269
+ getRefNameMapForAdapter(adapterConf: {
270
+ [x: string]: unknown;
271
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
272
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
273
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
274
+ } & {
275
+ getCanonicalAssemblyName(asmName: string): string | undefined;
276
+ getDisplayName(asmName: string): string;
277
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
278
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
279
+ }> & {
280
+ error: unknown;
281
+ loadingP: Promise<void> | undefined;
282
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
283
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
284
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
285
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
286
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
287
+ loadedGeneticCodes: Record<string, number> | undefined;
288
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
289
+ statusMessage: string | undefined;
290
+ statusProgress: number | undefined;
291
+ statusSource: string | undefined;
292
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
293
+ } & {
294
+ getConf(arg: string): any;
295
+ } & {
296
+ readonly name: string;
297
+ readonly aliases: string[];
298
+ readonly displayName: string;
299
+ readonly refNameColors: string[];
300
+ } & {
301
+ readonly allAliases: string[];
302
+ hasName(name: string): boolean;
303
+ } & {
304
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
305
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
306
+ } & {
307
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
308
+ regions: import("@jbrowse/core/util").Region[];
309
+ cytobands: import("@jbrowse/core/util").Feature[];
310
+ geneticCodes: Record<string, number>;
311
+ }): void;
312
+ setError(e: unknown): void;
313
+ setLoadingP(p?: Promise<void>): void;
314
+ loadPre(): Promise<void>;
315
+ } & {
316
+ load(): Promise<void>;
317
+ } & {
318
+ afterAttach(): void;
319
+ } & {
320
+ readonly initialized: boolean;
321
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
322
+ readonly allRefNames: string[] | undefined;
323
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
324
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
325
+ } & {
326
+ readonly refNames: string[] | undefined;
327
+ } & {
328
+ readonly refNameToIndex: Map<string, number> | undefined;
329
+ } & {
330
+ getCanonicalRefName(refName: string): string | undefined;
331
+ getRefNameColor(refName: string): string | undefined;
332
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
333
+ getGeneticCodeId(refName: string): number;
334
+ getSeqAdapterRefName(canonicalRefName: string): string;
335
+ } & {
336
+ getCanonicalRefName2(refName: string): string;
337
+ isValidRefName(refName: string): boolean;
338
+ } & {
339
+ getAliasesForRefName(refName: string): string[];
340
+ getRefNameMapForAdapter(adapterConf: {
341
+ [x: string]: unknown;
342
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
343
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
344
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
345
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
346
+ }, {
347
+ error: unknown;
348
+ loadingP: Promise<void> | undefined;
349
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
350
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
351
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
352
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
353
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
354
+ loadedGeneticCodes: Record<string, number> | undefined;
355
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
356
+ statusMessage: string | undefined;
357
+ statusProgress: number | undefined;
358
+ statusSource: string | undefined;
359
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
360
+ } & {
361
+ getConf(arg: string): any;
362
+ } & {
363
+ readonly name: string;
364
+ readonly aliases: string[];
365
+ readonly displayName: string;
366
+ readonly refNameColors: string[];
367
+ } & {
368
+ readonly allAliases: string[];
369
+ hasName(name: string): boolean;
370
+ } & {
371
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
372
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
373
+ } & {
374
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
375
+ regions: import("@jbrowse/core/util").Region[];
376
+ cytobands: import("@jbrowse/core/util").Feature[];
377
+ geneticCodes: Record<string, number>;
378
+ }): void;
379
+ setError(e: unknown): void;
380
+ setLoadingP(p?: Promise<void>): void;
381
+ loadPre(): Promise<void>;
382
+ } & {
383
+ load(): Promise<void>;
384
+ } & {
385
+ afterAttach(): void;
386
+ } & {
387
+ readonly initialized: boolean;
388
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
389
+ readonly allRefNames: string[] | undefined;
390
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
391
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
392
+ } & {
393
+ readonly refNames: string[] | undefined;
394
+ } & {
395
+ readonly refNameToIndex: Map<string, number> | undefined;
396
+ } & {
397
+ getCanonicalRefName(refName: string): string | undefined;
398
+ getRefNameColor(refName: string): string | undefined;
399
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
400
+ getGeneticCodeId(refName: string): number;
401
+ getSeqAdapterRefName(canonicalRefName: string): string;
402
+ } & {
403
+ getCanonicalRefName2(refName: string): string;
404
+ isValidRefName(refName: string): boolean;
405
+ } & {
406
+ getAliasesForRefName(refName: string): string[];
407
+ getRefNameMapForAdapter(adapterConf: {
408
+ [x: string]: unknown;
409
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
410
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
411
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
412
+ has(asmName: string): boolean;
413
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
414
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
415
+ }> & {
416
+ error: unknown;
417
+ loadingP: Promise<void> | undefined;
418
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
419
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
420
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
421
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
422
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
423
+ loadedGeneticCodes: Record<string, number> | undefined;
424
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
425
+ statusMessage: string | undefined;
426
+ statusProgress: number | undefined;
427
+ statusSource: string | undefined;
428
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
429
+ } & {
430
+ getConf(arg: string): any;
431
+ } & {
432
+ readonly name: string;
433
+ readonly aliases: string[];
434
+ readonly displayName: string;
435
+ readonly refNameColors: string[];
436
+ } & {
437
+ readonly allAliases: string[];
438
+ hasName(name: string): boolean;
439
+ } & {
440
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
441
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
442
+ } & {
443
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
444
+ regions: import("@jbrowse/core/util").Region[];
445
+ cytobands: import("@jbrowse/core/util").Feature[];
446
+ geneticCodes: Record<string, number>;
447
+ }): void;
448
+ setError(e: unknown): void;
449
+ setLoadingP(p?: Promise<void>): void;
450
+ loadPre(): Promise<void>;
451
+ } & {
452
+ load(): Promise<void>;
453
+ } & {
454
+ afterAttach(): void;
455
+ } & {
456
+ readonly initialized: boolean;
457
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
458
+ readonly allRefNames: string[] | undefined;
459
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
460
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
461
+ } & {
462
+ readonly refNames: string[] | undefined;
463
+ } & {
464
+ readonly refNameToIndex: Map<string, number> | undefined;
465
+ } & {
466
+ getCanonicalRefName(refName: string): string | undefined;
467
+ getRefNameColor(refName: string): string | undefined;
468
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
469
+ getGeneticCodeId(refName: string): number;
470
+ getSeqAdapterRefName(canonicalRefName: string): string;
471
+ } & {
472
+ getCanonicalRefName2(refName: string): string;
473
+ isValidRefName(refName: string): boolean;
474
+ } & {
475
+ getAliasesForRefName(refName: string): string[];
476
+ getRefNameMapForAdapter(adapterConf: {
477
+ [x: string]: unknown;
478
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
479
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
480
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
481
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
482
+ }, {
483
+ error: unknown;
484
+ loadingP: Promise<void> | undefined;
485
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
486
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
487
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
488
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
489
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
490
+ loadedGeneticCodes: Record<string, number> | undefined;
491
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
492
+ statusMessage: string | undefined;
493
+ statusProgress: number | undefined;
494
+ statusSource: string | undefined;
495
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
496
+ } & {
497
+ getConf(arg: string): any;
498
+ } & {
499
+ readonly name: string;
500
+ readonly aliases: string[];
501
+ readonly displayName: string;
502
+ readonly refNameColors: string[];
503
+ } & {
504
+ readonly allAliases: string[];
505
+ hasName(name: string): boolean;
506
+ } & {
507
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
508
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
509
+ } & {
510
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
511
+ regions: import("@jbrowse/core/util").Region[];
512
+ cytobands: import("@jbrowse/core/util").Feature[];
513
+ geneticCodes: Record<string, number>;
514
+ }): void;
515
+ setError(e: unknown): void;
516
+ setLoadingP(p?: Promise<void>): void;
517
+ loadPre(): Promise<void>;
518
+ } & {
519
+ load(): Promise<void>;
520
+ } & {
521
+ afterAttach(): void;
522
+ } & {
523
+ readonly initialized: boolean;
524
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
525
+ readonly allRefNames: string[] | undefined;
526
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
527
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
528
+ } & {
529
+ readonly refNames: string[] | undefined;
530
+ } & {
531
+ readonly refNameToIndex: Map<string, number> | undefined;
532
+ } & {
533
+ getCanonicalRefName(refName: string): string | undefined;
534
+ getRefNameColor(refName: string): string | undefined;
535
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
536
+ getGeneticCodeId(refName: string): number;
537
+ getSeqAdapterRefName(canonicalRefName: string): string;
538
+ } & {
539
+ getCanonicalRefName2(refName: string): string;
540
+ isValidRefName(refName: string): boolean;
541
+ } & {
542
+ getAliasesForRefName(refName: string): string[];
543
+ getRefNameMapForAdapter(adapterConf: {
544
+ [x: string]: unknown;
545
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
546
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
547
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
548
+ readonly assemblyNamesList: string[];
549
+ readonly configuredAssemblyNames: Set<string>;
550
+ readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
551
+ setSubschema(slotName: string, data: Record<string, unknown>): any;
552
+ setSlot(slotName: string, value: unknown): void;
553
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
554
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
555
+ } & {
556
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
557
+ } & {
558
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
559
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
560
+ }> & {
561
+ error: unknown;
562
+ loadingP: Promise<void> | undefined;
563
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
564
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
565
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
566
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
567
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
568
+ loadedGeneticCodes: Record<string, number> | undefined;
569
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
570
+ statusMessage: string | undefined;
571
+ statusProgress: number | undefined;
572
+ statusSource: string | undefined;
573
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
574
+ } & {
575
+ getConf(arg: string): any;
576
+ } & {
577
+ readonly name: string;
578
+ readonly aliases: string[];
579
+ readonly displayName: string;
580
+ readonly refNameColors: string[];
581
+ } & {
582
+ readonly allAliases: string[];
583
+ hasName(name: string): boolean;
584
+ } & {
585
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
586
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
587
+ } & {
588
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
589
+ regions: import("@jbrowse/core/util").Region[];
590
+ cytobands: import("@jbrowse/core/util").Feature[];
591
+ geneticCodes: Record<string, number>;
592
+ }): void;
593
+ setError(e: unknown): void;
594
+ setLoadingP(p?: Promise<void>): void;
595
+ loadPre(): Promise<void>;
596
+ } & {
597
+ load(): Promise<void>;
598
+ } & {
599
+ afterAttach(): void;
600
+ } & {
601
+ readonly initialized: boolean;
602
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
603
+ readonly allRefNames: string[] | undefined;
604
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
605
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
606
+ } & {
607
+ readonly refNames: string[] | undefined;
608
+ } & {
609
+ readonly refNameToIndex: Map<string, number> | undefined;
610
+ } & {
611
+ getCanonicalRefName(refName: string): string | undefined;
612
+ getRefNameColor(refName: string): string | undefined;
613
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
614
+ getGeneticCodeId(refName: string): number;
615
+ getSeqAdapterRefName(canonicalRefName: string): string;
616
+ } & {
617
+ getCanonicalRefName2(refName: string): string;
618
+ isValidRefName(refName: string): boolean;
619
+ } & {
620
+ getAliasesForRefName(refName: string): string[];
621
+ getRefNameMapForAdapter(adapterConf: {
622
+ [x: string]: unknown;
623
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
624
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
625
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
626
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
627
+ }, {
628
+ error: unknown;
629
+ loadingP: Promise<void> | undefined;
630
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
631
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
632
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
633
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
634
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
635
+ loadedGeneticCodes: Record<string, number> | undefined;
636
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
637
+ statusMessage: string | undefined;
638
+ statusProgress: number | undefined;
639
+ statusSource: string | undefined;
640
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
641
+ } & {
642
+ getConf(arg: string): any;
643
+ } & {
644
+ readonly name: string;
645
+ readonly aliases: string[];
646
+ readonly displayName: string;
647
+ readonly refNameColors: string[];
648
+ } & {
649
+ readonly allAliases: string[];
650
+ hasName(name: string): boolean;
651
+ } & {
652
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
653
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
654
+ } & {
655
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
656
+ regions: import("@jbrowse/core/util").Region[];
657
+ cytobands: import("@jbrowse/core/util").Feature[];
658
+ geneticCodes: Record<string, number>;
659
+ }): void;
660
+ setError(e: unknown): void;
661
+ setLoadingP(p?: Promise<void>): void;
662
+ loadPre(): Promise<void>;
663
+ } & {
664
+ load(): Promise<void>;
665
+ } & {
666
+ afterAttach(): void;
667
+ } & {
668
+ readonly initialized: boolean;
669
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
670
+ readonly allRefNames: string[] | undefined;
671
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
672
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
673
+ } & {
674
+ readonly refNames: string[] | undefined;
675
+ } & {
676
+ readonly refNameToIndex: Map<string, number> | undefined;
677
+ } & {
678
+ getCanonicalRefName(refName: string): string | undefined;
679
+ getRefNameColor(refName: string): string | undefined;
680
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
681
+ getGeneticCodeId(refName: string): number;
682
+ getSeqAdapterRefName(canonicalRefName: string): string;
683
+ } & {
684
+ getCanonicalRefName2(refName: string): string;
685
+ isValidRefName(refName: string): boolean;
686
+ } & {
687
+ getAliasesForRefName(refName: string): string[];
688
+ getRefNameMapForAdapter(adapterConf: {
689
+ [x: string]: unknown;
690
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
691
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
692
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
693
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
694
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
695
+ }> & {
696
+ error: unknown;
697
+ loadingP: Promise<void> | undefined;
698
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
699
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
700
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
701
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
702
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
703
+ loadedGeneticCodes: Record<string, number> | undefined;
704
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
705
+ statusMessage: string | undefined;
706
+ statusProgress: number | undefined;
707
+ statusSource: string | undefined;
708
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
709
+ } & {
710
+ getConf(arg: string): any;
711
+ } & {
712
+ readonly name: string;
713
+ readonly aliases: string[];
714
+ readonly displayName: string;
715
+ readonly refNameColors: string[];
716
+ } & {
717
+ readonly allAliases: string[];
718
+ hasName(name: string): boolean;
719
+ } & {
720
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
721
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
722
+ } & {
723
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
724
+ regions: import("@jbrowse/core/util").Region[];
725
+ cytobands: import("@jbrowse/core/util").Feature[];
726
+ geneticCodes: Record<string, number>;
727
+ }): void;
728
+ setError(e: unknown): void;
729
+ setLoadingP(p?: Promise<void>): void;
730
+ loadPre(): Promise<void>;
731
+ } & {
732
+ load(): Promise<void>;
733
+ } & {
734
+ afterAttach(): void;
735
+ } & {
736
+ readonly initialized: boolean;
737
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
738
+ readonly allRefNames: string[] | undefined;
739
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
740
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
741
+ } & {
742
+ readonly refNames: string[] | undefined;
743
+ } & {
744
+ readonly refNameToIndex: Map<string, number> | undefined;
745
+ } & {
746
+ getCanonicalRefName(refName: string): string | undefined;
747
+ getRefNameColor(refName: string): string | undefined;
748
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
749
+ getGeneticCodeId(refName: string): number;
750
+ getSeqAdapterRefName(canonicalRefName: string): string;
751
+ } & {
752
+ getCanonicalRefName2(refName: string): string;
753
+ isValidRefName(refName: string): boolean;
754
+ } & {
755
+ getAliasesForRefName(refName: string): string[];
756
+ getRefNameMapForAdapter(adapterConf: {
757
+ [x: string]: unknown;
758
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
759
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
760
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
761
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
762
+ }, {
763
+ error: unknown;
764
+ loadingP: Promise<void> | undefined;
765
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
766
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
767
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
768
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
769
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
770
+ loadedGeneticCodes: Record<string, number> | undefined;
771
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
772
+ statusMessage: string | undefined;
773
+ statusProgress: number | undefined;
774
+ statusSource: string | undefined;
775
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
776
+ } & {
777
+ getConf(arg: string): any;
778
+ } & {
779
+ readonly name: string;
780
+ readonly aliases: string[];
781
+ readonly displayName: string;
782
+ readonly refNameColors: string[];
783
+ } & {
784
+ readonly allAliases: string[];
785
+ hasName(name: string): boolean;
786
+ } & {
787
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
788
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
789
+ } & {
790
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
791
+ regions: import("@jbrowse/core/util").Region[];
792
+ cytobands: import("@jbrowse/core/util").Feature[];
793
+ geneticCodes: Record<string, number>;
794
+ }): void;
795
+ setError(e: unknown): void;
796
+ setLoadingP(p?: Promise<void>): void;
797
+ loadPre(): Promise<void>;
798
+ } & {
799
+ load(): Promise<void>;
800
+ } & {
801
+ afterAttach(): void;
802
+ } & {
803
+ readonly initialized: boolean;
804
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
805
+ readonly allRefNames: string[] | undefined;
806
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
807
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
808
+ } & {
809
+ readonly refNames: string[] | undefined;
810
+ } & {
811
+ readonly refNameToIndex: Map<string, number> | undefined;
812
+ } & {
813
+ getCanonicalRefName(refName: string): string | undefined;
814
+ getRefNameColor(refName: string): string | undefined;
815
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
816
+ getGeneticCodeId(refName: string): number;
817
+ getSeqAdapterRefName(canonicalRefName: string): string;
818
+ } & {
819
+ getCanonicalRefName2(refName: string): string;
820
+ isValidRefName(refName: string): boolean;
821
+ } & {
822
+ getAliasesForRefName(refName: string): string[];
823
+ getRefNameMapForAdapter(adapterConf: {
824
+ [x: string]: unknown;
825
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
826
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
827
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
828
+ getRefNameMapForAdapter(adapterConf: {
829
+ [x: string]: unknown;
830
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
831
+ isValidRefName(refName: string, assemblyName: string): boolean;
832
+ } & {
833
+ afterAttach(): void;
834
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
835
+ addAssembly(configuration: any): void;
836
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
837
+ }> & {
838
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
839
+ adminMode: boolean;
840
+ error: unknown;
841
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
842
+ pluginManager: PluginManager;
843
+ } & {
844
+ setError(error: unknown): void;
845
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
846
+ setDefaultSession(): void;
847
+ setSessionPath(path: string): void;
848
+ renameCurrentSession(newName: string): void;
849
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
850
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
851
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
852
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
853
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
854
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
855
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
856
+ }, {
857
+ error: unknown;
858
+ loadingP: Promise<void> | undefined;
859
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
860
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
861
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
862
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
863
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
864
+ loadedGeneticCodes: Record<string, number> | undefined;
865
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
866
+ statusMessage: string | undefined;
867
+ statusProgress: number | undefined;
868
+ statusSource: string | undefined;
869
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
870
+ } & {
871
+ getConf(arg: string): any;
872
+ } & {
873
+ readonly name: string;
874
+ readonly aliases: string[];
875
+ readonly displayName: string;
876
+ readonly refNameColors: string[];
877
+ } & {
878
+ readonly allAliases: string[];
879
+ hasName(name: string): boolean;
880
+ } & {
881
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
882
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
883
+ } & {
884
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
885
+ regions: import("@jbrowse/core/util").Region[];
886
+ cytobands: import("@jbrowse/core/util").Feature[];
887
+ geneticCodes: Record<string, number>;
888
+ }): void;
889
+ setError(e: unknown): void;
890
+ setLoadingP(p?: Promise<void>): void;
891
+ loadPre(): Promise<void>;
892
+ } & {
893
+ load(): Promise<void>;
894
+ } & {
895
+ afterAttach(): void;
896
+ } & {
897
+ readonly initialized: boolean;
898
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
899
+ readonly allRefNames: string[] | undefined;
900
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
901
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
902
+ } & {
903
+ readonly refNames: string[] | undefined;
904
+ } & {
905
+ readonly refNameToIndex: Map<string, number> | undefined;
906
+ } & {
907
+ getCanonicalRefName(refName: string): string | undefined;
908
+ getRefNameColor(refName: string): string | undefined;
909
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
910
+ getGeneticCodeId(refName: string): number;
911
+ getSeqAdapterRefName(canonicalRefName: string): string;
912
+ } & {
913
+ getCanonicalRefName2(refName: string): string;
914
+ isValidRefName(refName: string): boolean;
915
+ } & {
916
+ getAliasesForRefName(refName: string): string[];
917
+ getRefNameMapForAdapter(adapterConf: {
918
+ [x: string]: unknown;
919
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
920
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
921
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
922
+ }, {
923
+ unrecognizedReports: {
924
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
925
+ reportFor(session: unknown, name: string): {
926
+ handled: boolean;
927
+ claim?: Promise<void>;
928
+ } | undefined;
929
+ };
930
+ } & {
931
+ readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
932
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
933
+ }> & {
934
+ error: unknown;
935
+ loadingP: Promise<void> | undefined;
936
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
937
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
938
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
939
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
940
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
941
+ loadedGeneticCodes: Record<string, number> | undefined;
942
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
943
+ statusMessage: string | undefined;
944
+ statusProgress: number | undefined;
945
+ statusSource: string | undefined;
946
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
947
+ } & {
948
+ getConf(arg: string): any;
949
+ } & {
950
+ readonly name: string;
951
+ readonly aliases: string[];
952
+ readonly displayName: string;
953
+ readonly refNameColors: string[];
954
+ } & {
955
+ readonly allAliases: string[];
956
+ hasName(name: string): boolean;
957
+ } & {
958
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
959
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
960
+ } & {
961
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
962
+ regions: import("@jbrowse/core/util").Region[];
963
+ cytobands: import("@jbrowse/core/util").Feature[];
964
+ geneticCodes: Record<string, number>;
965
+ }): void;
966
+ setError(e: unknown): void;
967
+ setLoadingP(p?: Promise<void>): void;
968
+ loadPre(): Promise<void>;
969
+ } & {
970
+ load(): Promise<void>;
971
+ } & {
972
+ afterAttach(): void;
973
+ } & {
974
+ readonly initialized: boolean;
975
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
976
+ readonly allRefNames: string[] | undefined;
977
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
978
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
979
+ } & {
980
+ readonly refNames: string[] | undefined;
981
+ } & {
982
+ readonly refNameToIndex: Map<string, number> | undefined;
983
+ } & {
984
+ getCanonicalRefName(refName: string): string | undefined;
985
+ getRefNameColor(refName: string): string | undefined;
986
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
987
+ getGeneticCodeId(refName: string): number;
988
+ getSeqAdapterRefName(canonicalRefName: string): string;
989
+ } & {
990
+ getCanonicalRefName2(refName: string): string;
991
+ isValidRefName(refName: string): boolean;
992
+ } & {
993
+ getAliasesForRefName(refName: string): string[];
994
+ getRefNameMapForAdapter(adapterConf: {
995
+ [x: string]: unknown;
996
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
997
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
998
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
999
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1000
+ }, {
1001
+ error: unknown;
1002
+ loadingP: Promise<void> | undefined;
1003
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1004
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1005
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1006
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1007
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1008
+ loadedGeneticCodes: Record<string, number> | undefined;
1009
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1010
+ statusMessage: string | undefined;
1011
+ statusProgress: number | undefined;
1012
+ statusSource: string | undefined;
1013
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1014
+ } & {
1015
+ getConf(arg: string): any;
1016
+ } & {
1017
+ readonly name: string;
1018
+ readonly aliases: string[];
1019
+ readonly displayName: string;
1020
+ readonly refNameColors: string[];
1021
+ } & {
1022
+ readonly allAliases: string[];
1023
+ hasName(name: string): boolean;
1024
+ } & {
1025
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1026
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1027
+ } & {
1028
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1029
+ regions: import("@jbrowse/core/util").Region[];
1030
+ cytobands: import("@jbrowse/core/util").Feature[];
1031
+ geneticCodes: Record<string, number>;
1032
+ }): void;
1033
+ setError(e: unknown): void;
1034
+ setLoadingP(p?: Promise<void>): void;
1035
+ loadPre(): Promise<void>;
1036
+ } & {
1037
+ load(): Promise<void>;
1038
+ } & {
1039
+ afterAttach(): void;
1040
+ } & {
1041
+ readonly initialized: boolean;
1042
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1043
+ readonly allRefNames: string[] | undefined;
1044
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1045
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1046
+ } & {
1047
+ readonly refNames: string[] | undefined;
1048
+ } & {
1049
+ readonly refNameToIndex: Map<string, number> | undefined;
1050
+ } & {
1051
+ getCanonicalRefName(refName: string): string | undefined;
1052
+ getRefNameColor(refName: string): string | undefined;
1053
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1054
+ getGeneticCodeId(refName: string): number;
1055
+ getSeqAdapterRefName(canonicalRefName: string): string;
1056
+ } & {
1057
+ getCanonicalRefName2(refName: string): string;
1058
+ isValidRefName(refName: string): boolean;
1059
+ } & {
1060
+ getAliasesForRefName(refName: string): string[];
1061
+ getRefNameMapForAdapter(adapterConf: {
1062
+ [x: string]: unknown;
1063
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1064
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1065
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1066
+ } & {
1067
+ getCanonicalAssemblyName(asmName: string): string | undefined;
1068
+ getDisplayName(asmName: string): string;
1069
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1070
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1071
+ }> & {
1072
+ error: unknown;
1073
+ loadingP: Promise<void> | undefined;
1074
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1075
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1076
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1077
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1078
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1079
+ loadedGeneticCodes: Record<string, number> | undefined;
1080
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1081
+ statusMessage: string | undefined;
1082
+ statusProgress: number | undefined;
1083
+ statusSource: string | undefined;
1084
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1085
+ } & {
1086
+ getConf(arg: string): any;
1087
+ } & {
1088
+ readonly name: string;
1089
+ readonly aliases: string[];
1090
+ readonly displayName: string;
1091
+ readonly refNameColors: string[];
1092
+ } & {
1093
+ readonly allAliases: string[];
1094
+ hasName(name: string): boolean;
1095
+ } & {
1096
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1097
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1098
+ } & {
1099
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1100
+ regions: import("@jbrowse/core/util").Region[];
1101
+ cytobands: import("@jbrowse/core/util").Feature[];
1102
+ geneticCodes: Record<string, number>;
1103
+ }): void;
1104
+ setError(e: unknown): void;
1105
+ setLoadingP(p?: Promise<void>): void;
1106
+ loadPre(): Promise<void>;
1107
+ } & {
1108
+ load(): Promise<void>;
1109
+ } & {
1110
+ afterAttach(): void;
1111
+ } & {
1112
+ readonly initialized: boolean;
1113
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1114
+ readonly allRefNames: string[] | undefined;
1115
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1116
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1117
+ } & {
1118
+ readonly refNames: string[] | undefined;
1119
+ } & {
1120
+ readonly refNameToIndex: Map<string, number> | undefined;
1121
+ } & {
1122
+ getCanonicalRefName(refName: string): string | undefined;
1123
+ getRefNameColor(refName: string): string | undefined;
1124
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1125
+ getGeneticCodeId(refName: string): number;
1126
+ getSeqAdapterRefName(canonicalRefName: string): string;
1127
+ } & {
1128
+ getCanonicalRefName2(refName: string): string;
1129
+ isValidRefName(refName: string): boolean;
1130
+ } & {
1131
+ getAliasesForRefName(refName: string): string[];
1132
+ getRefNameMapForAdapter(adapterConf: {
1133
+ [x: string]: unknown;
1134
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1135
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1136
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1137
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1138
+ }, {
1139
+ error: unknown;
1140
+ loadingP: Promise<void> | undefined;
1141
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1142
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1143
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1144
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1145
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1146
+ loadedGeneticCodes: Record<string, number> | undefined;
1147
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1148
+ statusMessage: string | undefined;
1149
+ statusProgress: number | undefined;
1150
+ statusSource: string | undefined;
1151
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1152
+ } & {
1153
+ getConf(arg: string): any;
1154
+ } & {
1155
+ readonly name: string;
1156
+ readonly aliases: string[];
1157
+ readonly displayName: string;
1158
+ readonly refNameColors: string[];
1159
+ } & {
1160
+ readonly allAliases: string[];
1161
+ hasName(name: string): boolean;
1162
+ } & {
1163
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1164
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1165
+ } & {
1166
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1167
+ regions: import("@jbrowse/core/util").Region[];
1168
+ cytobands: import("@jbrowse/core/util").Feature[];
1169
+ geneticCodes: Record<string, number>;
1170
+ }): void;
1171
+ setError(e: unknown): void;
1172
+ setLoadingP(p?: Promise<void>): void;
1173
+ loadPre(): Promise<void>;
1174
+ } & {
1175
+ load(): Promise<void>;
1176
+ } & {
1177
+ afterAttach(): void;
1178
+ } & {
1179
+ readonly initialized: boolean;
1180
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1181
+ readonly allRefNames: string[] | undefined;
1182
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1183
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1184
+ } & {
1185
+ readonly refNames: string[] | undefined;
1186
+ } & {
1187
+ readonly refNameToIndex: Map<string, number> | undefined;
1188
+ } & {
1189
+ getCanonicalRefName(refName: string): string | undefined;
1190
+ getRefNameColor(refName: string): string | undefined;
1191
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1192
+ getGeneticCodeId(refName: string): number;
1193
+ getSeqAdapterRefName(canonicalRefName: string): string;
1194
+ } & {
1195
+ getCanonicalRefName2(refName: string): string;
1196
+ isValidRefName(refName: string): boolean;
1197
+ } & {
1198
+ getAliasesForRefName(refName: string): string[];
1199
+ getRefNameMapForAdapter(adapterConf: {
1200
+ [x: string]: unknown;
1201
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1202
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1203
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1204
+ has(asmName: string): boolean;
1205
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1206
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1207
+ }> & {
1208
+ error: unknown;
1209
+ loadingP: Promise<void> | undefined;
1210
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1211
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1212
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1213
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1214
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1215
+ loadedGeneticCodes: Record<string, number> | undefined;
1216
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1217
+ statusMessage: string | undefined;
1218
+ statusProgress: number | undefined;
1219
+ statusSource: string | undefined;
1220
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1221
+ } & {
1222
+ getConf(arg: string): any;
1223
+ } & {
1224
+ readonly name: string;
1225
+ readonly aliases: string[];
1226
+ readonly displayName: string;
1227
+ readonly refNameColors: string[];
1228
+ } & {
1229
+ readonly allAliases: string[];
1230
+ hasName(name: string): boolean;
1231
+ } & {
1232
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1233
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1234
+ } & {
1235
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1236
+ regions: import("@jbrowse/core/util").Region[];
1237
+ cytobands: import("@jbrowse/core/util").Feature[];
1238
+ geneticCodes: Record<string, number>;
1239
+ }): void;
1240
+ setError(e: unknown): void;
1241
+ setLoadingP(p?: Promise<void>): void;
1242
+ loadPre(): Promise<void>;
1243
+ } & {
1244
+ load(): Promise<void>;
1245
+ } & {
1246
+ afterAttach(): void;
1247
+ } & {
1248
+ readonly initialized: boolean;
1249
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1250
+ readonly allRefNames: string[] | undefined;
1251
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1252
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1253
+ } & {
1254
+ readonly refNames: string[] | undefined;
1255
+ } & {
1256
+ readonly refNameToIndex: Map<string, number> | undefined;
1257
+ } & {
1258
+ getCanonicalRefName(refName: string): string | undefined;
1259
+ getRefNameColor(refName: string): string | undefined;
1260
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1261
+ getGeneticCodeId(refName: string): number;
1262
+ getSeqAdapterRefName(canonicalRefName: string): string;
1263
+ } & {
1264
+ getCanonicalRefName2(refName: string): string;
1265
+ isValidRefName(refName: string): boolean;
1266
+ } & {
1267
+ getAliasesForRefName(refName: string): string[];
1268
+ getRefNameMapForAdapter(adapterConf: {
1269
+ [x: string]: unknown;
1270
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1271
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1272
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1273
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1274
+ }, {
1275
+ error: unknown;
1276
+ loadingP: Promise<void> | undefined;
1277
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1278
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1279
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1280
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1281
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1282
+ loadedGeneticCodes: Record<string, number> | undefined;
1283
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1284
+ statusMessage: string | undefined;
1285
+ statusProgress: number | undefined;
1286
+ statusSource: string | undefined;
1287
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1288
+ } & {
1289
+ getConf(arg: string): any;
1290
+ } & {
1291
+ readonly name: string;
1292
+ readonly aliases: string[];
1293
+ readonly displayName: string;
1294
+ readonly refNameColors: string[];
1295
+ } & {
1296
+ readonly allAliases: string[];
1297
+ hasName(name: string): boolean;
1298
+ } & {
1299
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1300
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1301
+ } & {
1302
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1303
+ regions: import("@jbrowse/core/util").Region[];
1304
+ cytobands: import("@jbrowse/core/util").Feature[];
1305
+ geneticCodes: Record<string, number>;
1306
+ }): void;
1307
+ setError(e: unknown): void;
1308
+ setLoadingP(p?: Promise<void>): void;
1309
+ loadPre(): Promise<void>;
1310
+ } & {
1311
+ load(): Promise<void>;
1312
+ } & {
1313
+ afterAttach(): void;
1314
+ } & {
1315
+ readonly initialized: boolean;
1316
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1317
+ readonly allRefNames: string[] | undefined;
1318
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1319
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1320
+ } & {
1321
+ readonly refNames: string[] | undefined;
1322
+ } & {
1323
+ readonly refNameToIndex: Map<string, number> | undefined;
1324
+ } & {
1325
+ getCanonicalRefName(refName: string): string | undefined;
1326
+ getRefNameColor(refName: string): string | undefined;
1327
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1328
+ getGeneticCodeId(refName: string): number;
1329
+ getSeqAdapterRefName(canonicalRefName: string): string;
1330
+ } & {
1331
+ getCanonicalRefName2(refName: string): string;
1332
+ isValidRefName(refName: string): boolean;
1333
+ } & {
1334
+ getAliasesForRefName(refName: string): string[];
1335
+ getRefNameMapForAdapter(adapterConf: {
1336
+ [x: string]: unknown;
1337
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1338
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1339
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1340
+ readonly assemblyNamesList: string[];
1341
+ readonly configuredAssemblyNames: Set<string>;
1342
+ readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1343
+ setSubschema(slotName: string, data: Record<string, unknown>): any;
1344
+ setSlot(slotName: string, value: unknown): void;
1345
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1346
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1347
+ } & {
1348
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
1349
+ } & {
1350
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1351
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1352
+ }> & {
1353
+ error: unknown;
1354
+ loadingP: Promise<void> | undefined;
1355
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1356
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1357
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1358
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1359
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1360
+ loadedGeneticCodes: Record<string, number> | undefined;
1361
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1362
+ statusMessage: string | undefined;
1363
+ statusProgress: number | undefined;
1364
+ statusSource: string | undefined;
1365
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1366
+ } & {
1367
+ getConf(arg: string): any;
1368
+ } & {
1369
+ readonly name: string;
1370
+ readonly aliases: string[];
1371
+ readonly displayName: string;
1372
+ readonly refNameColors: string[];
1373
+ } & {
1374
+ readonly allAliases: string[];
1375
+ hasName(name: string): boolean;
1376
+ } & {
1377
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1378
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1379
+ } & {
1380
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1381
+ regions: import("@jbrowse/core/util").Region[];
1382
+ cytobands: import("@jbrowse/core/util").Feature[];
1383
+ geneticCodes: Record<string, number>;
1384
+ }): void;
1385
+ setError(e: unknown): void;
1386
+ setLoadingP(p?: Promise<void>): void;
1387
+ loadPre(): Promise<void>;
1388
+ } & {
1389
+ load(): Promise<void>;
1390
+ } & {
1391
+ afterAttach(): void;
1392
+ } & {
1393
+ readonly initialized: boolean;
1394
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1395
+ readonly allRefNames: string[] | undefined;
1396
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1397
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1398
+ } & {
1399
+ readonly refNames: string[] | undefined;
1400
+ } & {
1401
+ readonly refNameToIndex: Map<string, number> | undefined;
1402
+ } & {
1403
+ getCanonicalRefName(refName: string): string | undefined;
1404
+ getRefNameColor(refName: string): string | undefined;
1405
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1406
+ getGeneticCodeId(refName: string): number;
1407
+ getSeqAdapterRefName(canonicalRefName: string): string;
1408
+ } & {
1409
+ getCanonicalRefName2(refName: string): string;
1410
+ isValidRefName(refName: string): boolean;
1411
+ } & {
1412
+ getAliasesForRefName(refName: string): string[];
1413
+ getRefNameMapForAdapter(adapterConf: {
1414
+ [x: string]: unknown;
1415
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1416
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1417
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1418
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1419
+ }, {
1420
+ error: unknown;
1421
+ loadingP: Promise<void> | undefined;
1422
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1423
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1424
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1425
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1426
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1427
+ loadedGeneticCodes: Record<string, number> | undefined;
1428
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1429
+ statusMessage: string | undefined;
1430
+ statusProgress: number | undefined;
1431
+ statusSource: string | undefined;
1432
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1433
+ } & {
1434
+ getConf(arg: string): any;
1435
+ } & {
1436
+ readonly name: string;
1437
+ readonly aliases: string[];
1438
+ readonly displayName: string;
1439
+ readonly refNameColors: string[];
1440
+ } & {
1441
+ readonly allAliases: string[];
1442
+ hasName(name: string): boolean;
1443
+ } & {
1444
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1445
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1446
+ } & {
1447
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1448
+ regions: import("@jbrowse/core/util").Region[];
1449
+ cytobands: import("@jbrowse/core/util").Feature[];
1450
+ geneticCodes: Record<string, number>;
1451
+ }): void;
1452
+ setError(e: unknown): void;
1453
+ setLoadingP(p?: Promise<void>): void;
1454
+ loadPre(): Promise<void>;
1455
+ } & {
1456
+ load(): Promise<void>;
1457
+ } & {
1458
+ afterAttach(): void;
1459
+ } & {
1460
+ readonly initialized: boolean;
1461
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1462
+ readonly allRefNames: string[] | undefined;
1463
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1464
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1465
+ } & {
1466
+ readonly refNames: string[] | undefined;
1467
+ } & {
1468
+ readonly refNameToIndex: Map<string, number> | undefined;
1469
+ } & {
1470
+ getCanonicalRefName(refName: string): string | undefined;
1471
+ getRefNameColor(refName: string): string | undefined;
1472
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1473
+ getGeneticCodeId(refName: string): number;
1474
+ getSeqAdapterRefName(canonicalRefName: string): string;
1475
+ } & {
1476
+ getCanonicalRefName2(refName: string): string;
1477
+ isValidRefName(refName: string): boolean;
1478
+ } & {
1479
+ getAliasesForRefName(refName: string): string[];
1480
+ getRefNameMapForAdapter(adapterConf: {
1481
+ [x: string]: unknown;
1482
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1483
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1484
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1485
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1486
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1487
+ }> & {
1488
+ error: unknown;
1489
+ loadingP: Promise<void> | undefined;
1490
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1491
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1492
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1493
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1494
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1495
+ loadedGeneticCodes: Record<string, number> | undefined;
1496
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1497
+ statusMessage: string | undefined;
1498
+ statusProgress: number | undefined;
1499
+ statusSource: string | undefined;
1500
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1501
+ } & {
1502
+ getConf(arg: string): any;
1503
+ } & {
1504
+ readonly name: string;
1505
+ readonly aliases: string[];
1506
+ readonly displayName: string;
1507
+ readonly refNameColors: string[];
1508
+ } & {
1509
+ readonly allAliases: string[];
1510
+ hasName(name: string): boolean;
1511
+ } & {
1512
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1513
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1514
+ } & {
1515
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1516
+ regions: import("@jbrowse/core/util").Region[];
1517
+ cytobands: import("@jbrowse/core/util").Feature[];
1518
+ geneticCodes: Record<string, number>;
1519
+ }): void;
1520
+ setError(e: unknown): void;
1521
+ setLoadingP(p?: Promise<void>): void;
1522
+ loadPre(): Promise<void>;
1523
+ } & {
1524
+ load(): Promise<void>;
1525
+ } & {
1526
+ afterAttach(): void;
1527
+ } & {
1528
+ readonly initialized: boolean;
1529
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1530
+ readonly allRefNames: string[] | undefined;
1531
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1532
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1533
+ } & {
1534
+ readonly refNames: string[] | undefined;
1535
+ } & {
1536
+ readonly refNameToIndex: Map<string, number> | undefined;
1537
+ } & {
1538
+ getCanonicalRefName(refName: string): string | undefined;
1539
+ getRefNameColor(refName: string): string | undefined;
1540
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1541
+ getGeneticCodeId(refName: string): number;
1542
+ getSeqAdapterRefName(canonicalRefName: string): string;
1543
+ } & {
1544
+ getCanonicalRefName2(refName: string): string;
1545
+ isValidRefName(refName: string): boolean;
1546
+ } & {
1547
+ getAliasesForRefName(refName: string): string[];
1548
+ getRefNameMapForAdapter(adapterConf: {
1549
+ [x: string]: unknown;
1550
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1551
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1552
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1553
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1554
+ }, {
1555
+ error: unknown;
1556
+ loadingP: Promise<void> | undefined;
1557
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1558
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1559
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1560
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1561
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1562
+ loadedGeneticCodes: Record<string, number> | undefined;
1563
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1564
+ statusMessage: string | undefined;
1565
+ statusProgress: number | undefined;
1566
+ statusSource: string | undefined;
1567
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1568
+ } & {
1569
+ getConf(arg: string): any;
1570
+ } & {
1571
+ readonly name: string;
1572
+ readonly aliases: string[];
1573
+ readonly displayName: string;
1574
+ readonly refNameColors: string[];
1575
+ } & {
1576
+ readonly allAliases: string[];
1577
+ hasName(name: string): boolean;
1578
+ } & {
1579
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1580
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1581
+ } & {
1582
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1583
+ regions: import("@jbrowse/core/util").Region[];
1584
+ cytobands: import("@jbrowse/core/util").Feature[];
1585
+ geneticCodes: Record<string, number>;
1586
+ }): void;
1587
+ setError(e: unknown): void;
1588
+ setLoadingP(p?: Promise<void>): void;
1589
+ loadPre(): Promise<void>;
1590
+ } & {
1591
+ load(): Promise<void>;
1592
+ } & {
1593
+ afterAttach(): void;
1594
+ } & {
1595
+ readonly initialized: boolean;
1596
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1597
+ readonly allRefNames: string[] | undefined;
1598
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1599
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1600
+ } & {
1601
+ readonly refNames: string[] | undefined;
1602
+ } & {
1603
+ readonly refNameToIndex: Map<string, number> | undefined;
1604
+ } & {
1605
+ getCanonicalRefName(refName: string): string | undefined;
1606
+ getRefNameColor(refName: string): string | undefined;
1607
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1608
+ getGeneticCodeId(refName: string): number;
1609
+ getSeqAdapterRefName(canonicalRefName: string): string;
1610
+ } & {
1611
+ getCanonicalRefName2(refName: string): string;
1612
+ isValidRefName(refName: string): boolean;
1613
+ } & {
1614
+ getAliasesForRefName(refName: string): string[];
1615
+ getRefNameMapForAdapter(adapterConf: {
1616
+ [x: string]: unknown;
1617
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1618
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1619
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1620
+ getRefNameMapForAdapter(adapterConf: {
1621
+ [x: string]: unknown;
1622
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1623
+ isValidRefName(refName: string, assemblyName: string): boolean;
1624
+ } & {
1625
+ afterAttach(): void;
1626
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1627
+ addAssembly(configuration: any): void;
1628
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
1629
+ }, {
1630
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1631
+ adminMode: boolean;
1632
+ error: unknown;
1633
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1634
+ pluginManager: PluginManager;
1635
+ } & {
1636
+ setError(error: unknown): void;
1637
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1638
+ setDefaultSession(): void;
1639
+ setSessionPath(path: string): void;
1640
+ renameCurrentSession(newName: string): void;
1641
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1642
+ } & {
1643
+ readonly jbrowse: any;
1644
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1645
+ readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1646
+ setSubschema(slotName: string, data: Record<string, unknown>): any;
1647
+ setSlot(slotName: string, value: unknown): void;
1648
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1649
+ readonly adminMode: boolean;
1650
+ readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1651
+ } & {
1652
+ readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
1653
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1654
+ readonly DialogProps: Record<string, unknown> | undefined;
1655
+ } & {
1656
+ getPreferenceDefault(key: string): unknown;
1657
+ getPreference(key: string): unknown;
1658
+ getDisplayTypeDefault(displayType: string, slot: string): unknown;
1659
+ getDisplayTypeDefaults(): {
1660
+ displayType: string;
1661
+ slot: string;
1662
+ value: unknown;
1663
+ }[];
1664
+ getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
1665
+ } & {
1666
+ readonly animationMode: import("@jbrowse/core/util").AnimationMode;
1667
+ readonly scrollZoom: boolean;
1668
+ readonly numberGrouping: boolean;
1669
+ } & {
1670
+ afterAttach(): void;
1671
+ setSelection(thing: unknown): void;
1672
+ clearSelection(): void;
1673
+ setHovered(thing: unknown): void;
1674
+ setHighlightsVisible(arg: boolean): void;
1675
+ revealHighlights(): void;
1676
+ setPreferenceOverride(key: string, value: unknown): void;
1677
+ clearPreferenceOverrides(): void;
1678
+ clearPreferenceOverride(key: string): void;
1679
+ resetPreferenceChange(path: string[]): void;
1680
+ setScrollZoom(flag: boolean): void;
1681
+ setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
1682
+ setName(str: string): void;
1683
+ setFocusedViewId(viewId: string | undefined): void;
1684
+ removeActiveDialog(): void;
1685
+ queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1686
+ } & {
1687
+ snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1688
+ errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
1689
+ } & {
1690
+ readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1691
+ } & {
1692
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
1693
+ notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
1694
+ setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
1695
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
1696
+ popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1697
+ removeSnackbarMessage(message: string): void;
1698
+ } & {
1699
+ afterAttach(): void;
1700
+ } & {
1701
+ readonly visibleWidget: import("@jbrowse/core/util").Widget | undefined;
1702
+ } & {
1703
+ poppedOut: boolean;
1704
+ } & {
1705
+ readonly drawerVisible: boolean;
1706
+ } & {
1707
+ setDrawerPosition(arg: import("@jbrowse/core/util").DrawerPosition): void;
1708
+ updateDrawerWidth(drawerWidth: number, availableWidth?: number): number;
1709
+ resizeDrawer(distance: number, availableWidth?: number): number;
1710
+ addWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
1711
+ showWidget(widget: any): void;
1712
+ hideWidget(widget: any): void;
1713
+ minimizeWidgetDrawer(): void;
1714
+ showWidgetDrawer(): void;
1715
+ popoutWidget(): void;
1716
+ returnWidgetToDrawer(): void;
1717
+ hideAllWidgets(): void;
1718
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
1719
+ trackId: string;
1720
+ }, opts?: {
1721
+ expandedDisplayId?: string;
1722
+ }): void;
1723
+ afterAttach(): void;
1724
+ } & {
1725
+ readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1726
+ } & {
1727
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: object): any;
1728
+ breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1729
+ teardownConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1730
+ deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1731
+ addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1732
+ clearConnections(): void;
1733
+ captureConnectionTrack(trackId: string): void;
1734
+ updateConnectionTrackConfig(trackConf: Record<string, unknown> & {
1735
+ trackId: string;
1736
+ }): void;
1737
+ setConnectionTrackConfig(trackId: string, connectionId: string, config: Record<string, unknown>): void;
1738
+ pruneConnectionTrackConfig(trackId: string): void;
1739
+ hydrateConnection(connectionId: string): void;
1740
+ } & {
1741
+ getReferringMultiple(trackIds: string[]): Map<string, import("@jbrowse/product-core").ReferringNode[]>;
1742
+ } & {
1743
+ getReferring(trackId: string): import("@jbrowse/product-core").ReferringNode[];
1744
+ } & {
1745
+ dereferenceTrack(trackId: string, referring: import("@jbrowse/product-core").ReferringNode[]): void;
1746
+ } & {
1747
+ getTrackListMenuItems(config: import("@jbrowse/core/configuration").AnyConfigurationModel, view?: import("@jbrowse/core/util").TrackActionView): import("@jbrowse/core/ui").MenuItem[];
1748
+ getTrackActionMenuItems({ config, view, }: {
1749
+ config: import("@jbrowse/core/configuration").AnyConfigurationModel;
1750
+ view?: import("@jbrowse/core/util").TrackActionView;
1751
+ }): import("@jbrowse/core/ui").MenuItem[];
1752
+ } & {
1753
+ readonly themeOptions: import("@jbrowse/core/ui").SerializableThemeArgs;
1754
+ readonly palette: import("@jbrowse/core/ui/palette").JBrowsePalette;
1755
+ readonly styleTheme: import("@jbrowse/core/ui/styleTheme").JBrowseStyleTheme;
1756
+ readonly theme: import("@mui/material").Theme;
1757
+ getActiveThemeOptions(_name?: string): import("@mui/material").ThemeOptions | undefined;
1758
+ } & {
1759
+ setThemeMode(mode: 'light' | 'dark'): void;
1760
+ } & {
1761
+ /**
1762
+ * #getter
1763
+ */
1764
+ readonly version: string;
1765
+ /**
1766
+ * #getter
1767
+ */
1768
+ readonly assemblyNames: string[];
1769
+ /**
1770
+ * #getter
1771
+ */
1772
+ readonly assemblyManager: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1773
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
1774
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1775
+ }, {
1776
+ error: unknown;
1777
+ loadingP: Promise<void> | undefined;
1778
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1779
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1780
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1781
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1782
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1783
+ loadedGeneticCodes: Record<string, number> | undefined;
1784
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1785
+ statusMessage: string | undefined;
1786
+ statusProgress: number | undefined;
1787
+ statusSource: string | undefined;
1788
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1789
+ } & {
1790
+ getConf(arg: string): any;
1791
+ } & {
1792
+ readonly name: string;
1793
+ readonly aliases: string[];
1794
+ readonly displayName: string;
1795
+ readonly refNameColors: string[];
1796
+ } & {
1797
+ readonly allAliases: string[];
1798
+ hasName(name: string): boolean;
1799
+ } & {
1800
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1801
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1802
+ } & {
1803
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1804
+ regions: import("@jbrowse/core/util").Region[];
1805
+ cytobands: import("@jbrowse/core/util").Feature[];
1806
+ geneticCodes: Record<string, number>;
1807
+ }): void;
1808
+ setError(e: unknown): void;
1809
+ setLoadingP(p?: Promise<void>): void;
1810
+ loadPre(): Promise<void>;
1811
+ } & {
1812
+ load(): Promise<void>;
1813
+ } & {
1814
+ afterAttach(): void;
1815
+ } & {
1816
+ readonly initialized: boolean;
1817
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1818
+ readonly allRefNames: string[] | undefined;
1819
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1820
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1821
+ } & {
1822
+ readonly refNames: string[] | undefined;
1823
+ } & {
1824
+ readonly refNameToIndex: Map<string, number> | undefined;
1825
+ } & {
1826
+ getCanonicalRefName(refName: string): string | undefined;
1827
+ getRefNameColor(refName: string): string | undefined;
1828
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1829
+ getGeneticCodeId(refName: string): number;
1830
+ getSeqAdapterRefName(canonicalRefName: string): string;
1831
+ } & {
1832
+ getCanonicalRefName2(refName: string): string;
1833
+ isValidRefName(refName: string): boolean;
1834
+ } & {
1835
+ getAliasesForRefName(refName: string): string[];
1836
+ getRefNameMapForAdapter(adapterConf: {
1837
+ [x: string]: unknown;
1838
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1839
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1840
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1841
+ }> & {
1842
+ unrecognizedReports: {
1843
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
1844
+ reportFor(session: unknown, name: string): {
1845
+ handled: boolean;
1846
+ claim?: Promise<void>;
1847
+ } | undefined;
1848
+ };
1849
+ } & {
1850
+ readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1851
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1852
+ }> & {
1853
+ error: unknown;
1854
+ loadingP: Promise<void> | undefined;
1855
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1856
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1857
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1858
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1859
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1860
+ loadedGeneticCodes: Record<string, number> | undefined;
1861
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1862
+ statusMessage: string | undefined;
1863
+ statusProgress: number | undefined;
1864
+ statusSource: string | undefined;
1865
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1866
+ } & {
1867
+ getConf(arg: string): any;
1868
+ } & {
1869
+ readonly name: string;
1870
+ readonly aliases: string[];
1871
+ readonly displayName: string;
1872
+ readonly refNameColors: string[];
1873
+ } & {
1874
+ readonly allAliases: string[];
1875
+ hasName(name: string): boolean;
1876
+ } & {
1877
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1878
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1879
+ } & {
1880
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1881
+ regions: import("@jbrowse/core/util").Region[];
1882
+ cytobands: import("@jbrowse/core/util").Feature[];
1883
+ geneticCodes: Record<string, number>;
1884
+ }): void;
1885
+ setError(e: unknown): void;
1886
+ setLoadingP(p?: Promise<void>): void;
1887
+ loadPre(): Promise<void>;
1888
+ } & {
1889
+ load(): Promise<void>;
1890
+ } & {
1891
+ afterAttach(): void;
1892
+ } & {
1893
+ readonly initialized: boolean;
1894
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1895
+ readonly allRefNames: string[] | undefined;
1896
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1897
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1898
+ } & {
1899
+ readonly refNames: string[] | undefined;
1900
+ } & {
1901
+ readonly refNameToIndex: Map<string, number> | undefined;
1902
+ } & {
1903
+ getCanonicalRefName(refName: string): string | undefined;
1904
+ getRefNameColor(refName: string): string | undefined;
1905
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1906
+ getGeneticCodeId(refName: string): number;
1907
+ getSeqAdapterRefName(canonicalRefName: string): string;
1908
+ } & {
1909
+ getCanonicalRefName2(refName: string): string;
1910
+ isValidRefName(refName: string): boolean;
1911
+ } & {
1912
+ getAliasesForRefName(refName: string): string[];
1913
+ getRefNameMapForAdapter(adapterConf: {
1914
+ [x: string]: unknown;
1915
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1916
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1917
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1918
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1919
+ }, {
1920
+ error: unknown;
1921
+ loadingP: Promise<void> | undefined;
1922
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1923
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1924
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1925
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1926
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1927
+ loadedGeneticCodes: Record<string, number> | undefined;
1928
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1929
+ statusMessage: string | undefined;
1930
+ statusProgress: number | undefined;
1931
+ statusSource: string | undefined;
1932
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1933
+ } & {
1934
+ getConf(arg: string): any;
1935
+ } & {
1936
+ readonly name: string;
1937
+ readonly aliases: string[];
1938
+ readonly displayName: string;
1939
+ readonly refNameColors: string[];
1940
+ } & {
1941
+ readonly allAliases: string[];
1942
+ hasName(name: string): boolean;
1943
+ } & {
1944
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1945
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1946
+ } & {
1947
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1948
+ regions: import("@jbrowse/core/util").Region[];
1949
+ cytobands: import("@jbrowse/core/util").Feature[];
1950
+ geneticCodes: Record<string, number>;
1951
+ }): void;
1952
+ setError(e: unknown): void;
1953
+ setLoadingP(p?: Promise<void>): void;
1954
+ loadPre(): Promise<void>;
1955
+ } & {
1956
+ load(): Promise<void>;
1957
+ } & {
1958
+ afterAttach(): void;
1959
+ } & {
1960
+ readonly initialized: boolean;
1961
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1962
+ readonly allRefNames: string[] | undefined;
1963
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1964
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1965
+ } & {
1966
+ readonly refNames: string[] | undefined;
1967
+ } & {
1968
+ readonly refNameToIndex: Map<string, number> | undefined;
1969
+ } & {
1970
+ getCanonicalRefName(refName: string): string | undefined;
1971
+ getRefNameColor(refName: string): string | undefined;
1972
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1973
+ getGeneticCodeId(refName: string): number;
1974
+ getSeqAdapterRefName(canonicalRefName: string): string;
1975
+ } & {
1976
+ getCanonicalRefName2(refName: string): string;
1977
+ isValidRefName(refName: string): boolean;
1978
+ } & {
1979
+ getAliasesForRefName(refName: string): string[];
1980
+ getRefNameMapForAdapter(adapterConf: {
1981
+ [x: string]: unknown;
1982
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1983
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1984
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1985
+ } & {
1986
+ getCanonicalAssemblyName(asmName: string): string | undefined;
1987
+ getDisplayName(asmName: string): string;
1988
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1989
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1990
+ }> & {
1991
+ error: unknown;
1992
+ loadingP: Promise<void> | undefined;
1993
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1994
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1995
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1996
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1997
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1998
+ loadedGeneticCodes: Record<string, number> | undefined;
1999
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2000
+ statusMessage: string | undefined;
2001
+ statusProgress: number | undefined;
2002
+ statusSource: string | undefined;
2003
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2004
+ } & {
2005
+ getConf(arg: string): any;
2006
+ } & {
2007
+ readonly name: string;
2008
+ readonly aliases: string[];
2009
+ readonly displayName: string;
2010
+ readonly refNameColors: string[];
2011
+ } & {
2012
+ readonly allAliases: string[];
2013
+ hasName(name: string): boolean;
2014
+ } & {
2015
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2016
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2017
+ } & {
2018
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2019
+ regions: import("@jbrowse/core/util").Region[];
2020
+ cytobands: import("@jbrowse/core/util").Feature[];
2021
+ geneticCodes: Record<string, number>;
2022
+ }): void;
2023
+ setError(e: unknown): void;
2024
+ setLoadingP(p?: Promise<void>): void;
2025
+ loadPre(): Promise<void>;
2026
+ } & {
2027
+ load(): Promise<void>;
2028
+ } & {
2029
+ afterAttach(): void;
2030
+ } & {
2031
+ readonly initialized: boolean;
2032
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2033
+ readonly allRefNames: string[] | undefined;
2034
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2035
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2036
+ } & {
2037
+ readonly refNames: string[] | undefined;
2038
+ } & {
2039
+ readonly refNameToIndex: Map<string, number> | undefined;
2040
+ } & {
2041
+ getCanonicalRefName(refName: string): string | undefined;
2042
+ getRefNameColor(refName: string): string | undefined;
2043
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2044
+ getGeneticCodeId(refName: string): number;
2045
+ getSeqAdapterRefName(canonicalRefName: string): string;
2046
+ } & {
2047
+ getCanonicalRefName2(refName: string): string;
2048
+ isValidRefName(refName: string): boolean;
2049
+ } & {
2050
+ getAliasesForRefName(refName: string): string[];
2051
+ getRefNameMapForAdapter(adapterConf: {
2052
+ [x: string]: unknown;
2053
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2054
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2055
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2056
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2057
+ }, {
2058
+ error: unknown;
2059
+ loadingP: Promise<void> | undefined;
2060
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2061
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2062
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2063
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2064
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2065
+ loadedGeneticCodes: Record<string, number> | undefined;
2066
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2067
+ statusMessage: string | undefined;
2068
+ statusProgress: number | undefined;
2069
+ statusSource: string | undefined;
2070
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2071
+ } & {
2072
+ getConf(arg: string): any;
2073
+ } & {
2074
+ readonly name: string;
2075
+ readonly aliases: string[];
2076
+ readonly displayName: string;
2077
+ readonly refNameColors: string[];
2078
+ } & {
2079
+ readonly allAliases: string[];
2080
+ hasName(name: string): boolean;
2081
+ } & {
2082
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2083
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2084
+ } & {
2085
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2086
+ regions: import("@jbrowse/core/util").Region[];
2087
+ cytobands: import("@jbrowse/core/util").Feature[];
2088
+ geneticCodes: Record<string, number>;
2089
+ }): void;
2090
+ setError(e: unknown): void;
2091
+ setLoadingP(p?: Promise<void>): void;
2092
+ loadPre(): Promise<void>;
2093
+ } & {
2094
+ load(): Promise<void>;
2095
+ } & {
2096
+ afterAttach(): void;
2097
+ } & {
2098
+ readonly initialized: boolean;
2099
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2100
+ readonly allRefNames: string[] | undefined;
2101
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2102
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2103
+ } & {
2104
+ readonly refNames: string[] | undefined;
2105
+ } & {
2106
+ readonly refNameToIndex: Map<string, number> | undefined;
2107
+ } & {
2108
+ getCanonicalRefName(refName: string): string | undefined;
2109
+ getRefNameColor(refName: string): string | undefined;
2110
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2111
+ getGeneticCodeId(refName: string): number;
2112
+ getSeqAdapterRefName(canonicalRefName: string): string;
2113
+ } & {
2114
+ getCanonicalRefName2(refName: string): string;
2115
+ isValidRefName(refName: string): boolean;
2116
+ } & {
2117
+ getAliasesForRefName(refName: string): string[];
2118
+ getRefNameMapForAdapter(adapterConf: {
2119
+ [x: string]: unknown;
2120
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2121
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2122
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2123
+ has(asmName: string): boolean;
2124
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2125
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2126
+ }> & {
2127
+ error: unknown;
2128
+ loadingP: Promise<void> | undefined;
2129
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2130
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2131
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2132
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2133
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2134
+ loadedGeneticCodes: Record<string, number> | undefined;
2135
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2136
+ statusMessage: string | undefined;
2137
+ statusProgress: number | undefined;
2138
+ statusSource: string | undefined;
2139
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2140
+ } & {
2141
+ getConf(arg: string): any;
2142
+ } & {
2143
+ readonly name: string;
2144
+ readonly aliases: string[];
2145
+ readonly displayName: string;
2146
+ readonly refNameColors: string[];
2147
+ } & {
2148
+ readonly allAliases: string[];
2149
+ hasName(name: string): boolean;
2150
+ } & {
2151
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2152
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2153
+ } & {
2154
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2155
+ regions: import("@jbrowse/core/util").Region[];
2156
+ cytobands: import("@jbrowse/core/util").Feature[];
2157
+ geneticCodes: Record<string, number>;
2158
+ }): void;
2159
+ setError(e: unknown): void;
2160
+ setLoadingP(p?: Promise<void>): void;
2161
+ loadPre(): Promise<void>;
2162
+ } & {
2163
+ load(): Promise<void>;
2164
+ } & {
2165
+ afterAttach(): void;
2166
+ } & {
2167
+ readonly initialized: boolean;
2168
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2169
+ readonly allRefNames: string[] | undefined;
2170
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2171
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2172
+ } & {
2173
+ readonly refNames: string[] | undefined;
2174
+ } & {
2175
+ readonly refNameToIndex: Map<string, number> | undefined;
2176
+ } & {
2177
+ getCanonicalRefName(refName: string): string | undefined;
2178
+ getRefNameColor(refName: string): string | undefined;
2179
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2180
+ getGeneticCodeId(refName: string): number;
2181
+ getSeqAdapterRefName(canonicalRefName: string): string;
2182
+ } & {
2183
+ getCanonicalRefName2(refName: string): string;
2184
+ isValidRefName(refName: string): boolean;
2185
+ } & {
2186
+ getAliasesForRefName(refName: string): string[];
2187
+ getRefNameMapForAdapter(adapterConf: {
2188
+ [x: string]: unknown;
2189
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2190
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2191
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2192
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2193
+ }, {
2194
+ error: unknown;
2195
+ loadingP: Promise<void> | undefined;
2196
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2197
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2198
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2199
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2200
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2201
+ loadedGeneticCodes: Record<string, number> | undefined;
2202
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2203
+ statusMessage: string | undefined;
2204
+ statusProgress: number | undefined;
2205
+ statusSource: string | undefined;
2206
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2207
+ } & {
2208
+ getConf(arg: string): any;
2209
+ } & {
2210
+ readonly name: string;
2211
+ readonly aliases: string[];
2212
+ readonly displayName: string;
2213
+ readonly refNameColors: string[];
2214
+ } & {
2215
+ readonly allAliases: string[];
2216
+ hasName(name: string): boolean;
2217
+ } & {
2218
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2219
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2220
+ } & {
2221
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2222
+ regions: import("@jbrowse/core/util").Region[];
2223
+ cytobands: import("@jbrowse/core/util").Feature[];
2224
+ geneticCodes: Record<string, number>;
2225
+ }): void;
2226
+ setError(e: unknown): void;
2227
+ setLoadingP(p?: Promise<void>): void;
2228
+ loadPre(): Promise<void>;
2229
+ } & {
2230
+ load(): Promise<void>;
2231
+ } & {
2232
+ afterAttach(): void;
2233
+ } & {
2234
+ readonly initialized: boolean;
2235
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2236
+ readonly allRefNames: string[] | undefined;
2237
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2238
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2239
+ } & {
2240
+ readonly refNames: string[] | undefined;
2241
+ } & {
2242
+ readonly refNameToIndex: Map<string, number> | undefined;
2243
+ } & {
2244
+ getCanonicalRefName(refName: string): string | undefined;
2245
+ getRefNameColor(refName: string): string | undefined;
2246
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2247
+ getGeneticCodeId(refName: string): number;
2248
+ getSeqAdapterRefName(canonicalRefName: string): string;
2249
+ } & {
2250
+ getCanonicalRefName2(refName: string): string;
2251
+ isValidRefName(refName: string): boolean;
2252
+ } & {
2253
+ getAliasesForRefName(refName: string): string[];
2254
+ getRefNameMapForAdapter(adapterConf: {
2255
+ [x: string]: unknown;
2256
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2257
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2258
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2259
+ readonly assemblyNamesList: string[];
2260
+ readonly configuredAssemblyNames: Set<string>;
2261
+ readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
2262
+ setSubschema(slotName: string, data: Record<string, unknown>): any;
2263
+ setSlot(slotName: string, value: unknown): void;
2264
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
2265
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2266
+ } & {
2267
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
2268
+ } & {
2269
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2270
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2271
+ }> & {
2272
+ error: unknown;
2273
+ loadingP: Promise<void> | undefined;
2274
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2275
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2276
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2277
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2278
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2279
+ loadedGeneticCodes: Record<string, number> | undefined;
2280
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2281
+ statusMessage: string | undefined;
2282
+ statusProgress: number | undefined;
2283
+ statusSource: string | undefined;
2284
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2285
+ } & {
2286
+ getConf(arg: string): any;
2287
+ } & {
2288
+ readonly name: string;
2289
+ readonly aliases: string[];
2290
+ readonly displayName: string;
2291
+ readonly refNameColors: string[];
2292
+ } & {
2293
+ readonly allAliases: string[];
2294
+ hasName(name: string): boolean;
2295
+ } & {
2296
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2297
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2298
+ } & {
2299
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2300
+ regions: import("@jbrowse/core/util").Region[];
2301
+ cytobands: import("@jbrowse/core/util").Feature[];
2302
+ geneticCodes: Record<string, number>;
2303
+ }): void;
2304
+ setError(e: unknown): void;
2305
+ setLoadingP(p?: Promise<void>): void;
2306
+ loadPre(): Promise<void>;
2307
+ } & {
2308
+ load(): Promise<void>;
2309
+ } & {
2310
+ afterAttach(): void;
2311
+ } & {
2312
+ readonly initialized: boolean;
2313
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2314
+ readonly allRefNames: string[] | undefined;
2315
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2316
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2317
+ } & {
2318
+ readonly refNames: string[] | undefined;
2319
+ } & {
2320
+ readonly refNameToIndex: Map<string, number> | undefined;
2321
+ } & {
2322
+ getCanonicalRefName(refName: string): string | undefined;
2323
+ getRefNameColor(refName: string): string | undefined;
2324
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2325
+ getGeneticCodeId(refName: string): number;
2326
+ getSeqAdapterRefName(canonicalRefName: string): string;
2327
+ } & {
2328
+ getCanonicalRefName2(refName: string): string;
2329
+ isValidRefName(refName: string): boolean;
2330
+ } & {
2331
+ getAliasesForRefName(refName: string): string[];
2332
+ getRefNameMapForAdapter(adapterConf: {
2333
+ [x: string]: unknown;
2334
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2335
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2336
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2337
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2338
+ }, {
2339
+ error: unknown;
2340
+ loadingP: Promise<void> | undefined;
2341
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2342
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2343
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2344
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2345
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2346
+ loadedGeneticCodes: Record<string, number> | undefined;
2347
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2348
+ statusMessage: string | undefined;
2349
+ statusProgress: number | undefined;
2350
+ statusSource: string | undefined;
2351
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2352
+ } & {
2353
+ getConf(arg: string): any;
2354
+ } & {
2355
+ readonly name: string;
2356
+ readonly aliases: string[];
2357
+ readonly displayName: string;
2358
+ readonly refNameColors: string[];
2359
+ } & {
2360
+ readonly allAliases: string[];
2361
+ hasName(name: string): boolean;
2362
+ } & {
2363
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2364
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2365
+ } & {
2366
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2367
+ regions: import("@jbrowse/core/util").Region[];
2368
+ cytobands: import("@jbrowse/core/util").Feature[];
2369
+ geneticCodes: Record<string, number>;
2370
+ }): void;
2371
+ setError(e: unknown): void;
2372
+ setLoadingP(p?: Promise<void>): void;
2373
+ loadPre(): Promise<void>;
2374
+ } & {
2375
+ load(): Promise<void>;
2376
+ } & {
2377
+ afterAttach(): void;
2378
+ } & {
2379
+ readonly initialized: boolean;
2380
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2381
+ readonly allRefNames: string[] | undefined;
2382
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2383
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2384
+ } & {
2385
+ readonly refNames: string[] | undefined;
2386
+ } & {
2387
+ readonly refNameToIndex: Map<string, number> | undefined;
2388
+ } & {
2389
+ getCanonicalRefName(refName: string): string | undefined;
2390
+ getRefNameColor(refName: string): string | undefined;
2391
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2392
+ getGeneticCodeId(refName: string): number;
2393
+ getSeqAdapterRefName(canonicalRefName: string): string;
2394
+ } & {
2395
+ getCanonicalRefName2(refName: string): string;
2396
+ isValidRefName(refName: string): boolean;
2397
+ } & {
2398
+ getAliasesForRefName(refName: string): string[];
2399
+ getRefNameMapForAdapter(adapterConf: {
2400
+ [x: string]: unknown;
2401
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2402
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2403
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
2404
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2405
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2406
+ }> & {
2407
+ error: unknown;
2408
+ loadingP: Promise<void> | undefined;
2409
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2410
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2411
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2412
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2413
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2414
+ loadedGeneticCodes: Record<string, number> | undefined;
2415
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2416
+ statusMessage: string | undefined;
2417
+ statusProgress: number | undefined;
2418
+ statusSource: string | undefined;
2419
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2420
+ } & {
2421
+ getConf(arg: string): any;
2422
+ } & {
2423
+ readonly name: string;
2424
+ readonly aliases: string[];
2425
+ readonly displayName: string;
2426
+ readonly refNameColors: string[];
2427
+ } & {
2428
+ readonly allAliases: string[];
2429
+ hasName(name: string): boolean;
2430
+ } & {
2431
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2432
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2433
+ } & {
2434
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2435
+ regions: import("@jbrowse/core/util").Region[];
2436
+ cytobands: import("@jbrowse/core/util").Feature[];
2437
+ geneticCodes: Record<string, number>;
2438
+ }): void;
2439
+ setError(e: unknown): void;
2440
+ setLoadingP(p?: Promise<void>): void;
2441
+ loadPre(): Promise<void>;
2442
+ } & {
2443
+ load(): Promise<void>;
2444
+ } & {
2445
+ afterAttach(): void;
2446
+ } & {
2447
+ readonly initialized: boolean;
2448
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2449
+ readonly allRefNames: string[] | undefined;
2450
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2451
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2452
+ } & {
2453
+ readonly refNames: string[] | undefined;
2454
+ } & {
2455
+ readonly refNameToIndex: Map<string, number> | undefined;
2456
+ } & {
2457
+ getCanonicalRefName(refName: string): string | undefined;
2458
+ getRefNameColor(refName: string): string | undefined;
2459
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2460
+ getGeneticCodeId(refName: string): number;
2461
+ getSeqAdapterRefName(canonicalRefName: string): string;
2462
+ } & {
2463
+ getCanonicalRefName2(refName: string): string;
2464
+ isValidRefName(refName: string): boolean;
2465
+ } & {
2466
+ getAliasesForRefName(refName: string): string[];
2467
+ getRefNameMapForAdapter(adapterConf: {
2468
+ [x: string]: unknown;
2469
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2470
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2471
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2472
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2473
+ }, {
2474
+ error: unknown;
2475
+ loadingP: Promise<void> | undefined;
2476
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2477
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2478
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2479
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2480
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2481
+ loadedGeneticCodes: Record<string, number> | undefined;
2482
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2483
+ statusMessage: string | undefined;
2484
+ statusProgress: number | undefined;
2485
+ statusSource: string | undefined;
2486
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2487
+ } & {
2488
+ getConf(arg: string): any;
2489
+ } & {
2490
+ readonly name: string;
2491
+ readonly aliases: string[];
2492
+ readonly displayName: string;
2493
+ readonly refNameColors: string[];
2494
+ } & {
2495
+ readonly allAliases: string[];
2496
+ hasName(name: string): boolean;
2497
+ } & {
2498
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2499
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2500
+ } & {
2501
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2502
+ regions: import("@jbrowse/core/util").Region[];
2503
+ cytobands: import("@jbrowse/core/util").Feature[];
2504
+ geneticCodes: Record<string, number>;
2505
+ }): void;
2506
+ setError(e: unknown): void;
2507
+ setLoadingP(p?: Promise<void>): void;
2508
+ loadPre(): Promise<void>;
2509
+ } & {
2510
+ load(): Promise<void>;
2511
+ } & {
2512
+ afterAttach(): void;
2513
+ } & {
2514
+ readonly initialized: boolean;
2515
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2516
+ readonly allRefNames: string[] | undefined;
2517
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2518
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2519
+ } & {
2520
+ readonly refNames: string[] | undefined;
2521
+ } & {
2522
+ readonly refNameToIndex: Map<string, number> | undefined;
2523
+ } & {
2524
+ getCanonicalRefName(refName: string): string | undefined;
2525
+ getRefNameColor(refName: string): string | undefined;
2526
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2527
+ getGeneticCodeId(refName: string): number;
2528
+ getSeqAdapterRefName(canonicalRefName: string): string;
2529
+ } & {
2530
+ getCanonicalRefName2(refName: string): string;
2531
+ isValidRefName(refName: string): boolean;
2532
+ } & {
2533
+ getAliasesForRefName(refName: string): string[];
2534
+ getRefNameMapForAdapter(adapterConf: {
2535
+ [x: string]: unknown;
2536
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2537
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2538
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2539
+ getRefNameMapForAdapter(adapterConf: {
2540
+ [x: string]: unknown;
2541
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2542
+ isValidRefName(refName: string, assemblyName: string): boolean;
2543
+ } & {
2544
+ afterAttach(): void;
2545
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
2546
+ addAssembly(configuration: any): void;
2547
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2548
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
2549
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2550
+ }, {
2551
+ error: unknown;
2552
+ loadingP: Promise<void> | undefined;
2553
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2554
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2555
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2556
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2557
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2558
+ loadedGeneticCodes: Record<string, number> | undefined;
2559
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2560
+ statusMessage: string | undefined;
2561
+ statusProgress: number | undefined;
2562
+ statusSource: string | undefined;
2563
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2564
+ } & {
2565
+ getConf(arg: string): any;
2566
+ } & {
2567
+ readonly name: string;
2568
+ readonly aliases: string[];
2569
+ readonly displayName: string;
2570
+ readonly refNameColors: string[];
2571
+ } & {
2572
+ readonly allAliases: string[];
2573
+ hasName(name: string): boolean;
2574
+ } & {
2575
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2576
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2577
+ } & {
2578
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2579
+ regions: import("@jbrowse/core/util").Region[];
2580
+ cytobands: import("@jbrowse/core/util").Feature[];
2581
+ geneticCodes: Record<string, number>;
2582
+ }): void;
2583
+ setError(e: unknown): void;
2584
+ setLoadingP(p?: Promise<void>): void;
2585
+ loadPre(): Promise<void>;
2586
+ } & {
2587
+ load(): Promise<void>;
2588
+ } & {
2589
+ afterAttach(): void;
2590
+ } & {
2591
+ readonly initialized: boolean;
2592
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2593
+ readonly allRefNames: string[] | undefined;
2594
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2595
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2596
+ } & {
2597
+ readonly refNames: string[] | undefined;
2598
+ } & {
2599
+ readonly refNameToIndex: Map<string, number> | undefined;
2600
+ } & {
2601
+ getCanonicalRefName(refName: string): string | undefined;
2602
+ getRefNameColor(refName: string): string | undefined;
2603
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2604
+ getGeneticCodeId(refName: string): number;
2605
+ getSeqAdapterRefName(canonicalRefName: string): string;
2606
+ } & {
2607
+ getCanonicalRefName2(refName: string): string;
2608
+ isValidRefName(refName: string): boolean;
2609
+ } & {
2610
+ getAliasesForRefName(refName: string): string[];
2611
+ getRefNameMapForAdapter(adapterConf: {
2612
+ [x: string]: unknown;
2613
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2614
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2615
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2616
+ }, {
2617
+ unrecognizedReports: {
2618
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
2619
+ reportFor(session: unknown, name: string): {
2620
+ handled: boolean;
2621
+ claim?: Promise<void>;
2622
+ } | undefined;
2623
+ };
2624
+ } & {
2625
+ readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2626
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2627
+ }> & {
2628
+ error: unknown;
2629
+ loadingP: Promise<void> | undefined;
2630
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2631
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2632
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2633
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2634
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2635
+ loadedGeneticCodes: Record<string, number> | undefined;
2636
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2637
+ statusMessage: string | undefined;
2638
+ statusProgress: number | undefined;
2639
+ statusSource: string | undefined;
2640
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2641
+ } & {
2642
+ getConf(arg: string): any;
2643
+ } & {
2644
+ readonly name: string;
2645
+ readonly aliases: string[];
2646
+ readonly displayName: string;
2647
+ readonly refNameColors: string[];
2648
+ } & {
2649
+ readonly allAliases: string[];
2650
+ hasName(name: string): boolean;
2651
+ } & {
2652
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2653
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2654
+ } & {
2655
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2656
+ regions: import("@jbrowse/core/util").Region[];
2657
+ cytobands: import("@jbrowse/core/util").Feature[];
2658
+ geneticCodes: Record<string, number>;
2659
+ }): void;
2660
+ setError(e: unknown): void;
2661
+ setLoadingP(p?: Promise<void>): void;
2662
+ loadPre(): Promise<void>;
2663
+ } & {
2664
+ load(): Promise<void>;
2665
+ } & {
2666
+ afterAttach(): void;
2667
+ } & {
2668
+ readonly initialized: boolean;
2669
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2670
+ readonly allRefNames: string[] | undefined;
2671
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2672
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2673
+ } & {
2674
+ readonly refNames: string[] | undefined;
2675
+ } & {
2676
+ readonly refNameToIndex: Map<string, number> | undefined;
2677
+ } & {
2678
+ getCanonicalRefName(refName: string): string | undefined;
2679
+ getRefNameColor(refName: string): string | undefined;
2680
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2681
+ getGeneticCodeId(refName: string): number;
2682
+ getSeqAdapterRefName(canonicalRefName: string): string;
2683
+ } & {
2684
+ getCanonicalRefName2(refName: string): string;
2685
+ isValidRefName(refName: string): boolean;
2686
+ } & {
2687
+ getAliasesForRefName(refName: string): string[];
2688
+ getRefNameMapForAdapter(adapterConf: {
2689
+ [x: string]: unknown;
2690
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2691
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2692
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2693
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2694
+ }, {
2695
+ error: unknown;
2696
+ loadingP: Promise<void> | undefined;
2697
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2698
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2699
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2700
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2701
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2702
+ loadedGeneticCodes: Record<string, number> | undefined;
2703
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2704
+ statusMessage: string | undefined;
2705
+ statusProgress: number | undefined;
2706
+ statusSource: string | undefined;
2707
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2708
+ } & {
2709
+ getConf(arg: string): any;
2710
+ } & {
2711
+ readonly name: string;
2712
+ readonly aliases: string[];
2713
+ readonly displayName: string;
2714
+ readonly refNameColors: string[];
2715
+ } & {
2716
+ readonly allAliases: string[];
2717
+ hasName(name: string): boolean;
2718
+ } & {
2719
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2720
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2721
+ } & {
2722
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2723
+ regions: import("@jbrowse/core/util").Region[];
2724
+ cytobands: import("@jbrowse/core/util").Feature[];
2725
+ geneticCodes: Record<string, number>;
2726
+ }): void;
2727
+ setError(e: unknown): void;
2728
+ setLoadingP(p?: Promise<void>): void;
2729
+ loadPre(): Promise<void>;
2730
+ } & {
2731
+ load(): Promise<void>;
2732
+ } & {
2733
+ afterAttach(): void;
2734
+ } & {
2735
+ readonly initialized: boolean;
2736
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2737
+ readonly allRefNames: string[] | undefined;
2738
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2739
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2740
+ } & {
2741
+ readonly refNames: string[] | undefined;
2742
+ } & {
2743
+ readonly refNameToIndex: Map<string, number> | undefined;
2744
+ } & {
2745
+ getCanonicalRefName(refName: string): string | undefined;
2746
+ getRefNameColor(refName: string): string | undefined;
2747
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2748
+ getGeneticCodeId(refName: string): number;
2749
+ getSeqAdapterRefName(canonicalRefName: string): string;
2750
+ } & {
2751
+ getCanonicalRefName2(refName: string): string;
2752
+ isValidRefName(refName: string): boolean;
2753
+ } & {
2754
+ getAliasesForRefName(refName: string): string[];
2755
+ getRefNameMapForAdapter(adapterConf: {
2756
+ [x: string]: unknown;
2757
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2758
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2759
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2760
+ } & {
2761
+ getCanonicalAssemblyName(asmName: string): string | undefined;
2762
+ getDisplayName(asmName: string): string;
2763
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2764
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2765
+ }> & {
2766
+ error: unknown;
2767
+ loadingP: Promise<void> | undefined;
2768
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2769
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2770
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2771
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2772
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2773
+ loadedGeneticCodes: Record<string, number> | undefined;
2774
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2775
+ statusMessage: string | undefined;
2776
+ statusProgress: number | undefined;
2777
+ statusSource: string | undefined;
2778
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2779
+ } & {
2780
+ getConf(arg: string): any;
2781
+ } & {
2782
+ readonly name: string;
2783
+ readonly aliases: string[];
2784
+ readonly displayName: string;
2785
+ readonly refNameColors: string[];
2786
+ } & {
2787
+ readonly allAliases: string[];
2788
+ hasName(name: string): boolean;
2789
+ } & {
2790
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2791
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2792
+ } & {
2793
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2794
+ regions: import("@jbrowse/core/util").Region[];
2795
+ cytobands: import("@jbrowse/core/util").Feature[];
2796
+ geneticCodes: Record<string, number>;
2797
+ }): void;
2798
+ setError(e: unknown): void;
2799
+ setLoadingP(p?: Promise<void>): void;
2800
+ loadPre(): Promise<void>;
2801
+ } & {
2802
+ load(): Promise<void>;
2803
+ } & {
2804
+ afterAttach(): void;
2805
+ } & {
2806
+ readonly initialized: boolean;
2807
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2808
+ readonly allRefNames: string[] | undefined;
2809
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2810
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2811
+ } & {
2812
+ readonly refNames: string[] | undefined;
2813
+ } & {
2814
+ readonly refNameToIndex: Map<string, number> | undefined;
2815
+ } & {
2816
+ getCanonicalRefName(refName: string): string | undefined;
2817
+ getRefNameColor(refName: string): string | undefined;
2818
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2819
+ getGeneticCodeId(refName: string): number;
2820
+ getSeqAdapterRefName(canonicalRefName: string): string;
2821
+ } & {
2822
+ getCanonicalRefName2(refName: string): string;
2823
+ isValidRefName(refName: string): boolean;
2824
+ } & {
2825
+ getAliasesForRefName(refName: string): string[];
2826
+ getRefNameMapForAdapter(adapterConf: {
2827
+ [x: string]: unknown;
2828
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2829
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2830
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2831
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2832
+ }, {
2833
+ error: unknown;
2834
+ loadingP: Promise<void> | undefined;
2835
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2836
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2837
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2838
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2839
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2840
+ loadedGeneticCodes: Record<string, number> | undefined;
2841
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2842
+ statusMessage: string | undefined;
2843
+ statusProgress: number | undefined;
2844
+ statusSource: string | undefined;
2845
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2846
+ } & {
2847
+ getConf(arg: string): any;
2848
+ } & {
2849
+ readonly name: string;
2850
+ readonly aliases: string[];
2851
+ readonly displayName: string;
2852
+ readonly refNameColors: string[];
2853
+ } & {
2854
+ readonly allAliases: string[];
2855
+ hasName(name: string): boolean;
2856
+ } & {
2857
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2858
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2859
+ } & {
2860
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2861
+ regions: import("@jbrowse/core/util").Region[];
2862
+ cytobands: import("@jbrowse/core/util").Feature[];
2863
+ geneticCodes: Record<string, number>;
2864
+ }): void;
2865
+ setError(e: unknown): void;
2866
+ setLoadingP(p?: Promise<void>): void;
2867
+ loadPre(): Promise<void>;
2868
+ } & {
2869
+ load(): Promise<void>;
2870
+ } & {
2871
+ afterAttach(): void;
2872
+ } & {
2873
+ readonly initialized: boolean;
2874
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2875
+ readonly allRefNames: string[] | undefined;
2876
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2877
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2878
+ } & {
2879
+ readonly refNames: string[] | undefined;
2880
+ } & {
2881
+ readonly refNameToIndex: Map<string, number> | undefined;
2882
+ } & {
2883
+ getCanonicalRefName(refName: string): string | undefined;
2884
+ getRefNameColor(refName: string): string | undefined;
2885
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2886
+ getGeneticCodeId(refName: string): number;
2887
+ getSeqAdapterRefName(canonicalRefName: string): string;
2888
+ } & {
2889
+ getCanonicalRefName2(refName: string): string;
2890
+ isValidRefName(refName: string): boolean;
2891
+ } & {
2892
+ getAliasesForRefName(refName: string): string[];
2893
+ getRefNameMapForAdapter(adapterConf: {
2894
+ [x: string]: unknown;
2895
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2896
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2897
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2898
+ has(asmName: string): boolean;
2899
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2900
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2901
+ }> & {
2902
+ error: unknown;
2903
+ loadingP: Promise<void> | undefined;
2904
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2905
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2906
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2907
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2908
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2909
+ loadedGeneticCodes: Record<string, number> | undefined;
2910
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2911
+ statusMessage: string | undefined;
2912
+ statusProgress: number | undefined;
2913
+ statusSource: string | undefined;
2914
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2915
+ } & {
2916
+ getConf(arg: string): any;
2917
+ } & {
2918
+ readonly name: string;
2919
+ readonly aliases: string[];
2920
+ readonly displayName: string;
2921
+ readonly refNameColors: string[];
2922
+ } & {
2923
+ readonly allAliases: string[];
2924
+ hasName(name: string): boolean;
2925
+ } & {
2926
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2927
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2928
+ } & {
2929
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2930
+ regions: import("@jbrowse/core/util").Region[];
2931
+ cytobands: import("@jbrowse/core/util").Feature[];
2932
+ geneticCodes: Record<string, number>;
2933
+ }): void;
2934
+ setError(e: unknown): void;
2935
+ setLoadingP(p?: Promise<void>): void;
2936
+ loadPre(): Promise<void>;
2937
+ } & {
2938
+ load(): Promise<void>;
2939
+ } & {
2940
+ afterAttach(): void;
2941
+ } & {
2942
+ readonly initialized: boolean;
2943
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2944
+ readonly allRefNames: string[] | undefined;
2945
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2946
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2947
+ } & {
2948
+ readonly refNames: string[] | undefined;
2949
+ } & {
2950
+ readonly refNameToIndex: Map<string, number> | undefined;
2951
+ } & {
2952
+ getCanonicalRefName(refName: string): string | undefined;
2953
+ getRefNameColor(refName: string): string | undefined;
2954
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2955
+ getGeneticCodeId(refName: string): number;
2956
+ getSeqAdapterRefName(canonicalRefName: string): string;
2957
+ } & {
2958
+ getCanonicalRefName2(refName: string): string;
2959
+ isValidRefName(refName: string): boolean;
2960
+ } & {
2961
+ getAliasesForRefName(refName: string): string[];
2962
+ getRefNameMapForAdapter(adapterConf: {
2963
+ [x: string]: unknown;
2964
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2965
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2966
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2967
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2968
+ }, {
2969
+ error: unknown;
2970
+ loadingP: Promise<void> | undefined;
2971
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2972
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2973
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2974
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2975
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2976
+ loadedGeneticCodes: Record<string, number> | undefined;
2977
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2978
+ statusMessage: string | undefined;
2979
+ statusProgress: number | undefined;
2980
+ statusSource: string | undefined;
2981
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2982
+ } & {
2983
+ getConf(arg: string): any;
2984
+ } & {
2985
+ readonly name: string;
2986
+ readonly aliases: string[];
2987
+ readonly displayName: string;
2988
+ readonly refNameColors: string[];
2989
+ } & {
2990
+ readonly allAliases: string[];
2991
+ hasName(name: string): boolean;
2992
+ } & {
2993
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2994
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2995
+ } & {
2996
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2997
+ regions: import("@jbrowse/core/util").Region[];
2998
+ cytobands: import("@jbrowse/core/util").Feature[];
2999
+ geneticCodes: Record<string, number>;
3000
+ }): void;
3001
+ setError(e: unknown): void;
3002
+ setLoadingP(p?: Promise<void>): void;
3003
+ loadPre(): Promise<void>;
3004
+ } & {
3005
+ load(): Promise<void>;
3006
+ } & {
3007
+ afterAttach(): void;
3008
+ } & {
3009
+ readonly initialized: boolean;
3010
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3011
+ readonly allRefNames: string[] | undefined;
3012
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3013
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3014
+ } & {
3015
+ readonly refNames: string[] | undefined;
3016
+ } & {
3017
+ readonly refNameToIndex: Map<string, number> | undefined;
3018
+ } & {
3019
+ getCanonicalRefName(refName: string): string | undefined;
3020
+ getRefNameColor(refName: string): string | undefined;
3021
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
3022
+ getGeneticCodeId(refName: string): number;
3023
+ getSeqAdapterRefName(canonicalRefName: string): string;
3024
+ } & {
3025
+ getCanonicalRefName2(refName: string): string;
3026
+ isValidRefName(refName: string): boolean;
3027
+ } & {
3028
+ getAliasesForRefName(refName: string): string[];
3029
+ getRefNameMapForAdapter(adapterConf: {
3030
+ [x: string]: unknown;
3031
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
3032
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
3033
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
3034
+ readonly assemblyNamesList: string[];
3035
+ readonly configuredAssemblyNames: Set<string>;
3036
+ readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
3037
+ setSubschema(slotName: string, data: Record<string, unknown>): any;
3038
+ setSlot(slotName: string, value: unknown): void;
3039
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
3040
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3041
+ } & {
3042
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
3043
+ } & {
3044
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
3045
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3046
+ }> & {
3047
+ error: unknown;
3048
+ loadingP: Promise<void> | undefined;
3049
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3050
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3051
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3052
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3053
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3054
+ loadedGeneticCodes: Record<string, number> | undefined;
3055
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3056
+ statusMessage: string | undefined;
3057
+ statusProgress: number | undefined;
3058
+ statusSource: string | undefined;
3059
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
3060
+ } & {
3061
+ getConf(arg: string): any;
3062
+ } & {
3063
+ readonly name: string;
3064
+ readonly aliases: string[];
3065
+ readonly displayName: string;
3066
+ readonly refNameColors: string[];
3067
+ } & {
3068
+ readonly allAliases: string[];
3069
+ hasName(name: string): boolean;
3070
+ } & {
3071
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
3072
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
3073
+ } & {
3074
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
3075
+ regions: import("@jbrowse/core/util").Region[];
3076
+ cytobands: import("@jbrowse/core/util").Feature[];
3077
+ geneticCodes: Record<string, number>;
3078
+ }): void;
3079
+ setError(e: unknown): void;
3080
+ setLoadingP(p?: Promise<void>): void;
3081
+ loadPre(): Promise<void>;
3082
+ } & {
3083
+ load(): Promise<void>;
3084
+ } & {
3085
+ afterAttach(): void;
3086
+ } & {
3087
+ readonly initialized: boolean;
3088
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3089
+ readonly allRefNames: string[] | undefined;
3090
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3091
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3092
+ } & {
3093
+ readonly refNames: string[] | undefined;
3094
+ } & {
3095
+ readonly refNameToIndex: Map<string, number> | undefined;
3096
+ } & {
3097
+ getCanonicalRefName(refName: string): string | undefined;
3098
+ getRefNameColor(refName: string): string | undefined;
3099
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
3100
+ getGeneticCodeId(refName: string): number;
3101
+ getSeqAdapterRefName(canonicalRefName: string): string;
3102
+ } & {
3103
+ getCanonicalRefName2(refName: string): string;
3104
+ isValidRefName(refName: string): boolean;
3105
+ } & {
3106
+ getAliasesForRefName(refName: string): string[];
3107
+ getRefNameMapForAdapter(adapterConf: {
3108
+ [x: string]: unknown;
3109
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
3110
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
3111
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3112
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3113
+ }, {
3114
+ error: unknown;
3115
+ loadingP: Promise<void> | undefined;
3116
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3117
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3118
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3119
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3120
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3121
+ loadedGeneticCodes: Record<string, number> | undefined;
3122
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3123
+ statusMessage: string | undefined;
3124
+ statusProgress: number | undefined;
3125
+ statusSource: string | undefined;
3126
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
3127
+ } & {
3128
+ getConf(arg: string): any;
3129
+ } & {
3130
+ readonly name: string;
3131
+ readonly aliases: string[];
3132
+ readonly displayName: string;
3133
+ readonly refNameColors: string[];
3134
+ } & {
3135
+ readonly allAliases: string[];
3136
+ hasName(name: string): boolean;
3137
+ } & {
3138
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
3139
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
3140
+ } & {
3141
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
3142
+ regions: import("@jbrowse/core/util").Region[];
3143
+ cytobands: import("@jbrowse/core/util").Feature[];
3144
+ geneticCodes: Record<string, number>;
3145
+ }): void;
3146
+ setError(e: unknown): void;
3147
+ setLoadingP(p?: Promise<void>): void;
3148
+ loadPre(): Promise<void>;
3149
+ } & {
3150
+ load(): Promise<void>;
3151
+ } & {
3152
+ afterAttach(): void;
3153
+ } & {
3154
+ readonly initialized: boolean;
3155
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3156
+ readonly allRefNames: string[] | undefined;
3157
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3158
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3159
+ } & {
3160
+ readonly refNames: string[] | undefined;
3161
+ } & {
3162
+ readonly refNameToIndex: Map<string, number> | undefined;
3163
+ } & {
3164
+ getCanonicalRefName(refName: string): string | undefined;
3165
+ getRefNameColor(refName: string): string | undefined;
3166
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
3167
+ getGeneticCodeId(refName: string): number;
3168
+ getSeqAdapterRefName(canonicalRefName: string): string;
3169
+ } & {
3170
+ getCanonicalRefName2(refName: string): string;
3171
+ isValidRefName(refName: string): boolean;
3172
+ } & {
3173
+ getAliasesForRefName(refName: string): string[];
3174
+ getRefNameMapForAdapter(adapterConf: {
3175
+ [x: string]: unknown;
3176
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
3177
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
3178
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
3179
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
3180
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3181
+ }> & {
3182
+ error: unknown;
3183
+ loadingP: Promise<void> | undefined;
3184
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3185
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3186
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3187
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3188
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3189
+ loadedGeneticCodes: Record<string, number> | undefined;
3190
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3191
+ statusMessage: string | undefined;
3192
+ statusProgress: number | undefined;
3193
+ statusSource: string | undefined;
3194
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
3195
+ } & {
3196
+ getConf(arg: string): any;
3197
+ } & {
3198
+ readonly name: string;
3199
+ readonly aliases: string[];
3200
+ readonly displayName: string;
3201
+ readonly refNameColors: string[];
3202
+ } & {
3203
+ readonly allAliases: string[];
3204
+ hasName(name: string): boolean;
3205
+ } & {
3206
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
3207
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
3208
+ } & {
3209
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
3210
+ regions: import("@jbrowse/core/util").Region[];
3211
+ cytobands: import("@jbrowse/core/util").Feature[];
3212
+ geneticCodes: Record<string, number>;
3213
+ }): void;
3214
+ setError(e: unknown): void;
3215
+ setLoadingP(p?: Promise<void>): void;
3216
+ loadPre(): Promise<void>;
3217
+ } & {
3218
+ load(): Promise<void>;
3219
+ } & {
3220
+ afterAttach(): void;
3221
+ } & {
3222
+ readonly initialized: boolean;
3223
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3224
+ readonly allRefNames: string[] | undefined;
3225
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3226
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3227
+ } & {
3228
+ readonly refNames: string[] | undefined;
3229
+ } & {
3230
+ readonly refNameToIndex: Map<string, number> | undefined;
3231
+ } & {
3232
+ getCanonicalRefName(refName: string): string | undefined;
3233
+ getRefNameColor(refName: string): string | undefined;
3234
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
3235
+ getGeneticCodeId(refName: string): number;
3236
+ getSeqAdapterRefName(canonicalRefName: string): string;
3237
+ } & {
3238
+ getCanonicalRefName2(refName: string): string;
3239
+ isValidRefName(refName: string): boolean;
3240
+ } & {
3241
+ getAliasesForRefName(refName: string): string[];
3242
+ getRefNameMapForAdapter(adapterConf: {
3243
+ [x: string]: unknown;
3244
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
3245
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
3246
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
3247
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
3248
+ }, {
3249
+ error: unknown;
3250
+ loadingP: Promise<void> | undefined;
3251
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3252
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3253
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3254
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3255
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3256
+ loadedGeneticCodes: Record<string, number> | undefined;
3257
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3258
+ statusMessage: string | undefined;
3259
+ statusProgress: number | undefined;
3260
+ statusSource: string | undefined;
3261
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
3262
+ } & {
3263
+ getConf(arg: string): any;
3264
+ } & {
3265
+ readonly name: string;
3266
+ readonly aliases: string[];
3267
+ readonly displayName: string;
3268
+ readonly refNameColors: string[];
3269
+ } & {
3270
+ readonly allAliases: string[];
3271
+ hasName(name: string): boolean;
3272
+ } & {
3273
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
3274
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
3275
+ } & {
3276
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
3277
+ regions: import("@jbrowse/core/util").Region[];
3278
+ cytobands: import("@jbrowse/core/util").Feature[];
3279
+ geneticCodes: Record<string, number>;
3280
+ }): void;
3281
+ setError(e: unknown): void;
3282
+ setLoadingP(p?: Promise<void>): void;
3283
+ loadPre(): Promise<void>;
3284
+ } & {
3285
+ load(): Promise<void>;
3286
+ } & {
3287
+ afterAttach(): void;
3288
+ } & {
3289
+ readonly initialized: boolean;
3290
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3291
+ readonly allRefNames: string[] | undefined;
3292
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3293
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3294
+ } & {
3295
+ readonly refNames: string[] | undefined;
3296
+ } & {
3297
+ readonly refNameToIndex: Map<string, number> | undefined;
3298
+ } & {
3299
+ getCanonicalRefName(refName: string): string | undefined;
3300
+ getRefNameColor(refName: string): string | undefined;
3301
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
3302
+ getGeneticCodeId(refName: string): number;
3303
+ getSeqAdapterRefName(canonicalRefName: string): string;
3304
+ } & {
3305
+ getCanonicalRefName2(refName: string): string;
3306
+ isValidRefName(refName: string): boolean;
3307
+ } & {
3308
+ getAliasesForRefName(refName: string): string[];
3309
+ getRefNameMapForAdapter(adapterConf: {
3310
+ [x: string]: unknown;
3311
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
3312
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
3313
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
3314
+ getRefNameMapForAdapter(adapterConf: {
3315
+ [x: string]: unknown;
3316
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
3317
+ isValidRefName(refName: string, assemblyName: string): boolean;
3318
+ } & {
3319
+ afterAttach(): void;
3320
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3321
+ addAssembly(configuration: any): void;
3322
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
3323
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
3324
+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
3325
+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
3326
+ widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
3327
+ activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
3328
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
3329
+ }> & import("@jbrowse/mobx-state-tree")._NotCustomized>;