@jbrowse/embedded-core 5.0.0-beta.1 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (12) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +250 -759
  2. package/esm/EmbeddedSessionMixin.js +19 -12
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +70 -345
  4. package/esm/EmbeddedSessionThemeMixin.js +31 -22
  5. package/esm/createEmbeddedRootModel.d.ts +192 -454
  6. package/esm/createEmbeddedRootModel.js +29 -16
  7. package/esm/ui/EmbeddedViewContainer.js +8 -8
  8. package/package.json +7 -7
  9. package/esm/ui/VersionAboutDialog.d.ts +0 -5
  10. package/esm/ui/VersionAboutDialog.js +0 -13
  11. package/esm/ui/ViewTitle.d.ts +0 -5
  12. package/esm/ui/ViewTitle.js +0 -65
package/esm/EmbeddedSessionMixin.d.ts CHANGED
@@ -4,7 +4,7 @@ export interface EmbeddedSessionParent {
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  version: string;
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  assemblyManager: AssemblyManager;
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  config: {
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- assemblyName: string;
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+ assemblyNames: string[];
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  };
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  }
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  /**
@@ -14,24 +14,25 @@ export interface EmbeddedSessionParent {
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  * they compose and the three getters that read the root model. The twin of
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  * {@link createEmbeddedRootModel} one level down.
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  *
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- * A mixin the product composes, deliberately, rather than a factory taking the
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- * product's view type and tracks mixin as parameters. That factory is the
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- * obvious shape and it does not work: `types.compose`'s overloads are declared
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- * over `IModelType<P, O, FC, FS>`, so a model handed in as a naked type
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- * parameter has nothing to infer those four from and the composed result
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- * degrades — `session.view` becomes `any`, which typechecks at every embedder
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- * call site and is caught by nothing. Keeping every argument to `compose`
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- * concrete is what keeps the products' views typed.
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+ * 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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- * So each product still spells out its own tracks mixin, `view` prop, and the
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- * `views`/`addView`/`removeView` members that read `self.view` — those are the
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- * ones that need its concrete view type.
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+ * 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]>;
@@ -42,11 +43,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  }, "connectionInstances" | "connectionTrackConfigs"> & {
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  connectionInstances: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
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  connectionTrackConfigs: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Record<string, import("@jbrowse/product-core").ConnectionTrackConfigEntry>, Record<string, import("@jbrowse/product-core").ConnectionTrackConfigEntry>, Record<string, import("@jbrowse/product-core").ConnectionTrackConfigEntry>>, [undefined]>;
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- }, never>, never>, "focusedViewId" | "heldForMissingPlugins" | "highlightsVisible" | "id" | "name"> & Omit<{
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+ }, 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;
@@ -65,7 +68,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  error: unknown;
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  loadingP: Promise<void> | undefined;
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  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
68
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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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;
@@ -103,7 +106,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  afterAttach(): void;
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  } & {
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  readonly initialized: boolean;
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- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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  readonly allRefNames: string[] | undefined;
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  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
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  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -121,6 +123,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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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;
@@ -136,141 +139,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  } | undefined;
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  };
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  } & {
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- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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- }> & {
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- error: unknown;
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- loadingP: Promise<void> | undefined;
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- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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- volatileRegions: 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>;
155
- } & {
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- getConf(arg: string): any;
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- } & {
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- readonly name: string;
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- readonly aliases: string[];
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- readonly displayName: string;
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- readonly refNameColors: string[];
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- } & {
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- readonly allAliases: string[];
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- hasName(name: string): boolean;
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- } & {
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- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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- } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
170
- regions: import("@jbrowse/core/util").Region[];
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- cytobands: import("@jbrowse/core/util").Feature[];
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- geneticCodes: Record<string, number>;
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- }): void;
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- setError(e: unknown): void;
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- setLoadingP(p?: Promise<void>): void;
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- loadPre(): Promise<void>;
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- } & {
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- load(): Promise<void>;
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- } & {
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- afterAttach(): void;
181
- } & {
182
- readonly initialized: boolean;
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- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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- readonly allRefNames: string[] | undefined;
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- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
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- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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- } & {
188
- readonly refNames: string[] | undefined;
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- } & {
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- readonly refNameToIndex: Map<string, number> | undefined;
191
- } & {
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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;
200
- } & {
201
- getAliasesForRefName(refName: string): string[];
202
- 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>;
205
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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- }, {
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- error: unknown;
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- loadingP: Promise<void> | undefined;
211
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
212
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
213
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
214
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
215
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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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;
219
- statusProgress: number | undefined;
220
- statusSource: string | undefined;
221
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
222
- } & {
223
- getConf(arg: string): any;
224
- } & {
225
- readonly name: string;
226
- readonly aliases: string[];
227
- readonly displayName: string;
228
- readonly refNameColors: string[];
229
- } & {
230
- readonly allAliases: string[];
231
- hasName(name: string): boolean;
232
- } & {
233
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
234
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
235
- } & {
236
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
237
- regions: import("@jbrowse/core/util").Region[];
238
- cytobands: import("@jbrowse/core/util").Feature[];
239
- geneticCodes: Record<string, number>;
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- }): void;
241
- setError(e: unknown): void;
242
- setLoadingP(p?: Promise<void>): void;
243
- loadPre(): Promise<void>;
244
- } & {
245
- load(): Promise<void>;
246
- } & {
247
- afterAttach(): void;
248
- } & {
249
- readonly initialized: boolean;
250
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
251
- readonly allRefNames: string[] | undefined;
252
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
253
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
254
- } & {
255
- readonly refNames: string[] | undefined;
256
- } & {
257
- readonly refNameToIndex: Map<string, number> | undefined;
258
- } & {
259
- getCanonicalRefName(refName: string): string | undefined;
260
- getRefNameColor(refName: string): string | undefined;
261
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
262
- getGeneticCodeId(refName: string): number;
263
- getSeqAdapterRefName(canonicalRefName: string): string;
264
- } & {
265
- getCanonicalRefName2(refName: string): string;
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- isValidRefName(refName: string): boolean;
267
- } & {
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- getAliasesForRefName(refName: string): string[];
269
- getRefNameMapForAdapter(adapterConf: {
270
- [x: string]: unknown;
271
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
272
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
273
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
142
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
274
143
  } & {
275
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  getCanonicalAssemblyName(asmName: string): string | undefined;
276
145
  getDisplayName(asmName: string): string;
@@ -280,7 +149,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
280
149
  error: unknown;
281
150
  loadingP: Promise<void> | undefined;
282
151
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
283
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
152
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
284
153
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
285
154
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
286
155
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -318,7 +187,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
318
187
  afterAttach(): void;
319
188
  } & {
320
189
  readonly initialized: boolean;
321
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
322
190
  readonly allRefNames: string[] | undefined;
323
191
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
324
192
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -336,6 +204,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
336
204
  getCanonicalRefName2(refName: string): string;
337
205
  isValidRefName(refName: string): boolean;
338
206
  } & {
207
+ getRefNamePosition(refName: string): number | undefined;
339
208
  getAliasesForRefName(refName: string): string[];
340
209
  getRefNameMapForAdapter(adapterConf: {
341
210
  [x: string]: unknown;
@@ -347,7 +216,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
347
216
  error: unknown;
348
217
  loadingP: Promise<void> | undefined;
349
218
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
350
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
219
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
351
220
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
352
221
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
353
222
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -385,7 +254,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
385
254
  afterAttach(): void;
386
255
  } & {
387
256
  readonly initialized: boolean;
388
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
389
257
  readonly allRefNames: string[] | undefined;
390
258
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
391
259
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -403,6 +271,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
403
271
  getCanonicalRefName2(refName: string): string;
404
272
  isValidRefName(refName: string): boolean;
405
273
  } & {
274
+ getRefNamePosition(refName: string): number | undefined;
406
275
  getAliasesForRefName(refName: string): string[];
407
276
  getRefNameMapForAdapter(adapterConf: {
408
277
  [x: string]: unknown;
@@ -416,7 +285,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
416
285
  error: unknown;
417
286
  loadingP: Promise<void> | undefined;
418
287
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
419
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
288
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
420
289
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
421
290
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
422
291
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -454,7 +323,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
454
323
  afterAttach(): void;
455
324
  } & {
456
325
  readonly initialized: boolean;
457
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
458
326
  readonly allRefNames: string[] | undefined;
459
327
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
460
328
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -472,6 +340,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
472
340
  getCanonicalRefName2(refName: string): string;
473
341
  isValidRefName(refName: string): boolean;
474
342
  } & {
343
+ getRefNamePosition(refName: string): number | undefined;
475
344
  getAliasesForRefName(refName: string): string[];
476
345
  getRefNameMapForAdapter(adapterConf: {
477
346
  [x: string]: unknown;
@@ -483,7 +352,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
483
352
  error: unknown;
484
353
  loadingP: Promise<void> | undefined;
485
354
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
486
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
355
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
487
356
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
488
357
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
489
358
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -521,7 +390,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
521
390
  afterAttach(): void;
522
391
  } & {
523
392
  readonly initialized: boolean;
524
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
525
393
  readonly allRefNames: string[] | undefined;
526
394
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
527
395
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -539,6 +407,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
539
407
  getCanonicalRefName2(refName: string): string;
540
408
  isValidRefName(refName: string): boolean;
541
409
  } & {
410
+ getRefNamePosition(refName: string): number | undefined;
542
411
  getAliasesForRefName(refName: string): string[];
543
412
  getRefNameMapForAdapter(adapterConf: {
544
413
  [x: string]: unknown;
@@ -546,11 +415,8 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
546
415
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
547
416
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
548
417
  readonly assemblyNamesList: string[];
549
- readonly configuredAssemblyNames: Set<string>;
550
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
551
- setSubschema(slotName: string, data: Record<string, unknown>): any;
552
- setSlot(slotName: string, value: unknown): void;
553
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
418
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
419
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
554
420
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
555
421
  } & {
556
422
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -561,7 +427,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
561
427
  error: unknown;
562
428
  loadingP: Promise<void> | undefined;
563
429
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
564
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
430
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
565
431
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
566
432
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
567
433
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -599,7 +465,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
599
465
  afterAttach(): void;
600
466
  } & {
601
467
  readonly initialized: boolean;
602
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
603
468
  readonly allRefNames: string[] | undefined;
604
469
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
605
470
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -617,6 +482,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
617
482
  getCanonicalRefName2(refName: string): string;
618
483
  isValidRefName(refName: string): boolean;
619
484
  } & {
485
+ getRefNamePosition(refName: string): number | undefined;
620
486
  getAliasesForRefName(refName: string): string[];
621
487
  getRefNameMapForAdapter(adapterConf: {
622
488
  [x: string]: unknown;
@@ -628,7 +494,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
628
494
  error: unknown;
629
495
  loadingP: Promise<void> | undefined;
630
496
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
631
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
497
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
632
498
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
633
499
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
634
500
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -666,7 +532,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
666
532
  afterAttach(): void;
667
533
  } & {
668
534
  readonly initialized: boolean;
669
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
670
535
  readonly allRefNames: string[] | undefined;
671
536
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
672
537
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -684,6 +549,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
684
549
  getCanonicalRefName2(refName: string): string;
685
550
  isValidRefName(refName: string): boolean;
686
551
  } & {
552
+ getRefNamePosition(refName: string): number | undefined;
687
553
  getAliasesForRefName(refName: string): string[];
688
554
  getRefNameMapForAdapter(adapterConf: {
689
555
  [x: string]: unknown;
@@ -696,7 +562,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
696
562
  error: unknown;
697
563
  loadingP: Promise<void> | undefined;
698
564
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
699
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
565
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
700
566
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
701
567
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
702
568
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -734,7 +600,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
734
600
  afterAttach(): void;
735
601
  } & {
736
602
  readonly initialized: boolean;
737
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
738
603
  readonly allRefNames: string[] | undefined;
739
604
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
740
605
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -752,6 +617,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
752
617
  getCanonicalRefName2(refName: string): string;
753
618
  isValidRefName(refName: string): boolean;
754
619
  } & {
620
+ getRefNamePosition(refName: string): number | undefined;
755
621
  getAliasesForRefName(refName: string): string[];
756
622
  getRefNameMapForAdapter(adapterConf: {
757
623
  [x: string]: unknown;
@@ -763,7 +629,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
763
629
  error: unknown;
764
630
  loadingP: Promise<void> | undefined;
765
631
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
766
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
632
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
767
633
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
768
634
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
769
635
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -801,7 +667,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
801
667
  afterAttach(): void;
802
668
  } & {
803
669
  readonly initialized: boolean;
804
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
805
670
  readonly allRefNames: string[] | undefined;
806
671
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
807
672
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -819,6 +684,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
819
684
  getCanonicalRefName2(refName: string): string;
820
685
  isValidRefName(refName: string): boolean;
821
686
  } & {
687
+ getRefNamePosition(refName: string): number | undefined;
822
688
  getAliasesForRefName(refName: string): string[];
823
689
  getRefNameMapForAdapter(adapterConf: {
824
690
  [x: string]: unknown;
@@ -857,7 +723,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
857
723
  error: unknown;
858
724
  loadingP: Promise<void> | undefined;
859
725
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
860
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
726
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
861
727
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
862
728
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
863
729
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -895,7 +761,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
895
761
  afterAttach(): void;
896
762
  } & {
897
763
  readonly initialized: boolean;
898
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
899
764
  readonly allRefNames: string[] | undefined;
900
765
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
901
766
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -913,6 +778,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
913
778
  getCanonicalRefName2(refName: string): string;
914
779
  isValidRefName(refName: string): boolean;
915
780
  } & {
781
+ getRefNamePosition(refName: string): number | undefined;
916
782
  getAliasesForRefName(refName: string): string[];
917
783
  getRefNameMapForAdapter(adapterConf: {
918
784
  [x: string]: unknown;
@@ -928,141 +794,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
928
794
  } | undefined;
929
795
  };
930
796
  } & {
931
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
932
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
933
- }> & {
934
- error: unknown;
935
- loadingP: Promise<void> | undefined;
936
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
937
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
938
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
939
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
940
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
941
- loadedGeneticCodes: Record<string, number> | undefined;
942
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
943
- statusMessage: string | undefined;
944
- statusProgress: number | undefined;
945
- statusSource: string | undefined;
946
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
947
- } & {
948
- getConf(arg: string): any;
949
- } & {
950
- readonly name: string;
951
- readonly aliases: string[];
952
- readonly displayName: string;
953
- readonly refNameColors: string[];
954
- } & {
955
- readonly allAliases: string[];
956
- hasName(name: string): boolean;
957
- } & {
958
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
959
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
960
- } & {
961
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
962
- regions: import("@jbrowse/core/util").Region[];
963
- cytobands: import("@jbrowse/core/util").Feature[];
964
- geneticCodes: Record<string, number>;
965
- }): void;
966
- setError(e: unknown): void;
967
- setLoadingP(p?: Promise<void>): void;
968
- loadPre(): Promise<void>;
969
- } & {
970
- load(): Promise<void>;
971
- } & {
972
- afterAttach(): void;
973
- } & {
974
- readonly initialized: boolean;
975
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
976
- readonly allRefNames: string[] | undefined;
977
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
978
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
979
- } & {
980
- readonly refNames: string[] | undefined;
981
- } & {
982
- readonly refNameToIndex: Map<string, number> | undefined;
983
- } & {
984
- getCanonicalRefName(refName: string): string | undefined;
985
- getRefNameColor(refName: string): string | undefined;
986
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
987
- getGeneticCodeId(refName: string): number;
988
- getSeqAdapterRefName(canonicalRefName: string): string;
989
- } & {
990
- getCanonicalRefName2(refName: string): string;
991
- isValidRefName(refName: string): boolean;
992
- } & {
993
- getAliasesForRefName(refName: string): string[];
994
- getRefNameMapForAdapter(adapterConf: {
995
- [x: string]: unknown;
996
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
997
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
998
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
999
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1000
- }, {
1001
- error: unknown;
1002
- loadingP: Promise<void> | undefined;
1003
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1004
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1005
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1006
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1007
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1008
- loadedGeneticCodes: Record<string, number> | undefined;
1009
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1010
- statusMessage: string | undefined;
1011
- statusProgress: number | undefined;
1012
- statusSource: string | undefined;
1013
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1014
- } & {
1015
- getConf(arg: string): any;
1016
- } & {
1017
- readonly name: string;
1018
- readonly aliases: string[];
1019
- readonly displayName: string;
1020
- readonly refNameColors: string[];
1021
- } & {
1022
- readonly allAliases: string[];
1023
- hasName(name: string): boolean;
1024
- } & {
1025
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1026
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1027
- } & {
1028
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1029
- regions: import("@jbrowse/core/util").Region[];
1030
- cytobands: import("@jbrowse/core/util").Feature[];
1031
- geneticCodes: Record<string, number>;
1032
- }): void;
1033
- setError(e: unknown): void;
1034
- setLoadingP(p?: Promise<void>): void;
1035
- loadPre(): Promise<void>;
1036
- } & {
1037
- load(): Promise<void>;
1038
- } & {
1039
- afterAttach(): void;
1040
- } & {
1041
- readonly initialized: boolean;
1042
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1043
- readonly allRefNames: string[] | undefined;
1044
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1045
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1046
- } & {
1047
- readonly refNames: string[] | undefined;
1048
- } & {
1049
- readonly refNameToIndex: Map<string, number> | undefined;
1050
- } & {
1051
- getCanonicalRefName(refName: string): string | undefined;
1052
- getRefNameColor(refName: string): string | undefined;
1053
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1054
- getGeneticCodeId(refName: string): number;
1055
- getSeqAdapterRefName(canonicalRefName: string): string;
1056
- } & {
1057
- getCanonicalRefName2(refName: string): string;
1058
- isValidRefName(refName: string): boolean;
1059
- } & {
1060
- getAliasesForRefName(refName: string): string[];
1061
- getRefNameMapForAdapter(adapterConf: {
1062
- [x: string]: unknown;
1063
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1064
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1065
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
797
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
1066
798
  } & {
1067
799
  getCanonicalAssemblyName(asmName: string): string | undefined;
1068
800
  getDisplayName(asmName: string): string;
@@ -1072,7 +804,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1072
804
  error: unknown;
1073
805
  loadingP: Promise<void> | undefined;
1074
806
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1075
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
807
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1076
808
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1077
809
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1078
810
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1110,7 +842,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1110
842
  afterAttach(): void;
1111
843
  } & {
1112
844
  readonly initialized: boolean;
1113
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1114
845
  readonly allRefNames: string[] | undefined;
1115
846
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1116
847
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1128,6 +859,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1128
859
  getCanonicalRefName2(refName: string): string;
1129
860
  isValidRefName(refName: string): boolean;
1130
861
  } & {
862
+ getRefNamePosition(refName: string): number | undefined;
1131
863
  getAliasesForRefName(refName: string): string[];
1132
864
  getRefNameMapForAdapter(adapterConf: {
1133
865
  [x: string]: unknown;
@@ -1139,7 +871,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1139
871
  error: unknown;
1140
872
  loadingP: Promise<void> | undefined;
1141
873
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1142
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
874
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1143
875
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1144
876
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1145
877
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1177,7 +909,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1177
909
  afterAttach(): void;
1178
910
  } & {
1179
911
  readonly initialized: boolean;
1180
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1181
912
  readonly allRefNames: string[] | undefined;
1182
913
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1183
914
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1195,6 +926,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1195
926
  getCanonicalRefName2(refName: string): string;
1196
927
  isValidRefName(refName: string): boolean;
1197
928
  } & {
929
+ getRefNamePosition(refName: string): number | undefined;
1198
930
  getAliasesForRefName(refName: string): string[];
1199
931
  getRefNameMapForAdapter(adapterConf: {
1200
932
  [x: string]: unknown;
@@ -1208,7 +940,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1208
940
  error: unknown;
1209
941
  loadingP: Promise<void> | undefined;
1210
942
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1211
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
943
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1212
944
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1213
945
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1214
946
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1246,7 +978,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1246
978
  afterAttach(): void;
1247
979
  } & {
1248
980
  readonly initialized: boolean;
1249
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1250
981
  readonly allRefNames: string[] | undefined;
1251
982
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1252
983
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1264,6 +995,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1264
995
  getCanonicalRefName2(refName: string): string;
1265
996
  isValidRefName(refName: string): boolean;
1266
997
  } & {
998
+ getRefNamePosition(refName: string): number | undefined;
1267
999
  getAliasesForRefName(refName: string): string[];
1268
1000
  getRefNameMapForAdapter(adapterConf: {
1269
1001
  [x: string]: unknown;
@@ -1275,7 +1007,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1275
1007
  error: unknown;
1276
1008
  loadingP: Promise<void> | undefined;
1277
1009
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1278
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1010
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1279
1011
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1280
1012
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1281
1013
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1313,7 +1045,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1313
1045
  afterAttach(): void;
1314
1046
  } & {
1315
1047
  readonly initialized: boolean;
1316
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1317
1048
  readonly allRefNames: string[] | undefined;
1318
1049
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1319
1050
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1331,6 +1062,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1331
1062
  getCanonicalRefName2(refName: string): string;
1332
1063
  isValidRefName(refName: string): boolean;
1333
1064
  } & {
1065
+ getRefNamePosition(refName: string): number | undefined;
1334
1066
  getAliasesForRefName(refName: string): string[];
1335
1067
  getRefNameMapForAdapter(adapterConf: {
1336
1068
  [x: string]: unknown;
@@ -1338,11 +1070,8 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1338
1070
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1339
1071
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1340
1072
  readonly assemblyNamesList: string[];
1341
- readonly configuredAssemblyNames: Set<string>;
1342
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1343
- setSubschema(slotName: string, data: Record<string, unknown>): any;
1344
- setSlot(slotName: string, value: unknown): void;
1345
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1073
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1074
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1346
1075
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1347
1076
  } & {
1348
1077
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1353,7 +1082,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1353
1082
  error: unknown;
1354
1083
  loadingP: Promise<void> | undefined;
1355
1084
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1356
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1085
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1357
1086
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1358
1087
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1359
1088
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1391,7 +1120,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1391
1120
  afterAttach(): void;
1392
1121
  } & {
1393
1122
  readonly initialized: boolean;
1394
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1395
1123
  readonly allRefNames: string[] | undefined;
1396
1124
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1397
1125
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1409,6 +1137,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1409
1137
  getCanonicalRefName2(refName: string): string;
1410
1138
  isValidRefName(refName: string): boolean;
1411
1139
  } & {
1140
+ getRefNamePosition(refName: string): number | undefined;
1412
1141
  getAliasesForRefName(refName: string): string[];
1413
1142
  getRefNameMapForAdapter(adapterConf: {
1414
1143
  [x: string]: unknown;
@@ -1420,7 +1149,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1420
1149
  error: unknown;
1421
1150
  loadingP: Promise<void> | undefined;
1422
1151
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1423
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1152
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1424
1153
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1425
1154
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1426
1155
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1458,7 +1187,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1458
1187
  afterAttach(): void;
1459
1188
  } & {
1460
1189
  readonly initialized: boolean;
1461
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1462
1190
  readonly allRefNames: string[] | undefined;
1463
1191
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1464
1192
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1476,6 +1204,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1476
1204
  getCanonicalRefName2(refName: string): string;
1477
1205
  isValidRefName(refName: string): boolean;
1478
1206
  } & {
1207
+ getRefNamePosition(refName: string): number | undefined;
1479
1208
  getAliasesForRefName(refName: string): string[];
1480
1209
  getRefNameMapForAdapter(adapterConf: {
1481
1210
  [x: string]: unknown;
@@ -1488,7 +1217,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1488
1217
  error: unknown;
1489
1218
  loadingP: Promise<void> | undefined;
1490
1219
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1491
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1220
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1492
1221
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1493
1222
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1494
1223
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1526,7 +1255,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1526
1255
  afterAttach(): void;
1527
1256
  } & {
1528
1257
  readonly initialized: boolean;
1529
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1530
1258
  readonly allRefNames: string[] | undefined;
1531
1259
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1532
1260
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1544,6 +1272,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1544
1272
  getCanonicalRefName2(refName: string): string;
1545
1273
  isValidRefName(refName: string): boolean;
1546
1274
  } & {
1275
+ getRefNamePosition(refName: string): number | undefined;
1547
1276
  getAliasesForRefName(refName: string): string[];
1548
1277
  getRefNameMapForAdapter(adapterConf: {
1549
1278
  [x: string]: unknown;
@@ -1555,7 +1284,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1555
1284
  error: unknown;
1556
1285
  loadingP: Promise<void> | undefined;
1557
1286
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1558
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1287
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1559
1288
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1560
1289
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1561
1290
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1593,7 +1322,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1593
1322
  afterAttach(): void;
1594
1323
  } & {
1595
1324
  readonly initialized: boolean;
1596
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1597
1325
  readonly allRefNames: string[] | undefined;
1598
1326
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1599
1327
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1611,6 +1339,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1611
1339
  getCanonicalRefName2(refName: string): string;
1612
1340
  isValidRefName(refName: string): boolean;
1613
1341
  } & {
1342
+ getRefNamePosition(refName: string): number | undefined;
1614
1343
  getAliasesForRefName(refName: string): string[];
1615
1344
  getRefNameMapForAdapter(adapterConf: {
1616
1345
  [x: string]: unknown;
@@ -1642,10 +1371,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1642
1371
  } & {
1643
1372
  readonly jbrowse: any;
1644
1373
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1645
- readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1646
- setSubschema(slotName: string, data: Record<string, unknown>): any;
1647
- setSlot(slotName: string, value: unknown): void;
1648
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1374
+ readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1649
1375
  readonly adminMode: boolean;
1650
1376
  readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1651
1377
  } & {
@@ -1655,12 +1381,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1655
1381
  } & {
1656
1382
  getPreferenceDefault(key: string): unknown;
1657
1383
  getPreference(key: string): unknown;
1658
- getDisplayTypeDefault(displayType: string, slot: string): unknown;
1659
- getDisplayTypeDefaults(): {
1660
- displayType: string;
1661
- slot: string;
1662
- value: unknown;
1663
- }[];
1664
1384
  getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
1665
1385
  } & {
1666
1386
  readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1672,253 +1392,129 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1672
1392
  clearSelection(): void;
1673
1393
  setHovered(thing: unknown): void;
1674
1394
  setHighlightsVisible(arg: boolean): void;
1675
- revealHighlights(): 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;
1676
1400
  setPreferenceOverride(key: string, value: unknown): void;
1677
1401
  clearPreferenceOverrides(): void;
1678
1402
  clearPreferenceOverride(key: string): void;
1679
- resetPreferenceChange(path: string[]): void;
1680
1403
  setScrollZoom(flag: boolean): void;
1681
- setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
1682
1404
  setName(str: string): void;
1683
- setFocusedViewId(viewId: string | undefined): void;
1684
- removeActiveDialog(): void;
1685
- queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1686
- } & {
1687
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1688
- errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
1689
- } & {
1690
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1691
- } & {
1692
- notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
1693
- notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
1694
- setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
1695
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
1696
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1697
- removeSnackbarMessage(message: string): void;
1698
- } & {
1699
- readonly visibleWidget: import("@jbrowse/core/util").Widget | undefined;
1700
- } & {
1701
- poppedOut: boolean;
1702
- } & {
1703
- readonly drawerVisible: boolean;
1704
- } & {
1705
- setDrawerPosition(arg: import("@jbrowse/core/util").DrawerPosition): void;
1706
- updateDrawerWidth(drawerWidth: number, availableWidth?: number): number;
1707
- resizeDrawer(distance: number, availableWidth?: number): number;
1708
- addWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
1709
- showWidget(widget: any): void;
1710
- hideWidget(widget: any): void;
1711
- minimizeWidgetDrawer(): void;
1712
- showWidgetDrawer(): void;
1713
- popoutWidget(): void;
1714
- returnWidgetToDrawer(): void;
1715
- hideAllWidgets(): void;
1716
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
1717
- trackId: string;
1718
- }, opts?: {
1719
- expandedDisplayId?: string;
1720
- }): void;
1721
- afterAttach(): void;
1722
- } & {
1723
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1724
- } & {
1725
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: object): any;
1726
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1727
- teardownConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1728
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1729
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1730
- clearConnections(): void;
1731
- captureConnectionTrack(trackId: string): void;
1732
- updateConnectionTrackConfig(trackConf: Record<string, unknown> & {
1733
- trackId: string;
1734
- }): void;
1735
- setConnectionTrackConfig(trackId: string, connectionId: string, config: Record<string, unknown>): void;
1736
- pruneConnectionTrackConfig(trackId: string): void;
1737
- hydrateConnection(connectionId: string): void;
1738
- } & {
1739
- getReferringMultiple(trackIds: string[]): Map<string, import("@jbrowse/product-core").ReferringNode[]>;
1740
- } & {
1741
- getReferring(trackId: string): import("@jbrowse/product-core").ReferringNode[];
1742
- } & {
1743
- dereferenceTrack(trackId: string, referring: import("@jbrowse/product-core").ReferringNode[]): void;
1744
- } & {
1745
- getTrackListMenuItems(config: import("@jbrowse/core/configuration").AnyConfigurationModel, view?: import("@jbrowse/core/util").TrackActionView): import("@jbrowse/core/ui").MenuItem[];
1746
- getTrackActionMenuItems({ config, view, }: {
1747
- config: import("@jbrowse/core/configuration").AnyConfigurationModel;
1748
- view?: import("@jbrowse/core/util").TrackActionView;
1749
- }): import("@jbrowse/core/ui").MenuItem[];
1750
- } & {
1751
- readonly themeOptions: import("@jbrowse/core/ui").SerializableThemeArgs;
1752
- readonly palette: import("@jbrowse/core/ui/palette").JBrowsePalette;
1753
- readonly styleTheme: import("@jbrowse/core/ui/styleTheme").JBrowseStyleTheme;
1754
- readonly theme: import("@mui/material").Theme;
1755
- getActiveThemeOptions(_name?: string): import("@mui/material").ThemeOptions | undefined;
1756
- } & {
1757
- setThemeMode(mode: 'light' | 'dark'): void;
1758
- } & {
1759
- /**
1760
- * #getter
1761
- */
1762
- readonly version: string;
1763
- /**
1764
- * #getter
1765
- */
1766
- readonly assemblyNames: string[];
1767
- /**
1768
- * #getter
1769
- */
1770
- readonly assemblyManager: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1771
- assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
1772
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1773
- }, {
1774
- error: unknown;
1775
- loadingP: Promise<void> | undefined;
1776
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1777
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1778
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1779
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1780
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1781
- loadedGeneticCodes: Record<string, number> | undefined;
1782
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1783
- statusMessage: string | undefined;
1784
- statusProgress: number | undefined;
1785
- statusSource: string | undefined;
1786
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1787
- } & {
1788
- getConf(arg: string): any;
1789
- } & {
1790
- readonly name: string;
1791
- readonly aliases: string[];
1792
- readonly displayName: string;
1793
- readonly refNameColors: string[];
1794
- } & {
1795
- readonly allAliases: string[];
1796
- hasName(name: string): boolean;
1797
- } & {
1798
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1799
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1800
- } & {
1801
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1802
- regions: import("@jbrowse/core/util").Region[];
1803
- cytobands: import("@jbrowse/core/util").Feature[];
1804
- geneticCodes: Record<string, number>;
1805
- }): void;
1806
- setError(e: unknown): void;
1807
- setLoadingP(p?: Promise<void>): void;
1808
- loadPre(): Promise<void>;
1809
- } & {
1810
- load(): Promise<void>;
1811
- } & {
1812
- afterAttach(): void;
1813
- } & {
1814
- readonly initialized: boolean;
1815
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1816
- readonly allRefNames: string[] | undefined;
1817
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1818
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1819
- } & {
1820
- readonly refNames: string[] | undefined;
1821
- } & {
1822
- readonly refNameToIndex: Map<string, number> | undefined;
1823
- } & {
1824
- getCanonicalRefName(refName: string): string | undefined;
1825
- getRefNameColor(refName: string): string | undefined;
1826
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1827
- getGeneticCodeId(refName: string): number;
1828
- getSeqAdapterRefName(canonicalRefName: string): string;
1829
- } & {
1830
- getCanonicalRefName2(refName: string): string;
1831
- isValidRefName(refName: string): boolean;
1832
- } & {
1833
- getAliasesForRefName(refName: string): string[];
1834
- getRefNameMapForAdapter(adapterConf: {
1835
- [x: string]: unknown;
1836
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1837
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1838
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1839
- }> & {
1840
- unrecognizedReports: {
1841
- report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
1842
- reportFor(session: unknown, name: string): {
1843
- handled: boolean;
1844
- claim?: Promise<void>;
1845
- } | undefined;
1846
- };
1847
- } & {
1848
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1849
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1850
- }> & {
1851
- error: unknown;
1852
- loadingP: Promise<void> | undefined;
1853
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1854
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1855
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1856
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1857
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1858
- loadedGeneticCodes: Record<string, number> | undefined;
1859
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1860
- statusMessage: string | undefined;
1861
- statusProgress: number | undefined;
1862
- statusSource: string | undefined;
1863
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1864
- } & {
1865
- getConf(arg: string): any;
1866
- } & {
1867
- readonly name: string;
1868
- readonly aliases: string[];
1869
- readonly displayName: string;
1870
- readonly refNameColors: string[];
1871
- } & {
1872
- readonly allAliases: string[];
1873
- hasName(name: string): boolean;
1874
- } & {
1875
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1876
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1877
- } & {
1878
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1879
- regions: import("@jbrowse/core/util").Region[];
1880
- cytobands: import("@jbrowse/core/util").Feature[];
1881
- geneticCodes: Record<string, number>;
1882
- }): void;
1883
- setError(e: unknown): void;
1884
- setLoadingP(p?: Promise<void>): void;
1885
- loadPre(): Promise<void>;
1886
- } & {
1887
- load(): Promise<void>;
1888
- } & {
1889
- afterAttach(): void;
1890
- } & {
1891
- readonly initialized: boolean;
1892
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1893
- readonly allRefNames: string[] | undefined;
1894
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1895
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1896
- } & {
1897
- readonly refNames: string[] | undefined;
1898
- } & {
1899
- readonly refNameToIndex: Map<string, number> | undefined;
1900
- } & {
1901
- getCanonicalRefName(refName: string): string | undefined;
1902
- getRefNameColor(refName: string): string | undefined;
1903
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1904
- getGeneticCodeId(refName: string): number;
1905
- getSeqAdapterRefName(canonicalRefName: string): string;
1906
- } & {
1907
- getCanonicalRefName2(refName: string): string;
1908
- isValidRefName(refName: string): boolean;
1909
- } & {
1910
- getAliasesForRefName(refName: string): string[];
1911
- getRefNameMapForAdapter(adapterConf: {
1912
- [x: string]: unknown;
1913
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1914
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1915
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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<{
1916
1512
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1917
1513
  }, {
1918
1514
  error: unknown;
1919
1515
  loadingP: Promise<void> | undefined;
1920
1516
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1921
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1517
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1922
1518
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1923
1519
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1924
1520
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1956,7 +1552,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1956
1552
  afterAttach(): void;
1957
1553
  } & {
1958
1554
  readonly initialized: boolean;
1959
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1960
1555
  readonly allRefNames: string[] | undefined;
1961
1556
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1962
1557
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1974,12 +1569,23 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1974
1569
  getCanonicalRefName2(refName: string): string;
1975
1570
  isValidRefName(refName: string): boolean;
1976
1571
  } & {
1572
+ getRefNamePosition(refName: string): number | undefined;
1977
1573
  getAliasesForRefName(refName: string): string[];
1978
1574
  getRefNameMapForAdapter(adapterConf: {
1979
1575
  [x: string]: unknown;
1980
1576
  }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1981
1577
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1982
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
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>;
1983
1589
  } & {
1984
1590
  getCanonicalAssemblyName(asmName: string): string | undefined;
1985
1591
  getDisplayName(asmName: string): string;
@@ -1989,7 +1595,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1989
1595
  error: unknown;
1990
1596
  loadingP: Promise<void> | undefined;
1991
1597
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1992
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1598
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1993
1599
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1994
1600
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1995
1601
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2027,7 +1633,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2027
1633
  afterAttach(): void;
2028
1634
  } & {
2029
1635
  readonly initialized: boolean;
2030
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2031
1636
  readonly allRefNames: string[] | undefined;
2032
1637
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2033
1638
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2045,6 +1650,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2045
1650
  getCanonicalRefName2(refName: string): string;
2046
1651
  isValidRefName(refName: string): boolean;
2047
1652
  } & {
1653
+ getRefNamePosition(refName: string): number | undefined;
2048
1654
  getAliasesForRefName(refName: string): string[];
2049
1655
  getRefNameMapForAdapter(adapterConf: {
2050
1656
  [x: string]: unknown;
@@ -2056,7 +1662,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2056
1662
  error: unknown;
2057
1663
  loadingP: Promise<void> | undefined;
2058
1664
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2059
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1665
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2060
1666
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2061
1667
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2062
1668
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2094,7 +1700,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2094
1700
  afterAttach(): void;
2095
1701
  } & {
2096
1702
  readonly initialized: boolean;
2097
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2098
1703
  readonly allRefNames: string[] | undefined;
2099
1704
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2100
1705
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2112,6 +1717,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2112
1717
  getCanonicalRefName2(refName: string): string;
2113
1718
  isValidRefName(refName: string): boolean;
2114
1719
  } & {
1720
+ getRefNamePosition(refName: string): number | undefined;
2115
1721
  getAliasesForRefName(refName: string): string[];
2116
1722
  getRefNameMapForAdapter(adapterConf: {
2117
1723
  [x: string]: unknown;
@@ -2125,7 +1731,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2125
1731
  error: unknown;
2126
1732
  loadingP: Promise<void> | undefined;
2127
1733
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2128
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1734
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2129
1735
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2130
1736
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2131
1737
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2163,7 +1769,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2163
1769
  afterAttach(): void;
2164
1770
  } & {
2165
1771
  readonly initialized: boolean;
2166
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2167
1772
  readonly allRefNames: string[] | undefined;
2168
1773
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2169
1774
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2181,6 +1786,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2181
1786
  getCanonicalRefName2(refName: string): string;
2182
1787
  isValidRefName(refName: string): boolean;
2183
1788
  } & {
1789
+ getRefNamePosition(refName: string): number | undefined;
2184
1790
  getAliasesForRefName(refName: string): string[];
2185
1791
  getRefNameMapForAdapter(adapterConf: {
2186
1792
  [x: string]: unknown;
@@ -2192,7 +1798,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2192
1798
  error: unknown;
2193
1799
  loadingP: Promise<void> | undefined;
2194
1800
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2195
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1801
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2196
1802
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2197
1803
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2198
1804
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2230,7 +1836,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2230
1836
  afterAttach(): void;
2231
1837
  } & {
2232
1838
  readonly initialized: boolean;
2233
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2234
1839
  readonly allRefNames: string[] | undefined;
2235
1840
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2236
1841
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2248,6 +1853,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2248
1853
  getCanonicalRefName2(refName: string): string;
2249
1854
  isValidRefName(refName: string): boolean;
2250
1855
  } & {
1856
+ getRefNamePosition(refName: string): number | undefined;
2251
1857
  getAliasesForRefName(refName: string): string[];
2252
1858
  getRefNameMapForAdapter(adapterConf: {
2253
1859
  [x: string]: unknown;
@@ -2255,11 +1861,8 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2255
1861
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2256
1862
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2257
1863
  readonly assemblyNamesList: string[];
2258
- readonly configuredAssemblyNames: Set<string>;
2259
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
2260
- setSubschema(slotName: string, data: Record<string, unknown>): any;
2261
- setSlot(slotName: string, value: unknown): void;
2262
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1864
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1865
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2263
1866
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2264
1867
  } & {
2265
1868
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -2270,7 +1873,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2270
1873
  error: unknown;
2271
1874
  loadingP: Promise<void> | undefined;
2272
1875
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2273
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1876
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2274
1877
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2275
1878
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2276
1879
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2308,7 +1911,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2308
1911
  afterAttach(): void;
2309
1912
  } & {
2310
1913
  readonly initialized: boolean;
2311
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2312
1914
  readonly allRefNames: string[] | undefined;
2313
1915
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2314
1916
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2326,6 +1928,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2326
1928
  getCanonicalRefName2(refName: string): string;
2327
1929
  isValidRefName(refName: string): boolean;
2328
1930
  } & {
1931
+ getRefNamePosition(refName: string): number | undefined;
2329
1932
  getAliasesForRefName(refName: string): string[];
2330
1933
  getRefNameMapForAdapter(adapterConf: {
2331
1934
  [x: string]: unknown;
@@ -2337,7 +1940,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2337
1940
  error: unknown;
2338
1941
  loadingP: Promise<void> | undefined;
2339
1942
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2340
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1943
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2341
1944
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2342
1945
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2343
1946
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2375,7 +1978,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2375
1978
  afterAttach(): void;
2376
1979
  } & {
2377
1980
  readonly initialized: boolean;
2378
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2379
1981
  readonly allRefNames: string[] | undefined;
2380
1982
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2381
1983
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2393,6 +1995,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2393
1995
  getCanonicalRefName2(refName: string): string;
2394
1996
  isValidRefName(refName: string): boolean;
2395
1997
  } & {
1998
+ getRefNamePosition(refName: string): number | undefined;
2396
1999
  getAliasesForRefName(refName: string): string[];
2397
2000
  getRefNameMapForAdapter(adapterConf: {
2398
2001
  [x: string]: unknown;
@@ -2405,7 +2008,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2405
2008
  error: unknown;
2406
2009
  loadingP: Promise<void> | undefined;
2407
2010
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2408
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2011
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2409
2012
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2410
2013
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2411
2014
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2443,7 +2046,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2443
2046
  afterAttach(): void;
2444
2047
  } & {
2445
2048
  readonly initialized: boolean;
2446
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2447
2049
  readonly allRefNames: string[] | undefined;
2448
2050
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2449
2051
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2461,6 +2063,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2461
2063
  getCanonicalRefName2(refName: string): string;
2462
2064
  isValidRefName(refName: string): boolean;
2463
2065
  } & {
2066
+ getRefNamePosition(refName: string): number | undefined;
2464
2067
  getAliasesForRefName(refName: string): string[];
2465
2068
  getRefNameMapForAdapter(adapterConf: {
2466
2069
  [x: string]: unknown;
@@ -2472,7 +2075,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2472
2075
  error: unknown;
2473
2076
  loadingP: Promise<void> | undefined;
2474
2077
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2475
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2078
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2476
2079
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2477
2080
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2478
2081
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2510,7 +2113,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2510
2113
  afterAttach(): void;
2511
2114
  } & {
2512
2115
  readonly initialized: boolean;
2513
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2514
2116
  readonly allRefNames: string[] | undefined;
2515
2117
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2516
2118
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2528,6 +2130,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2528
2130
  getCanonicalRefName2(refName: string): string;
2529
2131
  isValidRefName(refName: string): boolean;
2530
2132
  } & {
2133
+ getRefNamePosition(refName: string): number | undefined;
2531
2134
  getAliasesForRefName(refName: string): string[];
2532
2135
  getRefNameMapForAdapter(adapterConf: {
2533
2136
  [x: string]: unknown;
@@ -2549,7 +2152,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2549
2152
  error: unknown;
2550
2153
  loadingP: Promise<void> | undefined;
2551
2154
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2552
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2155
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2553
2156
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2554
2157
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2555
2158
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2587,7 +2190,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2587
2190
  afterAttach(): void;
2588
2191
  } & {
2589
2192
  readonly initialized: boolean;
2590
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2591
2193
  readonly allRefNames: string[] | undefined;
2592
2194
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2593
2195
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2605,6 +2207,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2605
2207
  getCanonicalRefName2(refName: string): string;
2606
2208
  isValidRefName(refName: string): boolean;
2607
2209
  } & {
2210
+ getRefNamePosition(refName: string): number | undefined;
2608
2211
  getAliasesForRefName(refName: string): string[];
2609
2212
  getRefNameMapForAdapter(adapterConf: {
2610
2213
  [x: string]: unknown;
@@ -2620,141 +2223,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2620
2223
  } | undefined;
2621
2224
  };
2622
2225
  } & {
2623
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
2624
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2625
- }> & {
2626
- error: unknown;
2627
- loadingP: Promise<void> | undefined;
2628
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2629
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2630
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2631
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2632
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2633
- loadedGeneticCodes: Record<string, number> | undefined;
2634
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2635
- statusMessage: string | undefined;
2636
- statusProgress: number | undefined;
2637
- statusSource: string | undefined;
2638
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2639
- } & {
2640
- getConf(arg: string): any;
2641
- } & {
2642
- readonly name: string;
2643
- readonly aliases: string[];
2644
- readonly displayName: string;
2645
- readonly refNameColors: string[];
2646
- } & {
2647
- readonly allAliases: string[];
2648
- hasName(name: string): boolean;
2649
- } & {
2650
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2651
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2652
- } & {
2653
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2654
- regions: import("@jbrowse/core/util").Region[];
2655
- cytobands: import("@jbrowse/core/util").Feature[];
2656
- geneticCodes: Record<string, number>;
2657
- }): void;
2658
- setError(e: unknown): void;
2659
- setLoadingP(p?: Promise<void>): void;
2660
- loadPre(): Promise<void>;
2661
- } & {
2662
- load(): Promise<void>;
2663
- } & {
2664
- afterAttach(): void;
2665
- } & {
2666
- readonly initialized: boolean;
2667
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2668
- readonly allRefNames: string[] | undefined;
2669
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2670
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2671
- } & {
2672
- readonly refNames: string[] | undefined;
2673
- } & {
2674
- readonly refNameToIndex: Map<string, number> | undefined;
2675
- } & {
2676
- getCanonicalRefName(refName: string): string | undefined;
2677
- getRefNameColor(refName: string): string | undefined;
2678
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2679
- getGeneticCodeId(refName: string): number;
2680
- getSeqAdapterRefName(canonicalRefName: string): string;
2681
- } & {
2682
- getCanonicalRefName2(refName: string): string;
2683
- isValidRefName(refName: string): boolean;
2684
- } & {
2685
- getAliasesForRefName(refName: string): string[];
2686
- getRefNameMapForAdapter(adapterConf: {
2687
- [x: string]: unknown;
2688
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2689
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2690
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2691
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2692
- }, {
2693
- error: unknown;
2694
- loadingP: Promise<void> | undefined;
2695
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2696
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2697
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2698
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2699
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2700
- loadedGeneticCodes: Record<string, number> | undefined;
2701
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2702
- statusMessage: string | undefined;
2703
- statusProgress: number | undefined;
2704
- statusSource: string | undefined;
2705
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
2706
- } & {
2707
- getConf(arg: string): any;
2708
- } & {
2709
- readonly name: string;
2710
- readonly aliases: string[];
2711
- readonly displayName: string;
2712
- readonly refNameColors: string[];
2713
- } & {
2714
- readonly allAliases: string[];
2715
- hasName(name: string): boolean;
2716
- } & {
2717
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2718
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2719
- } & {
2720
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2721
- regions: import("@jbrowse/core/util").Region[];
2722
- cytobands: import("@jbrowse/core/util").Feature[];
2723
- geneticCodes: Record<string, number>;
2724
- }): void;
2725
- setError(e: unknown): void;
2726
- setLoadingP(p?: Promise<void>): void;
2727
- loadPre(): Promise<void>;
2728
- } & {
2729
- load(): Promise<void>;
2730
- } & {
2731
- afterAttach(): void;
2732
- } & {
2733
- readonly initialized: boolean;
2734
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2735
- readonly allRefNames: string[] | undefined;
2736
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2737
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
2738
- } & {
2739
- readonly refNames: string[] | undefined;
2740
- } & {
2741
- readonly refNameToIndex: Map<string, number> | undefined;
2742
- } & {
2743
- getCanonicalRefName(refName: string): string | undefined;
2744
- getRefNameColor(refName: string): string | undefined;
2745
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
2746
- getGeneticCodeId(refName: string): number;
2747
- getSeqAdapterRefName(canonicalRefName: string): string;
2748
- } & {
2749
- getCanonicalRefName2(refName: string): string;
2750
- isValidRefName(refName: string): boolean;
2751
- } & {
2752
- getAliasesForRefName(refName: string): string[];
2753
- getRefNameMapForAdapter(adapterConf: {
2754
- [x: string]: unknown;
2755
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2756
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2757
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2226
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
2758
2227
  } & {
2759
2228
  getCanonicalAssemblyName(asmName: string): string | undefined;
2760
2229
  getDisplayName(asmName: string): string;
@@ -2764,7 +2233,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2764
2233
  error: unknown;
2765
2234
  loadingP: Promise<void> | undefined;
2766
2235
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2767
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2236
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2768
2237
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2769
2238
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2770
2239
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2802,7 +2271,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2802
2271
  afterAttach(): void;
2803
2272
  } & {
2804
2273
  readonly initialized: boolean;
2805
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2806
2274
  readonly allRefNames: string[] | undefined;
2807
2275
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2808
2276
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2820,6 +2288,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2820
2288
  getCanonicalRefName2(refName: string): string;
2821
2289
  isValidRefName(refName: string): boolean;
2822
2290
  } & {
2291
+ getRefNamePosition(refName: string): number | undefined;
2823
2292
  getAliasesForRefName(refName: string): string[];
2824
2293
  getRefNameMapForAdapter(adapterConf: {
2825
2294
  [x: string]: unknown;
@@ -2831,7 +2300,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2831
2300
  error: unknown;
2832
2301
  loadingP: Promise<void> | undefined;
2833
2302
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2834
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2303
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2835
2304
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2836
2305
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2837
2306
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2869,7 +2338,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2869
2338
  afterAttach(): void;
2870
2339
  } & {
2871
2340
  readonly initialized: boolean;
2872
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2873
2341
  readonly allRefNames: string[] | undefined;
2874
2342
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2875
2343
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2887,6 +2355,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2887
2355
  getCanonicalRefName2(refName: string): string;
2888
2356
  isValidRefName(refName: string): boolean;
2889
2357
  } & {
2358
+ getRefNamePosition(refName: string): number | undefined;
2890
2359
  getAliasesForRefName(refName: string): string[];
2891
2360
  getRefNameMapForAdapter(adapterConf: {
2892
2361
  [x: string]: unknown;
@@ -2900,7 +2369,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2900
2369
  error: unknown;
2901
2370
  loadingP: Promise<void> | undefined;
2902
2371
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2903
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2372
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2904
2373
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2905
2374
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2906
2375
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -2938,7 +2407,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2938
2407
  afterAttach(): void;
2939
2408
  } & {
2940
2409
  readonly initialized: boolean;
2941
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2942
2410
  readonly allRefNames: string[] | undefined;
2943
2411
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
2944
2412
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -2956,6 +2424,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2956
2424
  getCanonicalRefName2(refName: string): string;
2957
2425
  isValidRefName(refName: string): boolean;
2958
2426
  } & {
2427
+ getRefNamePosition(refName: string): number | undefined;
2959
2428
  getAliasesForRefName(refName: string): string[];
2960
2429
  getRefNameMapForAdapter(adapterConf: {
2961
2430
  [x: string]: unknown;
@@ -2967,7 +2436,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2967
2436
  error: unknown;
2968
2437
  loadingP: Promise<void> | undefined;
2969
2438
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2970
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2439
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2971
2440
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2972
2441
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2973
2442
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -3005,7 +2474,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3005
2474
  afterAttach(): void;
3006
2475
  } & {
3007
2476
  readonly initialized: boolean;
3008
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3009
2477
  readonly allRefNames: string[] | undefined;
3010
2478
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3011
2479
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -3023,6 +2491,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3023
2491
  getCanonicalRefName2(refName: string): string;
3024
2492
  isValidRefName(refName: string): boolean;
3025
2493
  } & {
2494
+ getRefNamePosition(refName: string): number | undefined;
3026
2495
  getAliasesForRefName(refName: string): string[];
3027
2496
  getRefNameMapForAdapter(adapterConf: {
3028
2497
  [x: string]: unknown;
@@ -3030,11 +2499,8 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3030
2499
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
3031
2500
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
3032
2501
  readonly assemblyNamesList: string[];
3033
- readonly configuredAssemblyNames: Set<string>;
3034
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
3035
- setSubschema(slotName: string, data: Record<string, unknown>): any;
3036
- setSlot(slotName: string, value: unknown): void;
3037
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
2502
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
2503
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3038
2504
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
3039
2505
  } & {
3040
2506
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -3045,7 +2511,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3045
2511
  error: unknown;
3046
2512
  loadingP: Promise<void> | undefined;
3047
2513
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3048
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2514
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3049
2515
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3050
2516
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3051
2517
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -3083,7 +2549,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3083
2549
  afterAttach(): void;
3084
2550
  } & {
3085
2551
  readonly initialized: boolean;
3086
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3087
2552
  readonly allRefNames: string[] | undefined;
3088
2553
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3089
2554
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -3101,6 +2566,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3101
2566
  getCanonicalRefName2(refName: string): string;
3102
2567
  isValidRefName(refName: string): boolean;
3103
2568
  } & {
2569
+ getRefNamePosition(refName: string): number | undefined;
3104
2570
  getAliasesForRefName(refName: string): string[];
3105
2571
  getRefNameMapForAdapter(adapterConf: {
3106
2572
  [x: string]: unknown;
@@ -3112,7 +2578,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3112
2578
  error: unknown;
3113
2579
  loadingP: Promise<void> | undefined;
3114
2580
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3115
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2581
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3116
2582
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3117
2583
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3118
2584
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -3150,7 +2616,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3150
2616
  afterAttach(): void;
3151
2617
  } & {
3152
2618
  readonly initialized: boolean;
3153
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3154
2619
  readonly allRefNames: string[] | undefined;
3155
2620
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3156
2621
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -3168,6 +2633,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3168
2633
  getCanonicalRefName2(refName: string): string;
3169
2634
  isValidRefName(refName: string): boolean;
3170
2635
  } & {
2636
+ getRefNamePosition(refName: string): number | undefined;
3171
2637
  getAliasesForRefName(refName: string): string[];
3172
2638
  getRefNameMapForAdapter(adapterConf: {
3173
2639
  [x: string]: unknown;
@@ -3180,7 +2646,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3180
2646
  error: unknown;
3181
2647
  loadingP: Promise<void> | undefined;
3182
2648
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3183
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2649
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3184
2650
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3185
2651
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3186
2652
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -3218,7 +2684,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3218
2684
  afterAttach(): void;
3219
2685
  } & {
3220
2686
  readonly initialized: boolean;
3221
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3222
2687
  readonly allRefNames: string[] | undefined;
3223
2688
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3224
2689
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -3236,6 +2701,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3236
2701
  getCanonicalRefName2(refName: string): string;
3237
2702
  isValidRefName(refName: string): boolean;
3238
2703
  } & {
2704
+ getRefNamePosition(refName: string): number | undefined;
3239
2705
  getAliasesForRefName(refName: string): string[];
3240
2706
  getRefNameMapForAdapter(adapterConf: {
3241
2707
  [x: string]: unknown;
@@ -3247,7 +2713,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3247
2713
  error: unknown;
3248
2714
  loadingP: Promise<void> | undefined;
3249
2715
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
3250
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2716
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3251
2717
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
3252
2718
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
3253
2719
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -3285,7 +2751,6 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3285
2751
  afterAttach(): void;
3286
2752
  } & {
3287
2753
  readonly initialized: boolean;
3288
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3289
2754
  readonly allRefNames: string[] | undefined;
3290
2755
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
3291
2756
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -3303,6 +2768,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3303
2768
  getCanonicalRefName2(refName: string): string;
3304
2769
  isValidRefName(refName: string): boolean;
3305
2770
  } & {
2771
+ getRefNamePosition(refName: string): number | undefined;
3306
2772
  getAliasesForRefName(refName: string): string[];
3307
2773
  getRefNameMapForAdapter(adapterConf: {
3308
2774
  [x: string]: unknown;
@@ -3318,10 +2784,35 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
3318
2784
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3319
2785
  addAssembly(configuration: any): void;
3320
2786
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
3321
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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<{
3322
2813
  drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
3323
2814
  drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
3324
2815
  widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
3325
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]>;
3326
2817
  minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
3327
- }> & import("@jbrowse/mobx-state-tree")._NotCustomized>;
2818
+ }>>;