@jbrowse/embedded-core 4.3.0 → 5.0.0-beta.10

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Files changed (19) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +2818 -0
  2. package/esm/EmbeddedSessionMixin.js +61 -0
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +1448 -0
  4. package/esm/EmbeddedSessionThemeMixin.js +113 -0
  5. package/esm/createEmbeddedRootModel.d.ts +1638 -0
  6. package/esm/createEmbeddedRootModel.js +126 -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 +14 -18
  11. package/package.json +12 -14
  12. package/esm/ui/ModalWidget.d.ts +0 -5
  13. package/esm/ui/ModalWidget.js +0 -32
  14. package/esm/ui/VersionAboutDialog.d.ts +0 -5
  15. package/esm/ui/VersionAboutDialog.js +0 -13
  16. package/esm/ui/ViewMenu.d.ts +0 -8
  17. package/esm/ui/ViewMenu.js +0 -8
  18. package/esm/ui/ViewTitle.d.ts +0 -5
  19. package/esm/ui/ViewTitle.js +0 -47
package/esm/EmbeddedSessionMixin.d.ts ADDED
@@ -0,0 +1,2818 @@
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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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+ assemblyNames: 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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+ * Each product composes this mixin. A factory taking the product's view type
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+ * and tracks mixin as parameters does not typecheck usefully:
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+ * `types.compose`'s overloads are declared over `IModelType<P, O, FC, FS>`, so
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+ * a model passed as a naked type parameter gives nothing to infer those four
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+ * from, and `session.view` becomes `any` at every embedder call site with no
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+ * type error. Passing only concrete types to `compose` keeps the products'
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+ * views typed.
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+ *
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+ * Each product therefore declares its tracks mixin, `view` prop, and the
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+ * `views`/`addView`/`removeView` members that read `self.view`, because those
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+ * members 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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+ highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
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+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ highlightLabelsVisible: 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]>;
46
+ }, never>, never>, "focusedViewId" | "heldForMissingPlugins" | "highlightLabelsVisible" | "highlights" | "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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+ highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
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+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ highlightLabelsVisible: 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;
69
+ loadingP: Promise<void> | undefined;
70
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ loadedGeneticCodes: Record<string, number> | undefined;
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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ statusMessage: string | undefined;
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+ statusProgress: number | undefined;
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+ statusSource: string | undefined;
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+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
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+ } & {
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+ getConf(arg: string): any;
83
+ } & {
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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;
94
+ } & {
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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>;
103
+ } & {
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+ load(): Promise<void>;
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+ } & {
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+ afterAttach(): void;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly allRefNames: string[] | undefined;
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+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ } & {
113
+ readonly refNames: string[] | undefined;
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+ } & {
115
+ readonly refNameToIndex: Map<string, number> | undefined;
116
+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
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+ getGeneticCodeId(refName: string): number;
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+ getSeqAdapterRefName(canonicalRefName: string): string;
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+ } & {
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+ getCanonicalRefName2(refName: string): string;
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+ isValidRefName(refName: string): boolean;
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+ } & {
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+ getRefNamePosition(refName: string): number | undefined;
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+ getAliasesForRefName(refName: string): string[];
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+ getRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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+ }, {
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+ unrecognizedReports: {
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+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
136
+ reportFor(session: unknown, name: string): {
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+ handled: boolean;
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+ claim?: Promise<void>;
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+ } | undefined;
140
+ };
141
+ } & {
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+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
143
+ } & {
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+ getCanonicalAssemblyName(asmName: string): string | undefined;
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+ getDisplayName(asmName: string): string;
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+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
148
+ }> & {
149
+ error: unknown;
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+ loadingP: Promise<void> | undefined;
151
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
152
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
153
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
154
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
155
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
156
+ loadedGeneticCodes: Record<string, number> | undefined;
157
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
158
+ statusMessage: string | undefined;
159
+ statusProgress: number | undefined;
160
+ statusSource: string | undefined;
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+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
162
+ } & {
163
+ getConf(arg: string): any;
164
+ } & {
165
+ readonly name: string;
166
+ readonly aliases: string[];
167
+ readonly displayName: string;
168
+ readonly refNameColors: string[];
169
+ } & {
170
+ readonly allAliases: string[];
171
+ hasName(name: string): boolean;
172
+ } & {
173
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
174
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
175
+ } & {
176
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
177
+ regions: import("@jbrowse/core/util").Region[];
178
+ cytobands: import("@jbrowse/core/util").Feature[];
179
+ geneticCodes: Record<string, number>;
180
+ }): void;
181
+ setError(e: unknown): void;
182
+ setLoadingP(p?: Promise<void>): void;
183
+ loadPre(): Promise<void>;
184
+ } & {
185
+ load(): Promise<void>;
186
+ } & {
187
+ afterAttach(): void;
188
+ } & {
189
+ readonly initialized: boolean;
190
+ readonly allRefNames: string[] | undefined;
191
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
192
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
193
+ } & {
194
+ readonly refNames: string[] | undefined;
195
+ } & {
196
+ readonly refNameToIndex: Map<string, number> | undefined;
197
+ } & {
198
+ getCanonicalRefName(refName: string): string | undefined;
199
+ getRefNameColor(refName: string): string | undefined;
200
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
201
+ getGeneticCodeId(refName: string): number;
202
+ getSeqAdapterRefName(canonicalRefName: string): string;
203
+ } & {
204
+ getCanonicalRefName2(refName: string): string;
205
+ isValidRefName(refName: string): boolean;
206
+ } & {
207
+ getRefNamePosition(refName: string): number | undefined;
208
+ getAliasesForRefName(refName: string): string[];
209
+ getRefNameMapForAdapter(adapterConf: {
210
+ [x: string]: unknown;
211
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
212
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
213
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
214
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
215
+ }, {
216
+ error: unknown;
217
+ loadingP: Promise<void> | undefined;
218
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
219
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
220
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
221
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
222
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
223
+ loadedGeneticCodes: Record<string, number> | undefined;
224
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
225
+ statusMessage: string | undefined;
226
+ statusProgress: number | undefined;
227
+ statusSource: string | undefined;
228
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
229
+ } & {
230
+ getConf(arg: string): any;
231
+ } & {
232
+ readonly name: string;
233
+ readonly aliases: string[];
234
+ readonly displayName: string;
235
+ readonly refNameColors: string[];
236
+ } & {
237
+ readonly allAliases: string[];
238
+ hasName(name: string): boolean;
239
+ } & {
240
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
241
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
242
+ } & {
243
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
244
+ regions: import("@jbrowse/core/util").Region[];
245
+ cytobands: import("@jbrowse/core/util").Feature[];
246
+ geneticCodes: Record<string, number>;
247
+ }): void;
248
+ setError(e: unknown): void;
249
+ setLoadingP(p?: Promise<void>): void;
250
+ loadPre(): Promise<void>;
251
+ } & {
252
+ load(): Promise<void>;
253
+ } & {
254
+ afterAttach(): void;
255
+ } & {
256
+ readonly initialized: boolean;
257
+ readonly allRefNames: string[] | undefined;
258
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
259
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
260
+ } & {
261
+ readonly refNames: string[] | undefined;
262
+ } & {
263
+ readonly refNameToIndex: Map<string, number> | undefined;
264
+ } & {
265
+ getCanonicalRefName(refName: string): string | undefined;
266
+ getRefNameColor(refName: string): string | undefined;
267
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
268
+ getGeneticCodeId(refName: string): number;
269
+ getSeqAdapterRefName(canonicalRefName: string): string;
270
+ } & {
271
+ getCanonicalRefName2(refName: string): string;
272
+ isValidRefName(refName: string): boolean;
273
+ } & {
274
+ getRefNamePosition(refName: string): number | undefined;
275
+ getAliasesForRefName(refName: string): string[];
276
+ getRefNameMapForAdapter(adapterConf: {
277
+ [x: string]: unknown;
278
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
279
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
280
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
281
+ has(asmName: string): boolean;
282
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
283
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
284
+ }> & {
285
+ error: unknown;
286
+ loadingP: Promise<void> | undefined;
287
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
288
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
289
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
290
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
291
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
292
+ loadedGeneticCodes: Record<string, number> | undefined;
293
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
294
+ statusMessage: string | undefined;
295
+ statusProgress: number | undefined;
296
+ statusSource: string | undefined;
297
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
298
+ } & {
299
+ getConf(arg: string): any;
300
+ } & {
301
+ readonly name: string;
302
+ readonly aliases: string[];
303
+ readonly displayName: string;
304
+ readonly refNameColors: string[];
305
+ } & {
306
+ readonly allAliases: string[];
307
+ hasName(name: string): boolean;
308
+ } & {
309
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
310
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
311
+ } & {
312
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
313
+ regions: import("@jbrowse/core/util").Region[];
314
+ cytobands: import("@jbrowse/core/util").Feature[];
315
+ geneticCodes: Record<string, number>;
316
+ }): void;
317
+ setError(e: unknown): void;
318
+ setLoadingP(p?: Promise<void>): void;
319
+ loadPre(): Promise<void>;
320
+ } & {
321
+ load(): Promise<void>;
322
+ } & {
323
+ afterAttach(): void;
324
+ } & {
325
+ readonly initialized: boolean;
326
+ readonly allRefNames: string[] | undefined;
327
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
328
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
329
+ } & {
330
+ readonly refNames: string[] | undefined;
331
+ } & {
332
+ readonly refNameToIndex: Map<string, number> | undefined;
333
+ } & {
334
+ getCanonicalRefName(refName: string): string | undefined;
335
+ getRefNameColor(refName: string): string | undefined;
336
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
337
+ getGeneticCodeId(refName: string): number;
338
+ getSeqAdapterRefName(canonicalRefName: string): string;
339
+ } & {
340
+ getCanonicalRefName2(refName: string): string;
341
+ isValidRefName(refName: string): boolean;
342
+ } & {
343
+ getRefNamePosition(refName: string): number | undefined;
344
+ getAliasesForRefName(refName: string): string[];
345
+ getRefNameMapForAdapter(adapterConf: {
346
+ [x: string]: unknown;
347
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
348
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
349
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
350
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
351
+ }, {
352
+ error: unknown;
353
+ loadingP: Promise<void> | undefined;
354
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
355
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
356
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
357
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
358
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
359
+ loadedGeneticCodes: Record<string, number> | undefined;
360
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
361
+ statusMessage: string | undefined;
362
+ statusProgress: number | undefined;
363
+ statusSource: string | undefined;
364
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
365
+ } & {
366
+ getConf(arg: string): any;
367
+ } & {
368
+ readonly name: string;
369
+ readonly aliases: string[];
370
+ readonly displayName: string;
371
+ readonly refNameColors: string[];
372
+ } & {
373
+ readonly allAliases: string[];
374
+ hasName(name: string): boolean;
375
+ } & {
376
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
377
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
378
+ } & {
379
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
380
+ regions: import("@jbrowse/core/util").Region[];
381
+ cytobands: import("@jbrowse/core/util").Feature[];
382
+ geneticCodes: Record<string, number>;
383
+ }): void;
384
+ setError(e: unknown): void;
385
+ setLoadingP(p?: Promise<void>): void;
386
+ loadPre(): Promise<void>;
387
+ } & {
388
+ load(): Promise<void>;
389
+ } & {
390
+ afterAttach(): void;
391
+ } & {
392
+ readonly initialized: boolean;
393
+ readonly allRefNames: string[] | undefined;
394
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
395
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
396
+ } & {
397
+ readonly refNames: string[] | undefined;
398
+ } & {
399
+ readonly refNameToIndex: Map<string, number> | undefined;
400
+ } & {
401
+ getCanonicalRefName(refName: string): string | undefined;
402
+ getRefNameColor(refName: string): string | undefined;
403
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
404
+ getGeneticCodeId(refName: string): number;
405
+ getSeqAdapterRefName(canonicalRefName: string): string;
406
+ } & {
407
+ getCanonicalRefName2(refName: string): string;
408
+ isValidRefName(refName: string): boolean;
409
+ } & {
410
+ getRefNamePosition(refName: string): number | undefined;
411
+ getAliasesForRefName(refName: string): string[];
412
+ getRefNameMapForAdapter(adapterConf: {
413
+ [x: string]: unknown;
414
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
415
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
416
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
417
+ readonly assemblyNamesList: string[];
418
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
419
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
420
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
421
+ } & {
422
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
423
+ } & {
424
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
425
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
426
+ }> & {
427
+ error: unknown;
428
+ loadingP: Promise<void> | undefined;
429
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
430
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
431
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
432
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
433
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
434
+ loadedGeneticCodes: Record<string, number> | undefined;
435
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
436
+ statusMessage: string | undefined;
437
+ statusProgress: number | undefined;
438
+ statusSource: string | undefined;
439
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
440
+ } & {
441
+ getConf(arg: string): any;
442
+ } & {
443
+ readonly name: string;
444
+ readonly aliases: string[];
445
+ readonly displayName: string;
446
+ readonly refNameColors: string[];
447
+ } & {
448
+ readonly allAliases: string[];
449
+ hasName(name: string): boolean;
450
+ } & {
451
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
452
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
453
+ } & {
454
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
455
+ regions: import("@jbrowse/core/util").Region[];
456
+ cytobands: import("@jbrowse/core/util").Feature[];
457
+ geneticCodes: Record<string, number>;
458
+ }): void;
459
+ setError(e: unknown): void;
460
+ setLoadingP(p?: Promise<void>): void;
461
+ loadPre(): Promise<void>;
462
+ } & {
463
+ load(): Promise<void>;
464
+ } & {
465
+ afterAttach(): void;
466
+ } & {
467
+ readonly initialized: boolean;
468
+ readonly allRefNames: string[] | undefined;
469
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
470
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
471
+ } & {
472
+ readonly refNames: string[] | undefined;
473
+ } & {
474
+ readonly refNameToIndex: Map<string, number> | undefined;
475
+ } & {
476
+ getCanonicalRefName(refName: string): string | undefined;
477
+ getRefNameColor(refName: string): string | undefined;
478
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
479
+ getGeneticCodeId(refName: string): number;
480
+ getSeqAdapterRefName(canonicalRefName: string): string;
481
+ } & {
482
+ getCanonicalRefName2(refName: string): string;
483
+ isValidRefName(refName: string): boolean;
484
+ } & {
485
+ getRefNamePosition(refName: string): number | undefined;
486
+ getAliasesForRefName(refName: string): string[];
487
+ getRefNameMapForAdapter(adapterConf: {
488
+ [x: string]: unknown;
489
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
490
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
491
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
492
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
493
+ }, {
494
+ error: unknown;
495
+ loadingP: Promise<void> | undefined;
496
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
497
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
498
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
499
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
500
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
501
+ loadedGeneticCodes: Record<string, number> | undefined;
502
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
503
+ statusMessage: string | undefined;
504
+ statusProgress: number | undefined;
505
+ statusSource: string | undefined;
506
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
507
+ } & {
508
+ getConf(arg: string): any;
509
+ } & {
510
+ readonly name: string;
511
+ readonly aliases: string[];
512
+ readonly displayName: string;
513
+ readonly refNameColors: string[];
514
+ } & {
515
+ readonly allAliases: string[];
516
+ hasName(name: string): boolean;
517
+ } & {
518
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
519
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
520
+ } & {
521
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
522
+ regions: import("@jbrowse/core/util").Region[];
523
+ cytobands: import("@jbrowse/core/util").Feature[];
524
+ geneticCodes: Record<string, number>;
525
+ }): void;
526
+ setError(e: unknown): void;
527
+ setLoadingP(p?: Promise<void>): void;
528
+ loadPre(): Promise<void>;
529
+ } & {
530
+ load(): Promise<void>;
531
+ } & {
532
+ afterAttach(): void;
533
+ } & {
534
+ readonly initialized: boolean;
535
+ readonly allRefNames: string[] | undefined;
536
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
537
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
538
+ } & {
539
+ readonly refNames: string[] | undefined;
540
+ } & {
541
+ readonly refNameToIndex: Map<string, number> | undefined;
542
+ } & {
543
+ getCanonicalRefName(refName: string): string | undefined;
544
+ getRefNameColor(refName: string): string | undefined;
545
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
546
+ getGeneticCodeId(refName: string): number;
547
+ getSeqAdapterRefName(canonicalRefName: string): string;
548
+ } & {
549
+ getCanonicalRefName2(refName: string): string;
550
+ isValidRefName(refName: string): boolean;
551
+ } & {
552
+ getRefNamePosition(refName: string): number | undefined;
553
+ getAliasesForRefName(refName: string): string[];
554
+ getRefNameMapForAdapter(adapterConf: {
555
+ [x: string]: unknown;
556
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
557
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
558
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
559
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
560
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
561
+ }> & {
562
+ error: unknown;
563
+ loadingP: Promise<void> | undefined;
564
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
565
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
566
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
567
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
568
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
569
+ loadedGeneticCodes: Record<string, number> | undefined;
570
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
571
+ statusMessage: string | undefined;
572
+ statusProgress: number | undefined;
573
+ statusSource: string | undefined;
574
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
575
+ } & {
576
+ getConf(arg: string): any;
577
+ } & {
578
+ readonly name: string;
579
+ readonly aliases: string[];
580
+ readonly displayName: string;
581
+ readonly refNameColors: string[];
582
+ } & {
583
+ readonly allAliases: string[];
584
+ hasName(name: string): boolean;
585
+ } & {
586
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
587
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
588
+ } & {
589
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
590
+ regions: import("@jbrowse/core/util").Region[];
591
+ cytobands: import("@jbrowse/core/util").Feature[];
592
+ geneticCodes: Record<string, number>;
593
+ }): void;
594
+ setError(e: unknown): void;
595
+ setLoadingP(p?: Promise<void>): void;
596
+ loadPre(): Promise<void>;
597
+ } & {
598
+ load(): Promise<void>;
599
+ } & {
600
+ afterAttach(): void;
601
+ } & {
602
+ readonly initialized: boolean;
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
+ getRefNamePosition(refName: string): number | undefined;
621
+ getAliasesForRefName(refName: string): string[];
622
+ getRefNameMapForAdapter(adapterConf: {
623
+ [x: string]: unknown;
624
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
625
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
626
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
627
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
628
+ }, {
629
+ error: unknown;
630
+ loadingP: Promise<void> | undefined;
631
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
632
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
633
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
634
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
635
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
636
+ loadedGeneticCodes: Record<string, number> | undefined;
637
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
638
+ statusMessage: string | undefined;
639
+ statusProgress: number | undefined;
640
+ statusSource: string | undefined;
641
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
642
+ } & {
643
+ getConf(arg: string): any;
644
+ } & {
645
+ readonly name: string;
646
+ readonly aliases: string[];
647
+ readonly displayName: string;
648
+ readonly refNameColors: string[];
649
+ } & {
650
+ readonly allAliases: string[];
651
+ hasName(name: string): boolean;
652
+ } & {
653
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
654
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
655
+ } & {
656
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
657
+ regions: import("@jbrowse/core/util").Region[];
658
+ cytobands: import("@jbrowse/core/util").Feature[];
659
+ geneticCodes: Record<string, number>;
660
+ }): void;
661
+ setError(e: unknown): void;
662
+ setLoadingP(p?: Promise<void>): void;
663
+ loadPre(): Promise<void>;
664
+ } & {
665
+ load(): Promise<void>;
666
+ } & {
667
+ afterAttach(): void;
668
+ } & {
669
+ readonly initialized: boolean;
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
+ getRefNamePosition(refName: string): number | undefined;
688
+ getAliasesForRefName(refName: string): string[];
689
+ getRefNameMapForAdapter(adapterConf: {
690
+ [x: string]: unknown;
691
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
692
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
693
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
694
+ getRefNameMapForAdapter(adapterConf: {
695
+ [x: string]: unknown;
696
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
697
+ isValidRefName(refName: string, assemblyName: string): boolean;
698
+ } & {
699
+ afterAttach(): void;
700
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
701
+ addAssembly(configuration: any): void;
702
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
703
+ }> & {
704
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
705
+ adminMode: boolean;
706
+ error: unknown;
707
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
708
+ pluginManager: PluginManager;
709
+ } & {
710
+ setError(error: unknown): void;
711
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
712
+ setDefaultSession(): void;
713
+ setSessionPath(path: string): void;
714
+ renameCurrentSession(newName: string): void;
715
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
716
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
717
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
718
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
719
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
720
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
721
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
722
+ }, {
723
+ error: unknown;
724
+ loadingP: Promise<void> | undefined;
725
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
726
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
727
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
728
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
729
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
730
+ loadedGeneticCodes: Record<string, number> | undefined;
731
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
732
+ statusMessage: string | undefined;
733
+ statusProgress: number | undefined;
734
+ statusSource: string | undefined;
735
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
736
+ } & {
737
+ getConf(arg: string): any;
738
+ } & {
739
+ readonly name: string;
740
+ readonly aliases: string[];
741
+ readonly displayName: string;
742
+ readonly refNameColors: string[];
743
+ } & {
744
+ readonly allAliases: string[];
745
+ hasName(name: string): boolean;
746
+ } & {
747
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
748
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
749
+ } & {
750
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
751
+ regions: import("@jbrowse/core/util").Region[];
752
+ cytobands: import("@jbrowse/core/util").Feature[];
753
+ geneticCodes: Record<string, number>;
754
+ }): void;
755
+ setError(e: unknown): void;
756
+ setLoadingP(p?: Promise<void>): void;
757
+ loadPre(): Promise<void>;
758
+ } & {
759
+ load(): Promise<void>;
760
+ } & {
761
+ afterAttach(): void;
762
+ } & {
763
+ readonly initialized: boolean;
764
+ readonly allRefNames: string[] | undefined;
765
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
766
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
767
+ } & {
768
+ readonly refNames: string[] | undefined;
769
+ } & {
770
+ readonly refNameToIndex: Map<string, number> | undefined;
771
+ } & {
772
+ getCanonicalRefName(refName: string): string | undefined;
773
+ getRefNameColor(refName: string): string | undefined;
774
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
775
+ getGeneticCodeId(refName: string): number;
776
+ getSeqAdapterRefName(canonicalRefName: string): string;
777
+ } & {
778
+ getCanonicalRefName2(refName: string): string;
779
+ isValidRefName(refName: string): boolean;
780
+ } & {
781
+ getRefNamePosition(refName: string): number | undefined;
782
+ getAliasesForRefName(refName: string): string[];
783
+ getRefNameMapForAdapter(adapterConf: {
784
+ [x: string]: unknown;
785
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
786
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
787
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
788
+ }, {
789
+ unrecognizedReports: {
790
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
791
+ reportFor(session: unknown, name: string): {
792
+ handled: boolean;
793
+ claim?: Promise<void>;
794
+ } | undefined;
795
+ };
796
+ } & {
797
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
798
+ } & {
799
+ getCanonicalAssemblyName(asmName: string): string | undefined;
800
+ getDisplayName(asmName: string): string;
801
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
802
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
803
+ }> & {
804
+ error: unknown;
805
+ loadingP: Promise<void> | undefined;
806
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
807
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
808
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
809
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
810
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
811
+ loadedGeneticCodes: Record<string, number> | undefined;
812
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
813
+ statusMessage: string | undefined;
814
+ statusProgress: number | undefined;
815
+ statusSource: string | undefined;
816
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
817
+ } & {
818
+ getConf(arg: string): any;
819
+ } & {
820
+ readonly name: string;
821
+ readonly aliases: string[];
822
+ readonly displayName: string;
823
+ readonly refNameColors: string[];
824
+ } & {
825
+ readonly allAliases: string[];
826
+ hasName(name: string): boolean;
827
+ } & {
828
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
829
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
830
+ } & {
831
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
832
+ regions: import("@jbrowse/core/util").Region[];
833
+ cytobands: import("@jbrowse/core/util").Feature[];
834
+ geneticCodes: Record<string, number>;
835
+ }): void;
836
+ setError(e: unknown): void;
837
+ setLoadingP(p?: Promise<void>): void;
838
+ loadPre(): Promise<void>;
839
+ } & {
840
+ load(): Promise<void>;
841
+ } & {
842
+ afterAttach(): void;
843
+ } & {
844
+ readonly initialized: boolean;
845
+ readonly allRefNames: string[] | undefined;
846
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
847
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
848
+ } & {
849
+ readonly refNames: string[] | undefined;
850
+ } & {
851
+ readonly refNameToIndex: Map<string, number> | undefined;
852
+ } & {
853
+ getCanonicalRefName(refName: string): string | undefined;
854
+ getRefNameColor(refName: string): string | undefined;
855
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
856
+ getGeneticCodeId(refName: string): number;
857
+ getSeqAdapterRefName(canonicalRefName: string): string;
858
+ } & {
859
+ getCanonicalRefName2(refName: string): string;
860
+ isValidRefName(refName: string): boolean;
861
+ } & {
862
+ getRefNamePosition(refName: string): number | undefined;
863
+ getAliasesForRefName(refName: string): string[];
864
+ getRefNameMapForAdapter(adapterConf: {
865
+ [x: string]: unknown;
866
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
867
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
868
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
869
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
870
+ }, {
871
+ error: unknown;
872
+ loadingP: Promise<void> | undefined;
873
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
874
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
875
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
876
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
877
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
878
+ loadedGeneticCodes: Record<string, number> | undefined;
879
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
880
+ statusMessage: string | undefined;
881
+ statusProgress: number | undefined;
882
+ statusSource: string | undefined;
883
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
884
+ } & {
885
+ getConf(arg: string): any;
886
+ } & {
887
+ readonly name: string;
888
+ readonly aliases: string[];
889
+ readonly displayName: string;
890
+ readonly refNameColors: string[];
891
+ } & {
892
+ readonly allAliases: string[];
893
+ hasName(name: string): boolean;
894
+ } & {
895
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
896
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
897
+ } & {
898
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
899
+ regions: import("@jbrowse/core/util").Region[];
900
+ cytobands: import("@jbrowse/core/util").Feature[];
901
+ geneticCodes: Record<string, number>;
902
+ }): void;
903
+ setError(e: unknown): void;
904
+ setLoadingP(p?: Promise<void>): void;
905
+ loadPre(): Promise<void>;
906
+ } & {
907
+ load(): Promise<void>;
908
+ } & {
909
+ afterAttach(): void;
910
+ } & {
911
+ readonly initialized: boolean;
912
+ readonly allRefNames: string[] | undefined;
913
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
914
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
915
+ } & {
916
+ readonly refNames: string[] | undefined;
917
+ } & {
918
+ readonly refNameToIndex: Map<string, number> | undefined;
919
+ } & {
920
+ getCanonicalRefName(refName: string): string | undefined;
921
+ getRefNameColor(refName: string): string | undefined;
922
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
923
+ getGeneticCodeId(refName: string): number;
924
+ getSeqAdapterRefName(canonicalRefName: string): string;
925
+ } & {
926
+ getCanonicalRefName2(refName: string): string;
927
+ isValidRefName(refName: string): boolean;
928
+ } & {
929
+ getRefNamePosition(refName: string): number | undefined;
930
+ getAliasesForRefName(refName: string): string[];
931
+ getRefNameMapForAdapter(adapterConf: {
932
+ [x: string]: unknown;
933
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
934
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
935
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
936
+ has(asmName: string): boolean;
937
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
938
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
939
+ }> & {
940
+ error: unknown;
941
+ loadingP: Promise<void> | undefined;
942
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
943
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
944
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
945
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
946
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
947
+ loadedGeneticCodes: Record<string, number> | undefined;
948
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
949
+ statusMessage: string | undefined;
950
+ statusProgress: number | undefined;
951
+ statusSource: string | undefined;
952
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
953
+ } & {
954
+ getConf(arg: string): any;
955
+ } & {
956
+ readonly name: string;
957
+ readonly aliases: string[];
958
+ readonly displayName: string;
959
+ readonly refNameColors: string[];
960
+ } & {
961
+ readonly allAliases: string[];
962
+ hasName(name: string): boolean;
963
+ } & {
964
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
965
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
966
+ } & {
967
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
968
+ regions: import("@jbrowse/core/util").Region[];
969
+ cytobands: import("@jbrowse/core/util").Feature[];
970
+ geneticCodes: Record<string, number>;
971
+ }): void;
972
+ setError(e: unknown): void;
973
+ setLoadingP(p?: Promise<void>): void;
974
+ loadPre(): Promise<void>;
975
+ } & {
976
+ load(): Promise<void>;
977
+ } & {
978
+ afterAttach(): void;
979
+ } & {
980
+ readonly initialized: boolean;
981
+ readonly allRefNames: string[] | undefined;
982
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
983
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
984
+ } & {
985
+ readonly refNames: string[] | undefined;
986
+ } & {
987
+ readonly refNameToIndex: Map<string, number> | undefined;
988
+ } & {
989
+ getCanonicalRefName(refName: string): string | undefined;
990
+ getRefNameColor(refName: string): string | undefined;
991
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
992
+ getGeneticCodeId(refName: string): number;
993
+ getSeqAdapterRefName(canonicalRefName: string): string;
994
+ } & {
995
+ getCanonicalRefName2(refName: string): string;
996
+ isValidRefName(refName: string): boolean;
997
+ } & {
998
+ getRefNamePosition(refName: string): number | undefined;
999
+ getAliasesForRefName(refName: string): string[];
1000
+ getRefNameMapForAdapter(adapterConf: {
1001
+ [x: string]: unknown;
1002
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1003
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1004
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1005
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1006
+ }, {
1007
+ error: unknown;
1008
+ loadingP: Promise<void> | undefined;
1009
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1010
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1011
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1012
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1013
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1014
+ loadedGeneticCodes: Record<string, number> | undefined;
1015
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1016
+ statusMessage: string | undefined;
1017
+ statusProgress: number | undefined;
1018
+ statusSource: string | undefined;
1019
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1020
+ } & {
1021
+ getConf(arg: string): any;
1022
+ } & {
1023
+ readonly name: string;
1024
+ readonly aliases: string[];
1025
+ readonly displayName: string;
1026
+ readonly refNameColors: string[];
1027
+ } & {
1028
+ readonly allAliases: string[];
1029
+ hasName(name: string): boolean;
1030
+ } & {
1031
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1032
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1033
+ } & {
1034
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1035
+ regions: import("@jbrowse/core/util").Region[];
1036
+ cytobands: import("@jbrowse/core/util").Feature[];
1037
+ geneticCodes: Record<string, number>;
1038
+ }): void;
1039
+ setError(e: unknown): void;
1040
+ setLoadingP(p?: Promise<void>): void;
1041
+ loadPre(): Promise<void>;
1042
+ } & {
1043
+ load(): Promise<void>;
1044
+ } & {
1045
+ afterAttach(): void;
1046
+ } & {
1047
+ readonly initialized: boolean;
1048
+ readonly allRefNames: string[] | undefined;
1049
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1050
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1051
+ } & {
1052
+ readonly refNames: string[] | undefined;
1053
+ } & {
1054
+ readonly refNameToIndex: Map<string, number> | undefined;
1055
+ } & {
1056
+ getCanonicalRefName(refName: string): string | undefined;
1057
+ getRefNameColor(refName: string): string | undefined;
1058
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1059
+ getGeneticCodeId(refName: string): number;
1060
+ getSeqAdapterRefName(canonicalRefName: string): string;
1061
+ } & {
1062
+ getCanonicalRefName2(refName: string): string;
1063
+ isValidRefName(refName: string): boolean;
1064
+ } & {
1065
+ getRefNamePosition(refName: string): number | undefined;
1066
+ getAliasesForRefName(refName: string): string[];
1067
+ getRefNameMapForAdapter(adapterConf: {
1068
+ [x: string]: unknown;
1069
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1070
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1071
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1072
+ readonly assemblyNamesList: string[];
1073
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1074
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1075
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1076
+ } & {
1077
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
1078
+ } & {
1079
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1080
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1081
+ }> & {
1082
+ error: unknown;
1083
+ loadingP: Promise<void> | undefined;
1084
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1085
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1086
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1087
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1088
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1089
+ loadedGeneticCodes: Record<string, number> | undefined;
1090
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1091
+ statusMessage: string | undefined;
1092
+ statusProgress: number | undefined;
1093
+ statusSource: string | undefined;
1094
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1095
+ } & {
1096
+ getConf(arg: string): any;
1097
+ } & {
1098
+ readonly name: string;
1099
+ readonly aliases: string[];
1100
+ readonly displayName: string;
1101
+ readonly refNameColors: string[];
1102
+ } & {
1103
+ readonly allAliases: string[];
1104
+ hasName(name: string): boolean;
1105
+ } & {
1106
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1107
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1108
+ } & {
1109
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1110
+ regions: import("@jbrowse/core/util").Region[];
1111
+ cytobands: import("@jbrowse/core/util").Feature[];
1112
+ geneticCodes: Record<string, number>;
1113
+ }): void;
1114
+ setError(e: unknown): void;
1115
+ setLoadingP(p?: Promise<void>): void;
1116
+ loadPre(): Promise<void>;
1117
+ } & {
1118
+ load(): Promise<void>;
1119
+ } & {
1120
+ afterAttach(): void;
1121
+ } & {
1122
+ readonly initialized: boolean;
1123
+ readonly allRefNames: string[] | undefined;
1124
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1125
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1126
+ } & {
1127
+ readonly refNames: string[] | undefined;
1128
+ } & {
1129
+ readonly refNameToIndex: Map<string, number> | undefined;
1130
+ } & {
1131
+ getCanonicalRefName(refName: string): string | undefined;
1132
+ getRefNameColor(refName: string): string | undefined;
1133
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1134
+ getGeneticCodeId(refName: string): number;
1135
+ getSeqAdapterRefName(canonicalRefName: string): string;
1136
+ } & {
1137
+ getCanonicalRefName2(refName: string): string;
1138
+ isValidRefName(refName: string): boolean;
1139
+ } & {
1140
+ getRefNamePosition(refName: string): number | undefined;
1141
+ getAliasesForRefName(refName: string): string[];
1142
+ getRefNameMapForAdapter(adapterConf: {
1143
+ [x: string]: unknown;
1144
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1145
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1146
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1147
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1148
+ }, {
1149
+ error: unknown;
1150
+ loadingP: Promise<void> | undefined;
1151
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1152
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1153
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1154
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1155
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1156
+ loadedGeneticCodes: Record<string, number> | undefined;
1157
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1158
+ statusMessage: string | undefined;
1159
+ statusProgress: number | undefined;
1160
+ statusSource: string | undefined;
1161
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1162
+ } & {
1163
+ getConf(arg: string): any;
1164
+ } & {
1165
+ readonly name: string;
1166
+ readonly aliases: string[];
1167
+ readonly displayName: string;
1168
+ readonly refNameColors: string[];
1169
+ } & {
1170
+ readonly allAliases: string[];
1171
+ hasName(name: string): boolean;
1172
+ } & {
1173
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1174
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1175
+ } & {
1176
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1177
+ regions: import("@jbrowse/core/util").Region[];
1178
+ cytobands: import("@jbrowse/core/util").Feature[];
1179
+ geneticCodes: Record<string, number>;
1180
+ }): void;
1181
+ setError(e: unknown): void;
1182
+ setLoadingP(p?: Promise<void>): void;
1183
+ loadPre(): Promise<void>;
1184
+ } & {
1185
+ load(): Promise<void>;
1186
+ } & {
1187
+ afterAttach(): void;
1188
+ } & {
1189
+ readonly initialized: boolean;
1190
+ readonly allRefNames: string[] | undefined;
1191
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1192
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1193
+ } & {
1194
+ readonly refNames: string[] | undefined;
1195
+ } & {
1196
+ readonly refNameToIndex: Map<string, number> | undefined;
1197
+ } & {
1198
+ getCanonicalRefName(refName: string): string | undefined;
1199
+ getRefNameColor(refName: string): string | undefined;
1200
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1201
+ getGeneticCodeId(refName: string): number;
1202
+ getSeqAdapterRefName(canonicalRefName: string): string;
1203
+ } & {
1204
+ getCanonicalRefName2(refName: string): string;
1205
+ isValidRefName(refName: string): boolean;
1206
+ } & {
1207
+ getRefNamePosition(refName: string): number | undefined;
1208
+ getAliasesForRefName(refName: string): string[];
1209
+ getRefNameMapForAdapter(adapterConf: {
1210
+ [x: string]: unknown;
1211
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1212
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1213
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1214
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1215
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1216
+ }> & {
1217
+ error: unknown;
1218
+ loadingP: Promise<void> | undefined;
1219
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1220
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1221
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1222
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1223
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1224
+ loadedGeneticCodes: Record<string, number> | undefined;
1225
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1226
+ statusMessage: string | undefined;
1227
+ statusProgress: number | undefined;
1228
+ statusSource: string | undefined;
1229
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1230
+ } & {
1231
+ getConf(arg: string): any;
1232
+ } & {
1233
+ readonly name: string;
1234
+ readonly aliases: string[];
1235
+ readonly displayName: string;
1236
+ readonly refNameColors: string[];
1237
+ } & {
1238
+ readonly allAliases: string[];
1239
+ hasName(name: string): boolean;
1240
+ } & {
1241
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1242
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1243
+ } & {
1244
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1245
+ regions: import("@jbrowse/core/util").Region[];
1246
+ cytobands: import("@jbrowse/core/util").Feature[];
1247
+ geneticCodes: Record<string, number>;
1248
+ }): void;
1249
+ setError(e: unknown): void;
1250
+ setLoadingP(p?: Promise<void>): void;
1251
+ loadPre(): Promise<void>;
1252
+ } & {
1253
+ load(): Promise<void>;
1254
+ } & {
1255
+ afterAttach(): void;
1256
+ } & {
1257
+ readonly initialized: boolean;
1258
+ readonly allRefNames: string[] | undefined;
1259
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1260
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1261
+ } & {
1262
+ readonly refNames: string[] | undefined;
1263
+ } & {
1264
+ readonly refNameToIndex: Map<string, number> | undefined;
1265
+ } & {
1266
+ getCanonicalRefName(refName: string): string | undefined;
1267
+ getRefNameColor(refName: string): string | undefined;
1268
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1269
+ getGeneticCodeId(refName: string): number;
1270
+ getSeqAdapterRefName(canonicalRefName: string): string;
1271
+ } & {
1272
+ getCanonicalRefName2(refName: string): string;
1273
+ isValidRefName(refName: string): boolean;
1274
+ } & {
1275
+ getRefNamePosition(refName: string): number | undefined;
1276
+ getAliasesForRefName(refName: string): string[];
1277
+ getRefNameMapForAdapter(adapterConf: {
1278
+ [x: string]: unknown;
1279
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1280
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1281
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1282
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1283
+ }, {
1284
+ error: unknown;
1285
+ loadingP: Promise<void> | undefined;
1286
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1287
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1288
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1289
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1290
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1291
+ loadedGeneticCodes: Record<string, number> | undefined;
1292
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1293
+ statusMessage: string | undefined;
1294
+ statusProgress: number | undefined;
1295
+ statusSource: string | undefined;
1296
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1297
+ } & {
1298
+ getConf(arg: string): any;
1299
+ } & {
1300
+ readonly name: string;
1301
+ readonly aliases: string[];
1302
+ readonly displayName: string;
1303
+ readonly refNameColors: string[];
1304
+ } & {
1305
+ readonly allAliases: string[];
1306
+ hasName(name: string): boolean;
1307
+ } & {
1308
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1309
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1310
+ } & {
1311
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1312
+ regions: import("@jbrowse/core/util").Region[];
1313
+ cytobands: import("@jbrowse/core/util").Feature[];
1314
+ geneticCodes: Record<string, number>;
1315
+ }): void;
1316
+ setError(e: unknown): void;
1317
+ setLoadingP(p?: Promise<void>): void;
1318
+ loadPre(): Promise<void>;
1319
+ } & {
1320
+ load(): Promise<void>;
1321
+ } & {
1322
+ afterAttach(): void;
1323
+ } & {
1324
+ readonly initialized: boolean;
1325
+ readonly allRefNames: string[] | undefined;
1326
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1327
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1328
+ } & {
1329
+ readonly refNames: string[] | undefined;
1330
+ } & {
1331
+ readonly refNameToIndex: Map<string, number> | undefined;
1332
+ } & {
1333
+ getCanonicalRefName(refName: string): string | undefined;
1334
+ getRefNameColor(refName: string): string | undefined;
1335
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1336
+ getGeneticCodeId(refName: string): number;
1337
+ getSeqAdapterRefName(canonicalRefName: string): string;
1338
+ } & {
1339
+ getCanonicalRefName2(refName: string): string;
1340
+ isValidRefName(refName: string): boolean;
1341
+ } & {
1342
+ getRefNamePosition(refName: string): number | undefined;
1343
+ getAliasesForRefName(refName: string): string[];
1344
+ getRefNameMapForAdapter(adapterConf: {
1345
+ [x: string]: unknown;
1346
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1347
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1348
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1349
+ getRefNameMapForAdapter(adapterConf: {
1350
+ [x: string]: unknown;
1351
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1352
+ isValidRefName(refName: string, assemblyName: string): boolean;
1353
+ } & {
1354
+ afterAttach(): void;
1355
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1356
+ addAssembly(configuration: any): void;
1357
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
1358
+ }, {
1359
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1360
+ adminMode: boolean;
1361
+ error: unknown;
1362
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1363
+ pluginManager: PluginManager;
1364
+ } & {
1365
+ setError(error: unknown): void;
1366
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1367
+ setDefaultSession(): void;
1368
+ setSessionPath(path: string): void;
1369
+ renameCurrentSession(newName: string): void;
1370
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1371
+ } & {
1372
+ readonly jbrowse: any;
1373
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1374
+ readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1375
+ readonly adminMode: boolean;
1376
+ readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1377
+ } & {
1378
+ readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
1379
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1380
+ readonly DialogProps: Record<string, unknown> | undefined;
1381
+ } & {
1382
+ getPreferenceDefault(key: string): unknown;
1383
+ getPreference(key: string): unknown;
1384
+ getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
1385
+ } & {
1386
+ readonly animationMode: import("@jbrowse/core/util").AnimationMode;
1387
+ readonly scrollZoom: boolean;
1388
+ readonly numberGrouping: boolean;
1389
+ } & {
1390
+ afterAttach(): void;
1391
+ setSelection(thing: unknown): void;
1392
+ clearSelection(): void;
1393
+ setHovered(thing: unknown): void;
1394
+ setHighlightsVisible(arg: boolean): void;
1395
+ setHighlightLabelsVisible(arg: boolean): void;
1396
+ addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
1397
+ removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
1398
+ updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
1399
+ setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
1400
+ setPreferenceOverride(key: string, value: unknown): void;
1401
+ clearPreferenceOverrides(): void;
1402
+ clearPreferenceOverride(key: string): void;
1403
+ setScrollZoom(flag: boolean): void;
1404
+ setName(str: string): void;
1405
+ setFocusedViewId(viewId: string | undefined): void;
1406
+ removeActiveDialog(): void;
1407
+ queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1408
+ removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1409
+ } & {
1410
+ snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1411
+ errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
1412
+ } & {
1413
+ readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1414
+ } & {
1415
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
1416
+ notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
1417
+ setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
1418
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
1419
+ popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1420
+ removeSnackbarMessage(message: string): void;
1421
+ } & {
1422
+ afterAttach(): void;
1423
+ } & {
1424
+ readonly visibleWidget: import("@jbrowse/core/util").Widget | undefined;
1425
+ } & {
1426
+ poppedOut: boolean;
1427
+ modalWidgets: boolean;
1428
+ } & {
1429
+ readonly drawerVisible: boolean;
1430
+ readonly modalWidgetVisible: boolean;
1431
+ } & {
1432
+ setDrawerPosition(arg: import("@jbrowse/core/util").DrawerPosition): void;
1433
+ updateDrawerWidth(drawerWidth: number, availableWidth?: number): number;
1434
+ resizeDrawer(distance: number, availableWidth?: number): number;
1435
+ addWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
1436
+ showWidget(widget: any): void;
1437
+ hideWidget(widget: any): void;
1438
+ minimizeWidgetDrawer(): void;
1439
+ showWidgetDrawer(): void;
1440
+ popoutWidget(): void;
1441
+ returnWidgetToDrawer(): void;
1442
+ setModalWidgets(flag: boolean): void;
1443
+ hideAllWidgets(): void;
1444
+ afterAttach(): void;
1445
+ } & {
1446
+ closeModalWidget(): void;
1447
+ openWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
1448
+ } & {
1449
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
1450
+ trackId: string;
1451
+ }, opts?: {
1452
+ expandedDisplayId?: string;
1453
+ }): void;
1454
+ } & {
1455
+ readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1456
+ } & {
1457
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: object): any;
1458
+ breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1459
+ teardownConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1460
+ deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1461
+ addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1462
+ clearConnections(): void;
1463
+ captureConnectionTrack(trackId: string): void;
1464
+ updateConnectionTrackConfig(trackConf: Record<string, unknown> & {
1465
+ trackId: string;
1466
+ }): void;
1467
+ setConnectionTrackConfig(trackId: string, connectionId: string, config: Record<string, unknown>): void;
1468
+ pruneConnectionTrackConfig(trackId: string): void;
1469
+ hydrateConnection(connectionId: string): void;
1470
+ } & {
1471
+ getReferringMultiple(trackIds: string[]): Map<string, import("@jbrowse/product-core").ReferringNode[]>;
1472
+ } & {
1473
+ getReferring(trackId: string): import("@jbrowse/product-core").ReferringNode[];
1474
+ } & {
1475
+ dereferenceTrack(trackId: string, referring: import("@jbrowse/product-core").ReferringNode[]): void;
1476
+ } & {
1477
+ getTrackListMenuItems(config: import("@jbrowse/core/configuration").AnyConfigurationModel, view?: import("@jbrowse/core/util").TrackActionView): import("@jbrowse/core/ui").MenuItem[];
1478
+ getTrackActionMenuItems({ config, view, }: {
1479
+ config: import("@jbrowse/core/configuration").AnyConfigurationModel;
1480
+ view?: import("@jbrowse/core/util").TrackActionView;
1481
+ }): import("@jbrowse/core/ui").MenuItem[];
1482
+ } & {
1483
+ sessionThemeMode: import("@jbrowse/core/ui/palette").PaletteMode | undefined;
1484
+ } & {
1485
+ readonly themeOptions: import("@jbrowse/core/ui").SerializableThemeArgs;
1486
+ readonly palette: import("@jbrowse/core/ui/palette").JBrowsePalette;
1487
+ readonly styleTheme: import("@jbrowse/core/ui/styleTheme").JBrowseStyleTheme;
1488
+ readonly theme: import("@mui/material").Theme;
1489
+ getActiveThemeOptions(_name?: string): import("@mui/material").ThemeOptions | undefined;
1490
+ } & {
1491
+ setThemeMode(mode: import("@jbrowse/core/ui/palette").PaletteMode): void;
1492
+ } & {
1493
+ /**
1494
+ * #getter
1495
+ * An embedded view is drawn with no title bar above it, so its menu lives
1496
+ * in the view's own controls.
1497
+ */
1498
+ readonly viewTitleBars: boolean;
1499
+ /**
1500
+ * #getter
1501
+ */
1502
+ readonly version: string;
1503
+ /**
1504
+ * #getter
1505
+ */
1506
+ readonly assemblyNames: string[];
1507
+ /**
1508
+ * #getter
1509
+ */
1510
+ readonly assemblyManager: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1511
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
1512
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1513
+ }, {
1514
+ error: unknown;
1515
+ loadingP: Promise<void> | undefined;
1516
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1517
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1518
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1519
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1520
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1521
+ loadedGeneticCodes: Record<string, number> | undefined;
1522
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1523
+ statusMessage: string | undefined;
1524
+ statusProgress: number | undefined;
1525
+ statusSource: string | undefined;
1526
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1527
+ } & {
1528
+ getConf(arg: string): any;
1529
+ } & {
1530
+ readonly name: string;
1531
+ readonly aliases: string[];
1532
+ readonly displayName: string;
1533
+ readonly refNameColors: string[];
1534
+ } & {
1535
+ readonly allAliases: string[];
1536
+ hasName(name: string): boolean;
1537
+ } & {
1538
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1539
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1540
+ } & {
1541
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1542
+ regions: import("@jbrowse/core/util").Region[];
1543
+ cytobands: import("@jbrowse/core/util").Feature[];
1544
+ geneticCodes: Record<string, number>;
1545
+ }): void;
1546
+ setError(e: unknown): void;
1547
+ setLoadingP(p?: Promise<void>): void;
1548
+ loadPre(): Promise<void>;
1549
+ } & {
1550
+ load(): Promise<void>;
1551
+ } & {
1552
+ afterAttach(): void;
1553
+ } & {
1554
+ readonly initialized: boolean;
1555
+ readonly allRefNames: string[] | undefined;
1556
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1557
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1558
+ } & {
1559
+ readonly refNames: string[] | undefined;
1560
+ } & {
1561
+ readonly refNameToIndex: Map<string, number> | undefined;
1562
+ } & {
1563
+ getCanonicalRefName(refName: string): string | undefined;
1564
+ getRefNameColor(refName: string): string | undefined;
1565
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1566
+ getGeneticCodeId(refName: string): number;
1567
+ getSeqAdapterRefName(canonicalRefName: string): string;
1568
+ } & {
1569
+ getCanonicalRefName2(refName: string): string;
1570
+ isValidRefName(refName: string): boolean;
1571
+ } & {
1572
+ getRefNamePosition(refName: string): number | undefined;
1573
+ getAliasesForRefName(refName: string): string[];
1574
+ getRefNameMapForAdapter(adapterConf: {
1575
+ [x: string]: unknown;
1576
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1577
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1578
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1579
+ }> & {
1580
+ unrecognizedReports: {
1581
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
1582
+ reportFor(session: unknown, name: string): {
1583
+ handled: boolean;
1584
+ claim?: Promise<void>;
1585
+ } | undefined;
1586
+ };
1587
+ } & {
1588
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
1589
+ } & {
1590
+ getCanonicalAssemblyName(asmName: string): string | undefined;
1591
+ getDisplayName(asmName: string): string;
1592
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1593
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1594
+ }> & {
1595
+ error: unknown;
1596
+ loadingP: Promise<void> | undefined;
1597
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1598
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1599
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1600
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1601
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1602
+ loadedGeneticCodes: Record<string, number> | undefined;
1603
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1604
+ statusMessage: string | undefined;
1605
+ statusProgress: number | undefined;
1606
+ statusSource: string | undefined;
1607
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1608
+ } & {
1609
+ getConf(arg: string): any;
1610
+ } & {
1611
+ readonly name: string;
1612
+ readonly aliases: string[];
1613
+ readonly displayName: string;
1614
+ readonly refNameColors: string[];
1615
+ } & {
1616
+ readonly allAliases: string[];
1617
+ hasName(name: string): boolean;
1618
+ } & {
1619
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1620
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1621
+ } & {
1622
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1623
+ regions: import("@jbrowse/core/util").Region[];
1624
+ cytobands: import("@jbrowse/core/util").Feature[];
1625
+ geneticCodes: Record<string, number>;
1626
+ }): void;
1627
+ setError(e: unknown): void;
1628
+ setLoadingP(p?: Promise<void>): void;
1629
+ loadPre(): Promise<void>;
1630
+ } & {
1631
+ load(): Promise<void>;
1632
+ } & {
1633
+ afterAttach(): void;
1634
+ } & {
1635
+ readonly initialized: boolean;
1636
+ readonly allRefNames: string[] | undefined;
1637
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1638
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1639
+ } & {
1640
+ readonly refNames: string[] | undefined;
1641
+ } & {
1642
+ readonly refNameToIndex: Map<string, number> | undefined;
1643
+ } & {
1644
+ getCanonicalRefName(refName: string): string | undefined;
1645
+ getRefNameColor(refName: string): string | undefined;
1646
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1647
+ getGeneticCodeId(refName: string): number;
1648
+ getSeqAdapterRefName(canonicalRefName: string): string;
1649
+ } & {
1650
+ getCanonicalRefName2(refName: string): string;
1651
+ isValidRefName(refName: string): boolean;
1652
+ } & {
1653
+ getRefNamePosition(refName: string): number | undefined;
1654
+ getAliasesForRefName(refName: string): string[];
1655
+ getRefNameMapForAdapter(adapterConf: {
1656
+ [x: string]: unknown;
1657
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1658
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1659
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1660
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1661
+ }, {
1662
+ error: unknown;
1663
+ loadingP: Promise<void> | undefined;
1664
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1665
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1666
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1667
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1668
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1669
+ loadedGeneticCodes: Record<string, number> | undefined;
1670
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1671
+ statusMessage: string | undefined;
1672
+ statusProgress: number | undefined;
1673
+ statusSource: string | undefined;
1674
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1675
+ } & {
1676
+ getConf(arg: string): any;
1677
+ } & {
1678
+ readonly name: string;
1679
+ readonly aliases: string[];
1680
+ readonly displayName: string;
1681
+ readonly refNameColors: string[];
1682
+ } & {
1683
+ readonly allAliases: string[];
1684
+ hasName(name: string): boolean;
1685
+ } & {
1686
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1687
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1688
+ } & {
1689
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1690
+ regions: import("@jbrowse/core/util").Region[];
1691
+ cytobands: import("@jbrowse/core/util").Feature[];
1692
+ geneticCodes: Record<string, number>;
1693
+ }): void;
1694
+ setError(e: unknown): void;
1695
+ setLoadingP(p?: Promise<void>): void;
1696
+ loadPre(): Promise<void>;
1697
+ } & {
1698
+ load(): Promise<void>;
1699
+ } & {
1700
+ afterAttach(): void;
1701
+ } & {
1702
+ readonly initialized: boolean;
1703
+ readonly allRefNames: string[] | undefined;
1704
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1705
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1706
+ } & {
1707
+ readonly refNames: string[] | undefined;
1708
+ } & {
1709
+ readonly refNameToIndex: Map<string, number> | undefined;
1710
+ } & {
1711
+ getCanonicalRefName(refName: string): string | undefined;
1712
+ getRefNameColor(refName: string): string | undefined;
1713
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1714
+ getGeneticCodeId(refName: string): number;
1715
+ getSeqAdapterRefName(canonicalRefName: string): string;
1716
+ } & {
1717
+ getCanonicalRefName2(refName: string): string;
1718
+ isValidRefName(refName: string): boolean;
1719
+ } & {
1720
+ getRefNamePosition(refName: string): number | undefined;
1721
+ getAliasesForRefName(refName: string): string[];
1722
+ getRefNameMapForAdapter(adapterConf: {
1723
+ [x: string]: unknown;
1724
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1725
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1726
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1727
+ has(asmName: string): boolean;
1728
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1729
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1730
+ }> & {
1731
+ error: unknown;
1732
+ loadingP: Promise<void> | undefined;
1733
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1734
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1735
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1736
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1737
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1738
+ loadedGeneticCodes: Record<string, number> | undefined;
1739
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1740
+ statusMessage: string | undefined;
1741
+ statusProgress: number | undefined;
1742
+ statusSource: string | undefined;
1743
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1744
+ } & {
1745
+ getConf(arg: string): any;
1746
+ } & {
1747
+ readonly name: string;
1748
+ readonly aliases: string[];
1749
+ readonly displayName: string;
1750
+ readonly refNameColors: string[];
1751
+ } & {
1752
+ readonly allAliases: string[];
1753
+ hasName(name: string): boolean;
1754
+ } & {
1755
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1756
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1757
+ } & {
1758
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1759
+ regions: import("@jbrowse/core/util").Region[];
1760
+ cytobands: import("@jbrowse/core/util").Feature[];
1761
+ geneticCodes: Record<string, number>;
1762
+ }): void;
1763
+ setError(e: unknown): void;
1764
+ setLoadingP(p?: Promise<void>): void;
1765
+ loadPre(): Promise<void>;
1766
+ } & {
1767
+ load(): Promise<void>;
1768
+ } & {
1769
+ afterAttach(): void;
1770
+ } & {
1771
+ readonly initialized: boolean;
1772
+ readonly allRefNames: string[] | undefined;
1773
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1774
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1775
+ } & {
1776
+ readonly refNames: string[] | undefined;
1777
+ } & {
1778
+ readonly refNameToIndex: Map<string, number> | undefined;
1779
+ } & {
1780
+ getCanonicalRefName(refName: string): string | undefined;
1781
+ getRefNameColor(refName: string): string | undefined;
1782
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1783
+ getGeneticCodeId(refName: string): number;
1784
+ getSeqAdapterRefName(canonicalRefName: string): string;
1785
+ } & {
1786
+ getCanonicalRefName2(refName: string): string;
1787
+ isValidRefName(refName: string): boolean;
1788
+ } & {
1789
+ getRefNamePosition(refName: string): number | undefined;
1790
+ getAliasesForRefName(refName: string): string[];
1791
+ getRefNameMapForAdapter(adapterConf: {
1792
+ [x: string]: unknown;
1793
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1794
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1795
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1796
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1797
+ }, {
1798
+ error: unknown;
1799
+ loadingP: Promise<void> | undefined;
1800
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1801
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1802
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1803
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1804
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1805
+ loadedGeneticCodes: Record<string, number> | undefined;
1806
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1807
+ statusMessage: string | undefined;
1808
+ statusProgress: number | undefined;
1809
+ statusSource: string | undefined;
1810
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1811
+ } & {
1812
+ getConf(arg: string): any;
1813
+ } & {
1814
+ readonly name: string;
1815
+ readonly aliases: string[];
1816
+ readonly displayName: string;
1817
+ readonly refNameColors: string[];
1818
+ } & {
1819
+ readonly allAliases: string[];
1820
+ hasName(name: string): boolean;
1821
+ } & {
1822
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1823
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1824
+ } & {
1825
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1826
+ regions: import("@jbrowse/core/util").Region[];
1827
+ cytobands: import("@jbrowse/core/util").Feature[];
1828
+ geneticCodes: Record<string, number>;
1829
+ }): void;
1830
+ setError(e: unknown): void;
1831
+ setLoadingP(p?: Promise<void>): void;
1832
+ loadPre(): Promise<void>;
1833
+ } & {
1834
+ load(): Promise<void>;
1835
+ } & {
1836
+ afterAttach(): void;
1837
+ } & {
1838
+ readonly initialized: boolean;
1839
+ readonly allRefNames: string[] | undefined;
1840
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1841
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1842
+ } & {
1843
+ readonly refNames: string[] | undefined;
1844
+ } & {
1845
+ readonly refNameToIndex: Map<string, number> | undefined;
1846
+ } & {
1847
+ getCanonicalRefName(refName: string): string | undefined;
1848
+ getRefNameColor(refName: string): string | undefined;
1849
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1850
+ getGeneticCodeId(refName: string): number;
1851
+ getSeqAdapterRefName(canonicalRefName: string): string;
1852
+ } & {
1853
+ getCanonicalRefName2(refName: string): string;
1854
+ isValidRefName(refName: string): boolean;
1855
+ } & {
1856
+ getRefNamePosition(refName: string): number | undefined;
1857
+ getAliasesForRefName(refName: string): string[];
1858
+ getRefNameMapForAdapter(adapterConf: {
1859
+ [x: string]: unknown;
1860
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1861
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1862
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1863
+ readonly assemblyNamesList: string[];
1864
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1865
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1866
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1867
+ } & {
1868
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
1869
+ } & {
1870
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1871
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1872
+ }> & {
1873
+ error: unknown;
1874
+ loadingP: Promise<void> | undefined;
1875
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1876
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1877
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1878
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1879
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1880
+ loadedGeneticCodes: Record<string, number> | undefined;
1881
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1882
+ statusMessage: string | undefined;
1883
+ statusProgress: number | undefined;
1884
+ statusSource: string | undefined;
1885
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1886
+ } & {
1887
+ getConf(arg: string): any;
1888
+ } & {
1889
+ readonly name: string;
1890
+ readonly aliases: string[];
1891
+ readonly displayName: string;
1892
+ readonly refNameColors: string[];
1893
+ } & {
1894
+ readonly allAliases: string[];
1895
+ hasName(name: string): boolean;
1896
+ } & {
1897
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1898
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1899
+ } & {
1900
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1901
+ regions: import("@jbrowse/core/util").Region[];
1902
+ cytobands: import("@jbrowse/core/util").Feature[];
1903
+ geneticCodes: Record<string, number>;
1904
+ }): void;
1905
+ setError(e: unknown): void;
1906
+ setLoadingP(p?: Promise<void>): void;
1907
+ loadPre(): Promise<void>;
1908
+ } & {
1909
+ load(): Promise<void>;
1910
+ } & {
1911
+ afterAttach(): void;
1912
+ } & {
1913
+ readonly initialized: boolean;
1914
+ readonly allRefNames: string[] | undefined;
1915
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1916
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1917
+ } & {
1918
+ readonly refNames: string[] | undefined;
1919
+ } & {
1920
+ readonly refNameToIndex: Map<string, number> | undefined;
1921
+ } & {
1922
+ getCanonicalRefName(refName: string): string | undefined;
1923
+ getRefNameColor(refName: string): string | undefined;
1924
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1925
+ getGeneticCodeId(refName: string): number;
1926
+ getSeqAdapterRefName(canonicalRefName: string): string;
1927
+ } & {
1928
+ getCanonicalRefName2(refName: string): string;
1929
+ isValidRefName(refName: string): boolean;
1930
+ } & {
1931
+ getRefNamePosition(refName: string): number | undefined;
1932
+ getAliasesForRefName(refName: string): string[];
1933
+ getRefNameMapForAdapter(adapterConf: {
1934
+ [x: string]: unknown;
1935
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1936
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1937
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1938
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1939
+ }, {
1940
+ error: unknown;
1941
+ loadingP: Promise<void> | undefined;
1942
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1943
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1944
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1945
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1946
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1947
+ loadedGeneticCodes: Record<string, number> | undefined;
1948
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1949
+ statusMessage: string | undefined;
1950
+ statusProgress: number | undefined;
1951
+ statusSource: string | undefined;
1952
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1953
+ } & {
1954
+ getConf(arg: string): any;
1955
+ } & {
1956
+ readonly name: string;
1957
+ readonly aliases: string[];
1958
+ readonly displayName: string;
1959
+ readonly refNameColors: string[];
1960
+ } & {
1961
+ readonly allAliases: string[];
1962
+ hasName(name: string): boolean;
1963
+ } & {
1964
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1965
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1966
+ } & {
1967
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1968
+ regions: import("@jbrowse/core/util").Region[];
1969
+ cytobands: import("@jbrowse/core/util").Feature[];
1970
+ geneticCodes: Record<string, number>;
1971
+ }): void;
1972
+ setError(e: unknown): void;
1973
+ setLoadingP(p?: Promise<void>): void;
1974
+ loadPre(): Promise<void>;
1975
+ } & {
1976
+ load(): Promise<void>;
1977
+ } & {
1978
+ afterAttach(): void;
1979
+ } & {
1980
+ readonly initialized: boolean;
1981
+ readonly allRefNames: string[] | undefined;
1982
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1983
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1984
+ } & {
1985
+ readonly refNames: string[] | undefined;
1986
+ } & {
1987
+ readonly refNameToIndex: Map<string, number> | undefined;
1988
+ } & {
1989
+ getCanonicalRefName(refName: string): string | undefined;
1990
+ getRefNameColor(refName: string): string | undefined;
1991
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1992
+ getGeneticCodeId(refName: string): number;
1993
+ getSeqAdapterRefName(canonicalRefName: string): string;
1994
+ } & {
1995
+ getCanonicalRefName2(refName: string): string;
1996
+ isValidRefName(refName: string): boolean;
1997
+ } & {
1998
+ getRefNamePosition(refName: string): number | undefined;
1999
+ getAliasesForRefName(refName: string): string[];
2000
+ getRefNameMapForAdapter(adapterConf: {
2001
+ [x: string]: unknown;
2002
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2003
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2004
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
2005
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2006
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2007
+ }> & {
2008
+ error: unknown;
2009
+ loadingP: Promise<void> | undefined;
2010
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2011
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2012
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2013
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2014
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2015
+ loadedGeneticCodes: Record<string, number> | undefined;
2016
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2017
+ statusMessage: string | undefined;
2018
+ statusProgress: number | undefined;
2019
+ statusSource: string | undefined;
2020
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2021
+ } & {
2022
+ getConf(arg: string): any;
2023
+ } & {
2024
+ readonly name: string;
2025
+ readonly aliases: string[];
2026
+ readonly displayName: string;
2027
+ readonly refNameColors: string[];
2028
+ } & {
2029
+ readonly allAliases: string[];
2030
+ hasName(name: string): boolean;
2031
+ } & {
2032
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2033
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2034
+ } & {
2035
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2036
+ regions: import("@jbrowse/core/util").Region[];
2037
+ cytobands: import("@jbrowse/core/util").Feature[];
2038
+ geneticCodes: Record<string, number>;
2039
+ }): void;
2040
+ setError(e: unknown): void;
2041
+ setLoadingP(p?: Promise<void>): void;
2042
+ loadPre(): Promise<void>;
2043
+ } & {
2044
+ load(): Promise<void>;
2045
+ } & {
2046
+ afterAttach(): void;
2047
+ } & {
2048
+ readonly initialized: boolean;
2049
+ readonly allRefNames: string[] | undefined;
2050
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2051
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2052
+ } & {
2053
+ readonly refNames: string[] | undefined;
2054
+ } & {
2055
+ readonly refNameToIndex: Map<string, number> | undefined;
2056
+ } & {
2057
+ getCanonicalRefName(refName: string): string | undefined;
2058
+ getRefNameColor(refName: string): string | undefined;
2059
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2060
+ getGeneticCodeId(refName: string): number;
2061
+ getSeqAdapterRefName(canonicalRefName: string): string;
2062
+ } & {
2063
+ getCanonicalRefName2(refName: string): string;
2064
+ isValidRefName(refName: string): boolean;
2065
+ } & {
2066
+ getRefNamePosition(refName: string): number | undefined;
2067
+ getAliasesForRefName(refName: string): string[];
2068
+ getRefNameMapForAdapter(adapterConf: {
2069
+ [x: string]: unknown;
2070
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2071
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2072
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2073
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2074
+ }, {
2075
+ error: unknown;
2076
+ loadingP: Promise<void> | undefined;
2077
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2078
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2079
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2080
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2081
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2082
+ loadedGeneticCodes: Record<string, number> | undefined;
2083
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2084
+ statusMessage: string | undefined;
2085
+ statusProgress: number | undefined;
2086
+ statusSource: string | undefined;
2087
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2088
+ } & {
2089
+ getConf(arg: string): any;
2090
+ } & {
2091
+ readonly name: string;
2092
+ readonly aliases: string[];
2093
+ readonly displayName: string;
2094
+ readonly refNameColors: string[];
2095
+ } & {
2096
+ readonly allAliases: string[];
2097
+ hasName(name: string): boolean;
2098
+ } & {
2099
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2100
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2101
+ } & {
2102
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2103
+ regions: import("@jbrowse/core/util").Region[];
2104
+ cytobands: import("@jbrowse/core/util").Feature[];
2105
+ geneticCodes: Record<string, number>;
2106
+ }): void;
2107
+ setError(e: unknown): void;
2108
+ setLoadingP(p?: Promise<void>): void;
2109
+ loadPre(): Promise<void>;
2110
+ } & {
2111
+ load(): Promise<void>;
2112
+ } & {
2113
+ afterAttach(): void;
2114
+ } & {
2115
+ readonly initialized: boolean;
2116
+ readonly allRefNames: string[] | undefined;
2117
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2118
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2119
+ } & {
2120
+ readonly refNames: string[] | undefined;
2121
+ } & {
2122
+ readonly refNameToIndex: Map<string, number> | undefined;
2123
+ } & {
2124
+ getCanonicalRefName(refName: string): string | undefined;
2125
+ getRefNameColor(refName: string): string | undefined;
2126
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2127
+ getGeneticCodeId(refName: string): number;
2128
+ getSeqAdapterRefName(canonicalRefName: string): string;
2129
+ } & {
2130
+ getCanonicalRefName2(refName: string): string;
2131
+ isValidRefName(refName: string): boolean;
2132
+ } & {
2133
+ getRefNamePosition(refName: string): number | undefined;
2134
+ getAliasesForRefName(refName: string): string[];
2135
+ getRefNameMapForAdapter(adapterConf: {
2136
+ [x: string]: unknown;
2137
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2138
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2139
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2140
+ getRefNameMapForAdapter(adapterConf: {
2141
+ [x: string]: unknown;
2142
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2143
+ isValidRefName(refName: string, assemblyName: string): boolean;
2144
+ } & {
2145
+ afterAttach(): void;
2146
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
2147
+ addAssembly(configuration: any): void;
2148
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2149
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
2150
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2151
+ }, {
2152
+ error: unknown;
2153
+ loadingP: Promise<void> | undefined;
2154
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2155
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2156
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2157
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2158
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2159
+ loadedGeneticCodes: Record<string, number> | undefined;
2160
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2161
+ statusMessage: string | undefined;
2162
+ statusProgress: number | undefined;
2163
+ statusSource: string | undefined;
2164
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2165
+ } & {
2166
+ getConf(arg: string): any;
2167
+ } & {
2168
+ readonly name: string;
2169
+ readonly aliases: string[];
2170
+ readonly displayName: string;
2171
+ readonly refNameColors: string[];
2172
+ } & {
2173
+ readonly allAliases: string[];
2174
+ hasName(name: string): boolean;
2175
+ } & {
2176
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2177
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2178
+ } & {
2179
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2180
+ regions: import("@jbrowse/core/util").Region[];
2181
+ cytobands: import("@jbrowse/core/util").Feature[];
2182
+ geneticCodes: Record<string, number>;
2183
+ }): void;
2184
+ setError(e: unknown): void;
2185
+ setLoadingP(p?: Promise<void>): void;
2186
+ loadPre(): Promise<void>;
2187
+ } & {
2188
+ load(): Promise<void>;
2189
+ } & {
2190
+ afterAttach(): void;
2191
+ } & {
2192
+ readonly initialized: boolean;
2193
+ readonly allRefNames: string[] | undefined;
2194
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2195
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2196
+ } & {
2197
+ readonly refNames: string[] | undefined;
2198
+ } & {
2199
+ readonly refNameToIndex: Map<string, number> | undefined;
2200
+ } & {
2201
+ getCanonicalRefName(refName: string): string | undefined;
2202
+ getRefNameColor(refName: string): string | undefined;
2203
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2204
+ getGeneticCodeId(refName: string): number;
2205
+ getSeqAdapterRefName(canonicalRefName: string): string;
2206
+ } & {
2207
+ getCanonicalRefName2(refName: string): string;
2208
+ isValidRefName(refName: string): boolean;
2209
+ } & {
2210
+ getRefNamePosition(refName: string): number | undefined;
2211
+ getAliasesForRefName(refName: string): string[];
2212
+ getRefNameMapForAdapter(adapterConf: {
2213
+ [x: string]: unknown;
2214
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2215
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2216
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2217
+ }, {
2218
+ unrecognizedReports: {
2219
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
2220
+ reportFor(session: unknown, name: string): {
2221
+ handled: boolean;
2222
+ claim?: Promise<void>;
2223
+ } | undefined;
2224
+ };
2225
+ } & {
2226
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
2227
+ } & {
2228
+ getCanonicalAssemblyName(asmName: string): string | undefined;
2229
+ getDisplayName(asmName: string): string;
2230
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2231
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2232
+ }> & {
2233
+ error: unknown;
2234
+ loadingP: Promise<void> | undefined;
2235
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2236
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2237
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2238
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2239
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2240
+ loadedGeneticCodes: Record<string, number> | undefined;
2241
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2242
+ statusMessage: string | undefined;
2243
+ statusProgress: number | undefined;
2244
+ statusSource: string | undefined;
2245
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2246
+ } & {
2247
+ getConf(arg: string): any;
2248
+ } & {
2249
+ readonly name: string;
2250
+ readonly aliases: string[];
2251
+ readonly displayName: string;
2252
+ readonly refNameColors: string[];
2253
+ } & {
2254
+ readonly allAliases: string[];
2255
+ hasName(name: string): boolean;
2256
+ } & {
2257
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2258
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2259
+ } & {
2260
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2261
+ regions: import("@jbrowse/core/util").Region[];
2262
+ cytobands: import("@jbrowse/core/util").Feature[];
2263
+ geneticCodes: Record<string, number>;
2264
+ }): void;
2265
+ setError(e: unknown): void;
2266
+ setLoadingP(p?: Promise<void>): void;
2267
+ loadPre(): Promise<void>;
2268
+ } & {
2269
+ load(): Promise<void>;
2270
+ } & {
2271
+ afterAttach(): void;
2272
+ } & {
2273
+ readonly initialized: boolean;
2274
+ readonly allRefNames: string[] | undefined;
2275
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2276
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2277
+ } & {
2278
+ readonly refNames: string[] | undefined;
2279
+ } & {
2280
+ readonly refNameToIndex: Map<string, number> | undefined;
2281
+ } & {
2282
+ getCanonicalRefName(refName: string): string | undefined;
2283
+ getRefNameColor(refName: string): string | undefined;
2284
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2285
+ getGeneticCodeId(refName: string): number;
2286
+ getSeqAdapterRefName(canonicalRefName: string): string;
2287
+ } & {
2288
+ getCanonicalRefName2(refName: string): string;
2289
+ isValidRefName(refName: string): boolean;
2290
+ } & {
2291
+ getRefNamePosition(refName: string): number | undefined;
2292
+ getAliasesForRefName(refName: string): string[];
2293
+ getRefNameMapForAdapter(adapterConf: {
2294
+ [x: string]: unknown;
2295
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2296
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2297
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2298
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2299
+ }, {
2300
+ error: unknown;
2301
+ loadingP: Promise<void> | undefined;
2302
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2303
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2304
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2305
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2306
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2307
+ loadedGeneticCodes: Record<string, number> | undefined;
2308
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2309
+ statusMessage: string | undefined;
2310
+ statusProgress: number | undefined;
2311
+ statusSource: string | undefined;
2312
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2313
+ } & {
2314
+ getConf(arg: string): any;
2315
+ } & {
2316
+ readonly name: string;
2317
+ readonly aliases: string[];
2318
+ readonly displayName: string;
2319
+ readonly refNameColors: string[];
2320
+ } & {
2321
+ readonly allAliases: string[];
2322
+ hasName(name: string): boolean;
2323
+ } & {
2324
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2325
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2326
+ } & {
2327
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2328
+ regions: import("@jbrowse/core/util").Region[];
2329
+ cytobands: import("@jbrowse/core/util").Feature[];
2330
+ geneticCodes: Record<string, number>;
2331
+ }): void;
2332
+ setError(e: unknown): void;
2333
+ setLoadingP(p?: Promise<void>): void;
2334
+ loadPre(): Promise<void>;
2335
+ } & {
2336
+ load(): Promise<void>;
2337
+ } & {
2338
+ afterAttach(): void;
2339
+ } & {
2340
+ readonly initialized: boolean;
2341
+ readonly allRefNames: string[] | undefined;
2342
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2343
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2344
+ } & {
2345
+ readonly refNames: string[] | undefined;
2346
+ } & {
2347
+ readonly refNameToIndex: Map<string, number> | undefined;
2348
+ } & {
2349
+ getCanonicalRefName(refName: string): string | undefined;
2350
+ getRefNameColor(refName: string): string | undefined;
2351
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2352
+ getGeneticCodeId(refName: string): number;
2353
+ getSeqAdapterRefName(canonicalRefName: string): string;
2354
+ } & {
2355
+ getCanonicalRefName2(refName: string): string;
2356
+ isValidRefName(refName: string): boolean;
2357
+ } & {
2358
+ getRefNamePosition(refName: string): number | undefined;
2359
+ getAliasesForRefName(refName: string): string[];
2360
+ getRefNameMapForAdapter(adapterConf: {
2361
+ [x: string]: unknown;
2362
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2363
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2364
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2365
+ has(asmName: string): boolean;
2366
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2367
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2368
+ }> & {
2369
+ error: unknown;
2370
+ loadingP: Promise<void> | undefined;
2371
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2372
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2373
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2374
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2375
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2376
+ loadedGeneticCodes: Record<string, number> | undefined;
2377
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2378
+ statusMessage: string | undefined;
2379
+ statusProgress: number | undefined;
2380
+ statusSource: string | undefined;
2381
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2382
+ } & {
2383
+ getConf(arg: string): any;
2384
+ } & {
2385
+ readonly name: string;
2386
+ readonly aliases: string[];
2387
+ readonly displayName: string;
2388
+ readonly refNameColors: string[];
2389
+ } & {
2390
+ readonly allAliases: string[];
2391
+ hasName(name: string): boolean;
2392
+ } & {
2393
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2394
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2395
+ } & {
2396
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2397
+ regions: import("@jbrowse/core/util").Region[];
2398
+ cytobands: import("@jbrowse/core/util").Feature[];
2399
+ geneticCodes: Record<string, number>;
2400
+ }): void;
2401
+ setError(e: unknown): void;
2402
+ setLoadingP(p?: Promise<void>): void;
2403
+ loadPre(): Promise<void>;
2404
+ } & {
2405
+ load(): Promise<void>;
2406
+ } & {
2407
+ afterAttach(): void;
2408
+ } & {
2409
+ readonly initialized: boolean;
2410
+ readonly allRefNames: string[] | undefined;
2411
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2412
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2413
+ } & {
2414
+ readonly refNames: string[] | undefined;
2415
+ } & {
2416
+ readonly refNameToIndex: Map<string, number> | undefined;
2417
+ } & {
2418
+ getCanonicalRefName(refName: string): string | undefined;
2419
+ getRefNameColor(refName: string): string | undefined;
2420
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2421
+ getGeneticCodeId(refName: string): number;
2422
+ getSeqAdapterRefName(canonicalRefName: string): string;
2423
+ } & {
2424
+ getCanonicalRefName2(refName: string): string;
2425
+ isValidRefName(refName: string): boolean;
2426
+ } & {
2427
+ getRefNamePosition(refName: string): number | undefined;
2428
+ getAliasesForRefName(refName: string): string[];
2429
+ getRefNameMapForAdapter(adapterConf: {
2430
+ [x: string]: unknown;
2431
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2432
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2433
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2434
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2435
+ }, {
2436
+ error: unknown;
2437
+ loadingP: Promise<void> | undefined;
2438
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2439
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2440
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2441
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2442
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2443
+ loadedGeneticCodes: Record<string, number> | undefined;
2444
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2445
+ statusMessage: string | undefined;
2446
+ statusProgress: number | undefined;
2447
+ statusSource: string | undefined;
2448
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2449
+ } & {
2450
+ getConf(arg: string): any;
2451
+ } & {
2452
+ readonly name: string;
2453
+ readonly aliases: string[];
2454
+ readonly displayName: string;
2455
+ readonly refNameColors: string[];
2456
+ } & {
2457
+ readonly allAliases: string[];
2458
+ hasName(name: string): boolean;
2459
+ } & {
2460
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2461
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2462
+ } & {
2463
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2464
+ regions: import("@jbrowse/core/util").Region[];
2465
+ cytobands: import("@jbrowse/core/util").Feature[];
2466
+ geneticCodes: Record<string, number>;
2467
+ }): void;
2468
+ setError(e: unknown): void;
2469
+ setLoadingP(p?: Promise<void>): void;
2470
+ loadPre(): Promise<void>;
2471
+ } & {
2472
+ load(): Promise<void>;
2473
+ } & {
2474
+ afterAttach(): void;
2475
+ } & {
2476
+ readonly initialized: boolean;
2477
+ readonly allRefNames: string[] | undefined;
2478
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2479
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2480
+ } & {
2481
+ readonly refNames: string[] | undefined;
2482
+ } & {
2483
+ readonly refNameToIndex: Map<string, number> | undefined;
2484
+ } & {
2485
+ getCanonicalRefName(refName: string): string | undefined;
2486
+ getRefNameColor(refName: string): string | undefined;
2487
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2488
+ getGeneticCodeId(refName: string): number;
2489
+ getSeqAdapterRefName(canonicalRefName: string): string;
2490
+ } & {
2491
+ getCanonicalRefName2(refName: string): string;
2492
+ isValidRefName(refName: string): boolean;
2493
+ } & {
2494
+ getRefNamePosition(refName: string): number | undefined;
2495
+ getAliasesForRefName(refName: string): string[];
2496
+ getRefNameMapForAdapter(adapterConf: {
2497
+ [x: string]: unknown;
2498
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2499
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2500
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2501
+ readonly assemblyNamesList: string[];
2502
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
2503
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2504
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2505
+ } & {
2506
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
2507
+ } & {
2508
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2509
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2510
+ }> & {
2511
+ error: unknown;
2512
+ loadingP: Promise<void> | undefined;
2513
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2514
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2515
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2516
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2517
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2518
+ loadedGeneticCodes: Record<string, number> | undefined;
2519
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2520
+ statusMessage: string | undefined;
2521
+ statusProgress: number | undefined;
2522
+ statusSource: string | undefined;
2523
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2524
+ } & {
2525
+ getConf(arg: string): any;
2526
+ } & {
2527
+ readonly name: string;
2528
+ readonly aliases: string[];
2529
+ readonly displayName: string;
2530
+ readonly refNameColors: string[];
2531
+ } & {
2532
+ readonly allAliases: string[];
2533
+ hasName(name: string): boolean;
2534
+ } & {
2535
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2536
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2537
+ } & {
2538
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2539
+ regions: import("@jbrowse/core/util").Region[];
2540
+ cytobands: import("@jbrowse/core/util").Feature[];
2541
+ geneticCodes: Record<string, number>;
2542
+ }): void;
2543
+ setError(e: unknown): void;
2544
+ setLoadingP(p?: Promise<void>): void;
2545
+ loadPre(): Promise<void>;
2546
+ } & {
2547
+ load(): Promise<void>;
2548
+ } & {
2549
+ afterAttach(): void;
2550
+ } & {
2551
+ readonly initialized: boolean;
2552
+ readonly allRefNames: string[] | undefined;
2553
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2554
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2555
+ } & {
2556
+ readonly refNames: string[] | undefined;
2557
+ } & {
2558
+ readonly refNameToIndex: Map<string, number> | undefined;
2559
+ } & {
2560
+ getCanonicalRefName(refName: string): string | undefined;
2561
+ getRefNameColor(refName: string): string | undefined;
2562
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2563
+ getGeneticCodeId(refName: string): number;
2564
+ getSeqAdapterRefName(canonicalRefName: string): string;
2565
+ } & {
2566
+ getCanonicalRefName2(refName: string): string;
2567
+ isValidRefName(refName: string): boolean;
2568
+ } & {
2569
+ getRefNamePosition(refName: string): number | undefined;
2570
+ getAliasesForRefName(refName: string): string[];
2571
+ getRefNameMapForAdapter(adapterConf: {
2572
+ [x: string]: unknown;
2573
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2574
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2575
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2576
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2577
+ }, {
2578
+ error: unknown;
2579
+ loadingP: Promise<void> | undefined;
2580
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2581
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2582
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2583
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2584
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2585
+ loadedGeneticCodes: Record<string, number> | undefined;
2586
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2587
+ statusMessage: string | undefined;
2588
+ statusProgress: number | undefined;
2589
+ statusSource: string | undefined;
2590
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2591
+ } & {
2592
+ getConf(arg: string): any;
2593
+ } & {
2594
+ readonly name: string;
2595
+ readonly aliases: string[];
2596
+ readonly displayName: string;
2597
+ readonly refNameColors: string[];
2598
+ } & {
2599
+ readonly allAliases: string[];
2600
+ hasName(name: string): boolean;
2601
+ } & {
2602
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2603
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2604
+ } & {
2605
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2606
+ regions: import("@jbrowse/core/util").Region[];
2607
+ cytobands: import("@jbrowse/core/util").Feature[];
2608
+ geneticCodes: Record<string, number>;
2609
+ }): void;
2610
+ setError(e: unknown): void;
2611
+ setLoadingP(p?: Promise<void>): void;
2612
+ loadPre(): Promise<void>;
2613
+ } & {
2614
+ load(): Promise<void>;
2615
+ } & {
2616
+ afterAttach(): void;
2617
+ } & {
2618
+ readonly initialized: boolean;
2619
+ readonly allRefNames: string[] | undefined;
2620
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2621
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2622
+ } & {
2623
+ readonly refNames: string[] | undefined;
2624
+ } & {
2625
+ readonly refNameToIndex: Map<string, number> | undefined;
2626
+ } & {
2627
+ getCanonicalRefName(refName: string): string | undefined;
2628
+ getRefNameColor(refName: string): string | undefined;
2629
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2630
+ getGeneticCodeId(refName: string): number;
2631
+ getSeqAdapterRefName(canonicalRefName: string): string;
2632
+ } & {
2633
+ getCanonicalRefName2(refName: string): string;
2634
+ isValidRefName(refName: string): boolean;
2635
+ } & {
2636
+ getRefNamePosition(refName: string): number | undefined;
2637
+ getAliasesForRefName(refName: string): string[];
2638
+ getRefNameMapForAdapter(adapterConf: {
2639
+ [x: string]: unknown;
2640
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2641
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2642
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
2643
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2644
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2645
+ }> & {
2646
+ error: unknown;
2647
+ loadingP: Promise<void> | undefined;
2648
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2649
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2650
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2651
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2652
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2653
+ loadedGeneticCodes: Record<string, number> | undefined;
2654
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2655
+ statusMessage: string | undefined;
2656
+ statusProgress: number | undefined;
2657
+ statusSource: string | undefined;
2658
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2659
+ } & {
2660
+ getConf(arg: string): any;
2661
+ } & {
2662
+ readonly name: string;
2663
+ readonly aliases: string[];
2664
+ readonly displayName: string;
2665
+ readonly refNameColors: string[];
2666
+ } & {
2667
+ readonly allAliases: string[];
2668
+ hasName(name: string): boolean;
2669
+ } & {
2670
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2671
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2672
+ } & {
2673
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2674
+ regions: import("@jbrowse/core/util").Region[];
2675
+ cytobands: import("@jbrowse/core/util").Feature[];
2676
+ geneticCodes: Record<string, number>;
2677
+ }): void;
2678
+ setError(e: unknown): void;
2679
+ setLoadingP(p?: Promise<void>): void;
2680
+ loadPre(): Promise<void>;
2681
+ } & {
2682
+ load(): Promise<void>;
2683
+ } & {
2684
+ afterAttach(): void;
2685
+ } & {
2686
+ readonly initialized: boolean;
2687
+ readonly allRefNames: string[] | undefined;
2688
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2689
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2690
+ } & {
2691
+ readonly refNames: string[] | undefined;
2692
+ } & {
2693
+ readonly refNameToIndex: Map<string, number> | undefined;
2694
+ } & {
2695
+ getCanonicalRefName(refName: string): string | undefined;
2696
+ getRefNameColor(refName: string): string | undefined;
2697
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2698
+ getGeneticCodeId(refName: string): number;
2699
+ getSeqAdapterRefName(canonicalRefName: string): string;
2700
+ } & {
2701
+ getCanonicalRefName2(refName: string): string;
2702
+ isValidRefName(refName: string): boolean;
2703
+ } & {
2704
+ getRefNamePosition(refName: string): number | undefined;
2705
+ getAliasesForRefName(refName: string): string[];
2706
+ getRefNameMapForAdapter(adapterConf: {
2707
+ [x: string]: unknown;
2708
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2709
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2710
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2711
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2712
+ }, {
2713
+ error: unknown;
2714
+ loadingP: Promise<void> | undefined;
2715
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2716
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2717
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2718
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2719
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2720
+ loadedGeneticCodes: Record<string, number> | undefined;
2721
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2722
+ statusMessage: string | undefined;
2723
+ statusProgress: number | undefined;
2724
+ statusSource: string | undefined;
2725
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2726
+ } & {
2727
+ getConf(arg: string): any;
2728
+ } & {
2729
+ readonly name: string;
2730
+ readonly aliases: string[];
2731
+ readonly displayName: string;
2732
+ readonly refNameColors: string[];
2733
+ } & {
2734
+ readonly allAliases: string[];
2735
+ hasName(name: string): boolean;
2736
+ } & {
2737
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2738
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2739
+ } & {
2740
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2741
+ regions: import("@jbrowse/core/util").Region[];
2742
+ cytobands: import("@jbrowse/core/util").Feature[];
2743
+ geneticCodes: Record<string, number>;
2744
+ }): void;
2745
+ setError(e: unknown): void;
2746
+ setLoadingP(p?: Promise<void>): void;
2747
+ loadPre(): Promise<void>;
2748
+ } & {
2749
+ load(): Promise<void>;
2750
+ } & {
2751
+ afterAttach(): void;
2752
+ } & {
2753
+ readonly initialized: boolean;
2754
+ readonly allRefNames: string[] | undefined;
2755
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2756
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2757
+ } & {
2758
+ readonly refNames: string[] | undefined;
2759
+ } & {
2760
+ readonly refNameToIndex: Map<string, number> | undefined;
2761
+ } & {
2762
+ getCanonicalRefName(refName: string): string | undefined;
2763
+ getRefNameColor(refName: string): string | undefined;
2764
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2765
+ getGeneticCodeId(refName: string): number;
2766
+ getSeqAdapterRefName(canonicalRefName: string): string;
2767
+ } & {
2768
+ getCanonicalRefName2(refName: string): string;
2769
+ isValidRefName(refName: string): boolean;
2770
+ } & {
2771
+ getRefNamePosition(refName: string): number | undefined;
2772
+ getAliasesForRefName(refName: string): string[];
2773
+ getRefNameMapForAdapter(adapterConf: {
2774
+ [x: string]: unknown;
2775
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2776
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2777
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2778
+ getRefNameMapForAdapter(adapterConf: {
2779
+ [x: string]: unknown;
2780
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2781
+ isValidRefName(refName: string, assemblyName: string): boolean;
2782
+ } & {
2783
+ afterAttach(): void;
2784
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
2785
+ addAssembly(configuration: any): void;
2786
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2787
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<Omit<Omit<Omit<{
2788
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
2789
+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
2790
+ focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
2791
+ highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
2792
+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2793
+ highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2794
+ 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]>;
2795
+ }, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
2796
+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
2797
+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
2798
+ widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
2799
+ 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]>;
2800
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2801
+ }, "connectionInstances" | "connectionTrackConfigs"> & {
2802
+ connectionInstances: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
2803
+ 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]>;
2804
+ }, never>, never>, "focusedViewId" | "heldForMissingPlugins" | "highlightLabelsVisible" | "highlights" | "highlightsVisible" | "id" | "name"> & Omit<{
2805
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
2806
+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
2807
+ focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
2808
+ highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
2809
+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2810
+ highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2811
+ 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]>;
2812
+ }, never>>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
2813
+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
2814
+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
2815
+ widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
2816
+ 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]>;
2817
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2818
+ }>>;