@jbrowse/embedded-core 5.0.0-beta.13 → 5.0.0-beta.14

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 (5) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +227 -185
  2. package/esm/EmbeddedSessionThemeMixin.d.ts +118 -94
  3. package/esm/EmbeddedSessionThemeMixin.js +1 -1
  4. package/esm/createEmbeddedRootModel.d.ts +110 -92
  5. package/package.json +6 -6
package/esm/EmbeddedSessionMixin.d.ts CHANGED
@@ -67,13 +67,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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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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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -92,7 +92,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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  } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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  regions: import("@jbrowse/core/util").Region[];
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -123,11 +123,12 @@ 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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+ isCircularRefName(refName: string): boolean;
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  getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
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  getRefNameMapForAdapter(adapterConf: {
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  [x: string]: unknown;
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- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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  }, {
@@ -148,13 +149,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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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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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -173,7 +174,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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  } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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  regions: import("@jbrowse/core/util").Region[];
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -204,24 +205,25 @@ 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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+ isCircularRefName(refName: string): boolean;
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  getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
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  getRefNameMapForAdapter(adapterConf: {
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  [x: string]: unknown;
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- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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  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;
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- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -240,7 +242,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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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;
242
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  } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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  regions: import("@jbrowse/core/util").Region[];
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -271,11 +273,12 @@ 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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+ isCircularRefName(refName: string): boolean;
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  getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
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  getRefNameMapForAdapter(adapterConf: {
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  [x: string]: unknown;
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- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
280
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
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  has(asmName: string): boolean;
@@ -284,13 +287,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
284
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  }> & {
285
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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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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -309,7 +312,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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  } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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  regions: import("@jbrowse/core/util").Region[];
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -340,24 +343,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
342
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  } & {
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+ isCircularRefName(refName: string): boolean;
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  getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
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  getRefNameMapForAdapter(adapterConf: {
346
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  [x: string]: unknown;
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- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
348
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
349
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
350
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  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
351
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  }, {
352
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  error: unknown;
353
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  loadingP: Promise<void> | undefined;
354
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
358
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
356
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").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;
360
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -376,7 +380,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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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;
378
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  } & {
379
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
383
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
380
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  regions: import("@jbrowse/core/util").Region[];
381
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -407,11 +411,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
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  getCanonicalRefName2(refName: string): string;
408
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  isValidRefName(refName: string): boolean;
409
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  } & {
414
+ isCircularRefName(refName: string): boolean;
410
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  getRefNamePosition(refName: string): number | undefined;
411
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  getAliasesForRefName(refName: string): string[];
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  getRefNameMapForAdapter(adapterConf: {
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  [x: string]: unknown;
414
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
419
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
415
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
416
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
417
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  readonly assemblyNamesList: string[];
@@ -426,13 +431,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
426
431
  }> & {
427
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  error: unknown;
428
433
  loadingP: Promise<void> | undefined;
429
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
434
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
430
435
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
431
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
436
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
432
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  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
433
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
434
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  loadedGeneticCodes: Record<string, number> | undefined;
435
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
440
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
436
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  statusMessage: string | undefined;
437
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  statusProgress: number | undefined;
438
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  statusSource: string | undefined;
@@ -451,7 +456,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
451
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
452
457
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
453
458
  } & {
454
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
459
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
455
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  regions: import("@jbrowse/core/util").Region[];
456
461
  cytobands: import("@jbrowse/core/util").Feature[];
457
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  geneticCodes: Record<string, number>;
@@ -482,24 +487,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
482
487
  getCanonicalRefName2(refName: string): string;
483
488
  isValidRefName(refName: string): boolean;
484
489
  } & {
490
+ isCircularRefName(refName: string): boolean;
485
491
  getRefNamePosition(refName: string): number | undefined;
486
492
  getAliasesForRefName(refName: string): string[];
487
493
  getRefNameMapForAdapter(adapterConf: {
488
494
  [x: string]: unknown;
489
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
495
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
490
496
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
491
497
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
492
498
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
493
499
  }, {
494
500
  error: unknown;
495
501
  loadingP: Promise<void> | undefined;
496
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
502
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
497
503
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
498
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
504
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
499
505
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
500
506
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
501
507
  loadedGeneticCodes: Record<string, number> | undefined;
502
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
508
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
503
509
  statusMessage: string | undefined;
504
510
  statusProgress: number | undefined;
505
511
  statusSource: string | undefined;
@@ -518,7 +524,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
518
524
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
519
525
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
520
526
  } & {
521
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
527
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
522
528
  regions: import("@jbrowse/core/util").Region[];
523
529
  cytobands: import("@jbrowse/core/util").Feature[];
524
530
  geneticCodes: Record<string, number>;
@@ -549,11 +555,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
549
555
  getCanonicalRefName2(refName: string): string;
550
556
  isValidRefName(refName: string): boolean;
551
557
  } & {
558
+ isCircularRefName(refName: string): boolean;
552
559
  getRefNamePosition(refName: string): number | undefined;
553
560
  getAliasesForRefName(refName: string): string[];
554
561
  getRefNameMapForAdapter(adapterConf: {
555
562
  [x: string]: unknown;
556
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
563
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
557
564
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
558
565
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
559
566
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -561,13 +568,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
561
568
  }> & {
562
569
  error: unknown;
563
570
  loadingP: Promise<void> | undefined;
564
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
571
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
565
572
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
566
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
573
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
567
574
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
568
575
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
569
576
  loadedGeneticCodes: Record<string, number> | undefined;
570
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
577
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
571
578
  statusMessage: string | undefined;
572
579
  statusProgress: number | undefined;
573
580
  statusSource: string | undefined;
@@ -586,7 +593,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
586
593
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
587
594
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
588
595
  } & {
589
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
596
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
590
597
  regions: import("@jbrowse/core/util").Region[];
591
598
  cytobands: import("@jbrowse/core/util").Feature[];
592
599
  geneticCodes: Record<string, number>;
@@ -617,24 +624,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
617
624
  getCanonicalRefName2(refName: string): string;
618
625
  isValidRefName(refName: string): boolean;
619
626
  } & {
627
+ isCircularRefName(refName: string): boolean;
620
628
  getRefNamePosition(refName: string): number | undefined;
621
629
  getAliasesForRefName(refName: string): string[];
622
630
  getRefNameMapForAdapter(adapterConf: {
623
631
  [x: string]: unknown;
624
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
632
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
625
633
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
626
634
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
627
635
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
628
636
  }, {
629
637
  error: unknown;
630
638
  loadingP: Promise<void> | undefined;
631
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
639
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
632
640
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
633
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
641
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
634
642
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
635
643
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
636
644
  loadedGeneticCodes: Record<string, number> | undefined;
637
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
645
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
638
646
  statusMessage: string | undefined;
639
647
  statusProgress: number | undefined;
640
648
  statusSource: string | undefined;
@@ -653,7 +661,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
653
661
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
654
662
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
655
663
  } & {
656
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
664
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
657
665
  regions: import("@jbrowse/core/util").Region[];
658
666
  cytobands: import("@jbrowse/core/util").Feature[];
659
667
  geneticCodes: Record<string, number>;
@@ -684,16 +692,17 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
684
692
  getCanonicalRefName2(refName: string): string;
685
693
  isValidRefName(refName: string): boolean;
686
694
  } & {
695
+ isCircularRefName(refName: string): boolean;
687
696
  getRefNamePosition(refName: string): number | undefined;
688
697
  getAliasesForRefName(refName: string): string[];
689
698
  getRefNameMapForAdapter(adapterConf: {
690
699
  [x: string]: unknown;
691
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
700
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
692
701
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
693
702
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
694
703
  getRefNameMapForAdapter(adapterConf: {
695
704
  [x: string]: unknown;
696
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
705
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
697
706
  isValidRefName(refName: string, assemblyName: string): boolean;
698
707
  } & {
699
708
  afterAttach(): void;
@@ -706,8 +715,11 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
706
715
  error: unknown;
707
716
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
708
717
  pluginManager: PluginManager;
718
+ detachDisposers: (() => void)[];
709
719
  } & {
710
720
  setError(error: unknown): void;
721
+ addDetachDisposer(disposer: () => void): void;
722
+ detach(): void;
711
723
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
712
724
  setDefaultSession(): void;
713
725
  setSessionPath(path: string): void;
@@ -722,13 +734,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
722
734
  }, {
723
735
  error: unknown;
724
736
  loadingP: Promise<void> | undefined;
725
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
737
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
726
738
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
727
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
739
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
728
740
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
729
741
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
730
742
  loadedGeneticCodes: Record<string, number> | undefined;
731
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
743
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
732
744
  statusMessage: string | undefined;
733
745
  statusProgress: number | undefined;
734
746
  statusSource: string | undefined;
@@ -747,7 +759,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
747
759
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
748
760
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
749
761
  } & {
750
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
762
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
751
763
  regions: import("@jbrowse/core/util").Region[];
752
764
  cytobands: import("@jbrowse/core/util").Feature[];
753
765
  geneticCodes: Record<string, number>;
@@ -778,11 +790,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
778
790
  getCanonicalRefName2(refName: string): string;
779
791
  isValidRefName(refName: string): boolean;
780
792
  } & {
793
+ isCircularRefName(refName: string): boolean;
781
794
  getRefNamePosition(refName: string): number | undefined;
782
795
  getAliasesForRefName(refName: string): string[];
783
796
  getRefNameMapForAdapter(adapterConf: {
784
797
  [x: string]: unknown;
785
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
798
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
786
799
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
787
800
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
788
801
  }, {
@@ -803,13 +816,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
803
816
  }> & {
804
817
  error: unknown;
805
818
  loadingP: Promise<void> | undefined;
806
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
819
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
807
820
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
808
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
821
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
809
822
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
810
823
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
811
824
  loadedGeneticCodes: Record<string, number> | undefined;
812
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
825
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
813
826
  statusMessage: string | undefined;
814
827
  statusProgress: number | undefined;
815
828
  statusSource: string | undefined;
@@ -828,7 +841,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
828
841
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
829
842
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
830
843
  } & {
831
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
844
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
832
845
  regions: import("@jbrowse/core/util").Region[];
833
846
  cytobands: import("@jbrowse/core/util").Feature[];
834
847
  geneticCodes: Record<string, number>;
@@ -859,24 +872,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
859
872
  getCanonicalRefName2(refName: string): string;
860
873
  isValidRefName(refName: string): boolean;
861
874
  } & {
875
+ isCircularRefName(refName: string): boolean;
862
876
  getRefNamePosition(refName: string): number | undefined;
863
877
  getAliasesForRefName(refName: string): string[];
864
878
  getRefNameMapForAdapter(adapterConf: {
865
879
  [x: string]: unknown;
866
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
880
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
867
881
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
868
882
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
869
883
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
870
884
  }, {
871
885
  error: unknown;
872
886
  loadingP: Promise<void> | undefined;
873
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
887
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
874
888
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
875
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
889
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
876
890
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
877
891
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
878
892
  loadedGeneticCodes: Record<string, number> | undefined;
879
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
893
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
880
894
  statusMessage: string | undefined;
881
895
  statusProgress: number | undefined;
882
896
  statusSource: string | undefined;
@@ -895,7 +909,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
895
909
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
896
910
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
897
911
  } & {
898
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
912
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
899
913
  regions: import("@jbrowse/core/util").Region[];
900
914
  cytobands: import("@jbrowse/core/util").Feature[];
901
915
  geneticCodes: Record<string, number>;
@@ -926,11 +940,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
926
940
  getCanonicalRefName2(refName: string): string;
927
941
  isValidRefName(refName: string): boolean;
928
942
  } & {
943
+ isCircularRefName(refName: string): boolean;
929
944
  getRefNamePosition(refName: string): number | undefined;
930
945
  getAliasesForRefName(refName: string): string[];
931
946
  getRefNameMapForAdapter(adapterConf: {
932
947
  [x: string]: unknown;
933
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
948
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
934
949
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
935
950
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
936
951
  has(asmName: string): boolean;
@@ -939,13 +954,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
939
954
  }> & {
940
955
  error: unknown;
941
956
  loadingP: Promise<void> | undefined;
942
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
957
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
943
958
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
944
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
959
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
945
960
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
946
961
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
947
962
  loadedGeneticCodes: Record<string, number> | undefined;
948
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
963
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
949
964
  statusMessage: string | undefined;
950
965
  statusProgress: number | undefined;
951
966
  statusSource: string | undefined;
@@ -964,7 +979,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
964
979
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
965
980
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
966
981
  } & {
967
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
982
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
968
983
  regions: import("@jbrowse/core/util").Region[];
969
984
  cytobands: import("@jbrowse/core/util").Feature[];
970
985
  geneticCodes: Record<string, number>;
@@ -995,24 +1010,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
995
1010
  getCanonicalRefName2(refName: string): string;
996
1011
  isValidRefName(refName: string): boolean;
997
1012
  } & {
1013
+ isCircularRefName(refName: string): boolean;
998
1014
  getRefNamePosition(refName: string): number | undefined;
999
1015
  getAliasesForRefName(refName: string): string[];
1000
1016
  getRefNameMapForAdapter(adapterConf: {
1001
1017
  [x: string]: unknown;
1002
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1018
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1003
1019
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1004
1020
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1005
1021
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1006
1022
  }, {
1007
1023
  error: unknown;
1008
1024
  loadingP: Promise<void> | undefined;
1009
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1025
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1010
1026
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1011
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1027
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1012
1028
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1013
1029
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1014
1030
  loadedGeneticCodes: Record<string, number> | undefined;
1015
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1031
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1016
1032
  statusMessage: string | undefined;
1017
1033
  statusProgress: number | undefined;
1018
1034
  statusSource: string | undefined;
@@ -1031,7 +1047,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1031
1047
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1032
1048
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1033
1049
  } & {
1034
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1050
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1035
1051
  regions: import("@jbrowse/core/util").Region[];
1036
1052
  cytobands: import("@jbrowse/core/util").Feature[];
1037
1053
  geneticCodes: Record<string, number>;
@@ -1062,11 +1078,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1062
1078
  getCanonicalRefName2(refName: string): string;
1063
1079
  isValidRefName(refName: string): boolean;
1064
1080
  } & {
1081
+ isCircularRefName(refName: string): boolean;
1065
1082
  getRefNamePosition(refName: string): number | undefined;
1066
1083
  getAliasesForRefName(refName: string): string[];
1067
1084
  getRefNameMapForAdapter(adapterConf: {
1068
1085
  [x: string]: unknown;
1069
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1086
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1070
1087
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1071
1088
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1072
1089
  readonly assemblyNamesList: string[];
@@ -1081,13 +1098,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1081
1098
  }> & {
1082
1099
  error: unknown;
1083
1100
  loadingP: Promise<void> | undefined;
1084
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1101
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1085
1102
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1086
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1103
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1087
1104
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1088
1105
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1089
1106
  loadedGeneticCodes: Record<string, number> | undefined;
1090
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1107
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1091
1108
  statusMessage: string | undefined;
1092
1109
  statusProgress: number | undefined;
1093
1110
  statusSource: string | undefined;
@@ -1106,7 +1123,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1106
1123
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1107
1124
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1108
1125
  } & {
1109
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1126
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1110
1127
  regions: import("@jbrowse/core/util").Region[];
1111
1128
  cytobands: import("@jbrowse/core/util").Feature[];
1112
1129
  geneticCodes: Record<string, number>;
@@ -1137,24 +1154,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1137
1154
  getCanonicalRefName2(refName: string): string;
1138
1155
  isValidRefName(refName: string): boolean;
1139
1156
  } & {
1157
+ isCircularRefName(refName: string): boolean;
1140
1158
  getRefNamePosition(refName: string): number | undefined;
1141
1159
  getAliasesForRefName(refName: string): string[];
1142
1160
  getRefNameMapForAdapter(adapterConf: {
1143
1161
  [x: string]: unknown;
1144
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1162
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1145
1163
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1146
1164
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1147
1165
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1148
1166
  }, {
1149
1167
  error: unknown;
1150
1168
  loadingP: Promise<void> | undefined;
1151
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1169
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1152
1170
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1153
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1171
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1154
1172
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1155
1173
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1156
1174
  loadedGeneticCodes: Record<string, number> | undefined;
1157
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1175
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1158
1176
  statusMessage: string | undefined;
1159
1177
  statusProgress: number | undefined;
1160
1178
  statusSource: string | undefined;
@@ -1173,7 +1191,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1173
1191
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1174
1192
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1175
1193
  } & {
1176
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1194
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1177
1195
  regions: import("@jbrowse/core/util").Region[];
1178
1196
  cytobands: import("@jbrowse/core/util").Feature[];
1179
1197
  geneticCodes: Record<string, number>;
@@ -1204,11 +1222,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1204
1222
  getCanonicalRefName2(refName: string): string;
1205
1223
  isValidRefName(refName: string): boolean;
1206
1224
  } & {
1225
+ isCircularRefName(refName: string): boolean;
1207
1226
  getRefNamePosition(refName: string): number | undefined;
1208
1227
  getAliasesForRefName(refName: string): string[];
1209
1228
  getRefNameMapForAdapter(adapterConf: {
1210
1229
  [x: string]: unknown;
1211
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1230
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1212
1231
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1213
1232
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1214
1233
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1216,13 +1235,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1216
1235
  }> & {
1217
1236
  error: unknown;
1218
1237
  loadingP: Promise<void> | undefined;
1219
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1238
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1220
1239
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1221
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1240
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1222
1241
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1223
1242
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1224
1243
  loadedGeneticCodes: Record<string, number> | undefined;
1225
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1244
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1226
1245
  statusMessage: string | undefined;
1227
1246
  statusProgress: number | undefined;
1228
1247
  statusSource: string | undefined;
@@ -1241,7 +1260,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1241
1260
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1242
1261
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1243
1262
  } & {
1244
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1263
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1245
1264
  regions: import("@jbrowse/core/util").Region[];
1246
1265
  cytobands: import("@jbrowse/core/util").Feature[];
1247
1266
  geneticCodes: Record<string, number>;
@@ -1272,24 +1291,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1272
1291
  getCanonicalRefName2(refName: string): string;
1273
1292
  isValidRefName(refName: string): boolean;
1274
1293
  } & {
1294
+ isCircularRefName(refName: string): boolean;
1275
1295
  getRefNamePosition(refName: string): number | undefined;
1276
1296
  getAliasesForRefName(refName: string): string[];
1277
1297
  getRefNameMapForAdapter(adapterConf: {
1278
1298
  [x: string]: unknown;
1279
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1299
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1280
1300
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1281
1301
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1282
1302
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1283
1303
  }, {
1284
1304
  error: unknown;
1285
1305
  loadingP: Promise<void> | undefined;
1286
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1306
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1287
1307
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1288
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1308
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1289
1309
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1290
1310
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1291
1311
  loadedGeneticCodes: Record<string, number> | undefined;
1292
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1312
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1293
1313
  statusMessage: string | undefined;
1294
1314
  statusProgress: number | undefined;
1295
1315
  statusSource: string | undefined;
@@ -1308,7 +1328,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1308
1328
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1309
1329
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1310
1330
  } & {
1311
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1331
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1312
1332
  regions: import("@jbrowse/core/util").Region[];
1313
1333
  cytobands: import("@jbrowse/core/util").Feature[];
1314
1334
  geneticCodes: Record<string, number>;
@@ -1339,16 +1359,17 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1339
1359
  getCanonicalRefName2(refName: string): string;
1340
1360
  isValidRefName(refName: string): boolean;
1341
1361
  } & {
1362
+ isCircularRefName(refName: string): boolean;
1342
1363
  getRefNamePosition(refName: string): number | undefined;
1343
1364
  getAliasesForRefName(refName: string): string[];
1344
1365
  getRefNameMapForAdapter(adapterConf: {
1345
1366
  [x: string]: unknown;
1346
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1367
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1347
1368
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1348
1369
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1349
1370
  getRefNameMapForAdapter(adapterConf: {
1350
1371
  [x: string]: unknown;
1351
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1372
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1352
1373
  isValidRefName(refName: string, assemblyName: string): boolean;
1353
1374
  } & {
1354
1375
  afterAttach(): void;
@@ -1361,8 +1382,11 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1361
1382
  error: unknown;
1362
1383
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1363
1384
  pluginManager: PluginManager;
1385
+ detachDisposers: (() => void)[];
1364
1386
  } & {
1365
1387
  setError(error: unknown): void;
1388
+ addDetachDisposer(disposer: () => void): void;
1389
+ detach(): void;
1366
1390
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1367
1391
  setDefaultSession(): void;
1368
1392
  setSessionPath(path: string): void;
@@ -1404,7 +1428,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1404
1428
  setName(str: string): void;
1405
1429
  setFocusedViewId(viewId: string | undefined): void;
1406
1430
  removeActiveDialog(): void;
1407
- queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1431
+ queueDialog<T extends import("@jbrowse/core/util").DialogComponentType>(callback: (doneCallback: () => void) => [T, React.ComponentProps<T>]): void;
1408
1432
  removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1409
1433
  } & {
1410
1434
  snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
@@ -1513,13 +1537,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1513
1537
  }, {
1514
1538
  error: unknown;
1515
1539
  loadingP: Promise<void> | undefined;
1516
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1540
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1517
1541
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1518
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1542
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1519
1543
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1520
1544
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1521
1545
  loadedGeneticCodes: Record<string, number> | undefined;
1522
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1546
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1523
1547
  statusMessage: string | undefined;
1524
1548
  statusProgress: number | undefined;
1525
1549
  statusSource: string | undefined;
@@ -1538,7 +1562,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1538
1562
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1539
1563
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1540
1564
  } & {
1541
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1565
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1542
1566
  regions: import("@jbrowse/core/util").Region[];
1543
1567
  cytobands: import("@jbrowse/core/util").Feature[];
1544
1568
  geneticCodes: Record<string, number>;
@@ -1569,11 +1593,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1569
1593
  getCanonicalRefName2(refName: string): string;
1570
1594
  isValidRefName(refName: string): boolean;
1571
1595
  } & {
1596
+ isCircularRefName(refName: string): boolean;
1572
1597
  getRefNamePosition(refName: string): number | undefined;
1573
1598
  getAliasesForRefName(refName: string): string[];
1574
1599
  getRefNameMapForAdapter(adapterConf: {
1575
1600
  [x: string]: unknown;
1576
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1601
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1577
1602
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1578
1603
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1579
1604
  }> & {
@@ -1594,13 +1619,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1594
1619
  }> & {
1595
1620
  error: unknown;
1596
1621
  loadingP: Promise<void> | undefined;
1597
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1622
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1598
1623
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1599
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1624
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1600
1625
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1601
1626
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1602
1627
  loadedGeneticCodes: Record<string, number> | undefined;
1603
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1628
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1604
1629
  statusMessage: string | undefined;
1605
1630
  statusProgress: number | undefined;
1606
1631
  statusSource: string | undefined;
@@ -1619,7 +1644,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1619
1644
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1620
1645
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1621
1646
  } & {
1622
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1647
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1623
1648
  regions: import("@jbrowse/core/util").Region[];
1624
1649
  cytobands: import("@jbrowse/core/util").Feature[];
1625
1650
  geneticCodes: Record<string, number>;
@@ -1650,24 +1675,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1650
1675
  getCanonicalRefName2(refName: string): string;
1651
1676
  isValidRefName(refName: string): boolean;
1652
1677
  } & {
1678
+ isCircularRefName(refName: string): boolean;
1653
1679
  getRefNamePosition(refName: string): number | undefined;
1654
1680
  getAliasesForRefName(refName: string): string[];
1655
1681
  getRefNameMapForAdapter(adapterConf: {
1656
1682
  [x: string]: unknown;
1657
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1683
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1658
1684
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1659
1685
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1660
1686
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1661
1687
  }, {
1662
1688
  error: unknown;
1663
1689
  loadingP: Promise<void> | undefined;
1664
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1690
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1665
1691
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1666
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1692
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1667
1693
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1668
1694
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1669
1695
  loadedGeneticCodes: Record<string, number> | undefined;
1670
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1696
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1671
1697
  statusMessage: string | undefined;
1672
1698
  statusProgress: number | undefined;
1673
1699
  statusSource: string | undefined;
@@ -1686,7 +1712,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1686
1712
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1687
1713
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1688
1714
  } & {
1689
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1715
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1690
1716
  regions: import("@jbrowse/core/util").Region[];
1691
1717
  cytobands: import("@jbrowse/core/util").Feature[];
1692
1718
  geneticCodes: Record<string, number>;
@@ -1717,11 +1743,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1717
1743
  getCanonicalRefName2(refName: string): string;
1718
1744
  isValidRefName(refName: string): boolean;
1719
1745
  } & {
1746
+ isCircularRefName(refName: string): boolean;
1720
1747
  getRefNamePosition(refName: string): number | undefined;
1721
1748
  getAliasesForRefName(refName: string): string[];
1722
1749
  getRefNameMapForAdapter(adapterConf: {
1723
1750
  [x: string]: unknown;
1724
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1751
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1725
1752
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1726
1753
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1727
1754
  has(asmName: string): boolean;
@@ -1730,13 +1757,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1730
1757
  }> & {
1731
1758
  error: unknown;
1732
1759
  loadingP: Promise<void> | undefined;
1733
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1760
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1734
1761
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1735
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1762
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1736
1763
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1737
1764
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1738
1765
  loadedGeneticCodes: Record<string, number> | undefined;
1739
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1766
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1740
1767
  statusMessage: string | undefined;
1741
1768
  statusProgress: number | undefined;
1742
1769
  statusSource: string | undefined;
@@ -1755,7 +1782,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1755
1782
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1756
1783
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1757
1784
  } & {
1758
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1785
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1759
1786
  regions: import("@jbrowse/core/util").Region[];
1760
1787
  cytobands: import("@jbrowse/core/util").Feature[];
1761
1788
  geneticCodes: Record<string, number>;
@@ -1786,24 +1813,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1786
1813
  getCanonicalRefName2(refName: string): string;
1787
1814
  isValidRefName(refName: string): boolean;
1788
1815
  } & {
1816
+ isCircularRefName(refName: string): boolean;
1789
1817
  getRefNamePosition(refName: string): number | undefined;
1790
1818
  getAliasesForRefName(refName: string): string[];
1791
1819
  getRefNameMapForAdapter(adapterConf: {
1792
1820
  [x: string]: unknown;
1793
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1821
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1794
1822
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1795
1823
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1796
1824
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1797
1825
  }, {
1798
1826
  error: unknown;
1799
1827
  loadingP: Promise<void> | undefined;
1800
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1828
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1801
1829
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1802
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1830
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1803
1831
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1804
1832
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1805
1833
  loadedGeneticCodes: Record<string, number> | undefined;
1806
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1834
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1807
1835
  statusMessage: string | undefined;
1808
1836
  statusProgress: number | undefined;
1809
1837
  statusSource: string | undefined;
@@ -1822,7 +1850,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1822
1850
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1823
1851
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1824
1852
  } & {
1825
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1853
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1826
1854
  regions: import("@jbrowse/core/util").Region[];
1827
1855
  cytobands: import("@jbrowse/core/util").Feature[];
1828
1856
  geneticCodes: Record<string, number>;
@@ -1853,11 +1881,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1853
1881
  getCanonicalRefName2(refName: string): string;
1854
1882
  isValidRefName(refName: string): boolean;
1855
1883
  } & {
1884
+ isCircularRefName(refName: string): boolean;
1856
1885
  getRefNamePosition(refName: string): number | undefined;
1857
1886
  getAliasesForRefName(refName: string): string[];
1858
1887
  getRefNameMapForAdapter(adapterConf: {
1859
1888
  [x: string]: unknown;
1860
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1889
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1861
1890
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1862
1891
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1863
1892
  readonly assemblyNamesList: string[];
@@ -1872,13 +1901,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1872
1901
  }> & {
1873
1902
  error: unknown;
1874
1903
  loadingP: Promise<void> | undefined;
1875
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1904
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1876
1905
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1877
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1906
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1878
1907
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1879
1908
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1880
1909
  loadedGeneticCodes: Record<string, number> | undefined;
1881
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1910
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1882
1911
  statusMessage: string | undefined;
1883
1912
  statusProgress: number | undefined;
1884
1913
  statusSource: string | undefined;
@@ -1897,7 +1926,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1897
1926
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1898
1927
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1899
1928
  } & {
1900
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1929
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1901
1930
  regions: import("@jbrowse/core/util").Region[];
1902
1931
  cytobands: import("@jbrowse/core/util").Feature[];
1903
1932
  geneticCodes: Record<string, number>;
@@ -1928,24 +1957,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1928
1957
  getCanonicalRefName2(refName: string): string;
1929
1958
  isValidRefName(refName: string): boolean;
1930
1959
  } & {
1960
+ isCircularRefName(refName: string): boolean;
1931
1961
  getRefNamePosition(refName: string): number | undefined;
1932
1962
  getAliasesForRefName(refName: string): string[];
1933
1963
  getRefNameMapForAdapter(adapterConf: {
1934
1964
  [x: string]: unknown;
1935
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1965
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1936
1966
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1937
1967
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1938
1968
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1939
1969
  }, {
1940
1970
  error: unknown;
1941
1971
  loadingP: Promise<void> | undefined;
1942
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1972
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1943
1973
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1944
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1974
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1945
1975
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1946
1976
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1947
1977
  loadedGeneticCodes: Record<string, number> | undefined;
1948
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1978
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1949
1979
  statusMessage: string | undefined;
1950
1980
  statusProgress: number | undefined;
1951
1981
  statusSource: string | undefined;
@@ -1964,7 +1994,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1964
1994
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1965
1995
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1966
1996
  } & {
1967
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1997
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1968
1998
  regions: import("@jbrowse/core/util").Region[];
1969
1999
  cytobands: import("@jbrowse/core/util").Feature[];
1970
2000
  geneticCodes: Record<string, number>;
@@ -1995,11 +2025,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
1995
2025
  getCanonicalRefName2(refName: string): string;
1996
2026
  isValidRefName(refName: string): boolean;
1997
2027
  } & {
2028
+ isCircularRefName(refName: string): boolean;
1998
2029
  getRefNamePosition(refName: string): number | undefined;
1999
2030
  getAliasesForRefName(refName: string): string[];
2000
2031
  getRefNameMapForAdapter(adapterConf: {
2001
2032
  [x: string]: unknown;
2002
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2033
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2003
2034
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2004
2035
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
2005
2036
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -2007,13 +2038,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2007
2038
  }> & {
2008
2039
  error: unknown;
2009
2040
  loadingP: Promise<void> | undefined;
2010
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2041
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2011
2042
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2012
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2043
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2013
2044
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2014
2045
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2015
2046
  loadedGeneticCodes: Record<string, number> | undefined;
2016
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2047
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2017
2048
  statusMessage: string | undefined;
2018
2049
  statusProgress: number | undefined;
2019
2050
  statusSource: string | undefined;
@@ -2032,7 +2063,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2032
2063
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2033
2064
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2034
2065
  } & {
2035
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2066
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2036
2067
  regions: import("@jbrowse/core/util").Region[];
2037
2068
  cytobands: import("@jbrowse/core/util").Feature[];
2038
2069
  geneticCodes: Record<string, number>;
@@ -2063,24 +2094,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2063
2094
  getCanonicalRefName2(refName: string): string;
2064
2095
  isValidRefName(refName: string): boolean;
2065
2096
  } & {
2097
+ isCircularRefName(refName: string): boolean;
2066
2098
  getRefNamePosition(refName: string): number | undefined;
2067
2099
  getAliasesForRefName(refName: string): string[];
2068
2100
  getRefNameMapForAdapter(adapterConf: {
2069
2101
  [x: string]: unknown;
2070
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2102
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2071
2103
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2072
2104
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2073
2105
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2074
2106
  }, {
2075
2107
  error: unknown;
2076
2108
  loadingP: Promise<void> | undefined;
2077
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2109
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2078
2110
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2079
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2111
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2080
2112
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2081
2113
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2082
2114
  loadedGeneticCodes: Record<string, number> | undefined;
2083
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2115
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2084
2116
  statusMessage: string | undefined;
2085
2117
  statusProgress: number | undefined;
2086
2118
  statusSource: string | undefined;
@@ -2099,7 +2131,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2099
2131
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2100
2132
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2101
2133
  } & {
2102
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2134
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2103
2135
  regions: import("@jbrowse/core/util").Region[];
2104
2136
  cytobands: import("@jbrowse/core/util").Feature[];
2105
2137
  geneticCodes: Record<string, number>;
@@ -2130,16 +2162,17 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2130
2162
  getCanonicalRefName2(refName: string): string;
2131
2163
  isValidRefName(refName: string): boolean;
2132
2164
  } & {
2165
+ isCircularRefName(refName: string): boolean;
2133
2166
  getRefNamePosition(refName: string): number | undefined;
2134
2167
  getAliasesForRefName(refName: string): string[];
2135
2168
  getRefNameMapForAdapter(adapterConf: {
2136
2169
  [x: string]: unknown;
2137
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2170
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2138
2171
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2139
2172
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2140
2173
  getRefNameMapForAdapter(adapterConf: {
2141
2174
  [x: string]: unknown;
2142
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2175
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2143
2176
  isValidRefName(refName: string, assemblyName: string): boolean;
2144
2177
  } & {
2145
2178
  afterAttach(): void;
@@ -2151,13 +2184,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2151
2184
  }, {
2152
2185
  error: unknown;
2153
2186
  loadingP: Promise<void> | undefined;
2154
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2187
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2155
2188
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2156
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2189
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2157
2190
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2158
2191
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2159
2192
  loadedGeneticCodes: Record<string, number> | undefined;
2160
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2193
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2161
2194
  statusMessage: string | undefined;
2162
2195
  statusProgress: number | undefined;
2163
2196
  statusSource: string | undefined;
@@ -2176,7 +2209,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2176
2209
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2177
2210
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2178
2211
  } & {
2179
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2212
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2180
2213
  regions: import("@jbrowse/core/util").Region[];
2181
2214
  cytobands: import("@jbrowse/core/util").Feature[];
2182
2215
  geneticCodes: Record<string, number>;
@@ -2207,11 +2240,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2207
2240
  getCanonicalRefName2(refName: string): string;
2208
2241
  isValidRefName(refName: string): boolean;
2209
2242
  } & {
2243
+ isCircularRefName(refName: string): boolean;
2210
2244
  getRefNamePosition(refName: string): number | undefined;
2211
2245
  getAliasesForRefName(refName: string): string[];
2212
2246
  getRefNameMapForAdapter(adapterConf: {
2213
2247
  [x: string]: unknown;
2214
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2248
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2215
2249
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2216
2250
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2217
2251
  }, {
@@ -2232,13 +2266,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2232
2266
  }> & {
2233
2267
  error: unknown;
2234
2268
  loadingP: Promise<void> | undefined;
2235
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2269
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2236
2270
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2237
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2271
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2238
2272
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2239
2273
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2240
2274
  loadedGeneticCodes: Record<string, number> | undefined;
2241
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2275
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2242
2276
  statusMessage: string | undefined;
2243
2277
  statusProgress: number | undefined;
2244
2278
  statusSource: string | undefined;
@@ -2257,7 +2291,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2257
2291
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2258
2292
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2259
2293
  } & {
2260
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2294
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2261
2295
  regions: import("@jbrowse/core/util").Region[];
2262
2296
  cytobands: import("@jbrowse/core/util").Feature[];
2263
2297
  geneticCodes: Record<string, number>;
@@ -2288,24 +2322,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2288
2322
  getCanonicalRefName2(refName: string): string;
2289
2323
  isValidRefName(refName: string): boolean;
2290
2324
  } & {
2325
+ isCircularRefName(refName: string): boolean;
2291
2326
  getRefNamePosition(refName: string): number | undefined;
2292
2327
  getAliasesForRefName(refName: string): string[];
2293
2328
  getRefNameMapForAdapter(adapterConf: {
2294
2329
  [x: string]: unknown;
2295
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2330
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2296
2331
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2297
2332
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2298
2333
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2299
2334
  }, {
2300
2335
  error: unknown;
2301
2336
  loadingP: Promise<void> | undefined;
2302
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2337
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2303
2338
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2304
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2339
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2305
2340
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2306
2341
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2307
2342
  loadedGeneticCodes: Record<string, number> | undefined;
2308
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2343
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2309
2344
  statusMessage: string | undefined;
2310
2345
  statusProgress: number | undefined;
2311
2346
  statusSource: string | undefined;
@@ -2324,7 +2359,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2324
2359
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2325
2360
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2326
2361
  } & {
2327
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2362
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2328
2363
  regions: import("@jbrowse/core/util").Region[];
2329
2364
  cytobands: import("@jbrowse/core/util").Feature[];
2330
2365
  geneticCodes: Record<string, number>;
@@ -2355,11 +2390,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2355
2390
  getCanonicalRefName2(refName: string): string;
2356
2391
  isValidRefName(refName: string): boolean;
2357
2392
  } & {
2393
+ isCircularRefName(refName: string): boolean;
2358
2394
  getRefNamePosition(refName: string): number | undefined;
2359
2395
  getAliasesForRefName(refName: string): string[];
2360
2396
  getRefNameMapForAdapter(adapterConf: {
2361
2397
  [x: string]: unknown;
2362
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2398
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2363
2399
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2364
2400
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2365
2401
  has(asmName: string): boolean;
@@ -2368,13 +2404,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2368
2404
  }> & {
2369
2405
  error: unknown;
2370
2406
  loadingP: Promise<void> | undefined;
2371
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2407
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2372
2408
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2373
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2409
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2374
2410
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2375
2411
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2376
2412
  loadedGeneticCodes: Record<string, number> | undefined;
2377
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2413
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2378
2414
  statusMessage: string | undefined;
2379
2415
  statusProgress: number | undefined;
2380
2416
  statusSource: string | undefined;
@@ -2393,7 +2429,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2393
2429
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2394
2430
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2395
2431
  } & {
2396
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2432
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2397
2433
  regions: import("@jbrowse/core/util").Region[];
2398
2434
  cytobands: import("@jbrowse/core/util").Feature[];
2399
2435
  geneticCodes: Record<string, number>;
@@ -2424,24 +2460,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2424
2460
  getCanonicalRefName2(refName: string): string;
2425
2461
  isValidRefName(refName: string): boolean;
2426
2462
  } & {
2463
+ isCircularRefName(refName: string): boolean;
2427
2464
  getRefNamePosition(refName: string): number | undefined;
2428
2465
  getAliasesForRefName(refName: string): string[];
2429
2466
  getRefNameMapForAdapter(adapterConf: {
2430
2467
  [x: string]: unknown;
2431
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2468
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2432
2469
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2433
2470
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2434
2471
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2435
2472
  }, {
2436
2473
  error: unknown;
2437
2474
  loadingP: Promise<void> | undefined;
2438
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2475
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2439
2476
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2440
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2477
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2441
2478
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2442
2479
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2443
2480
  loadedGeneticCodes: Record<string, number> | undefined;
2444
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2481
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2445
2482
  statusMessage: string | undefined;
2446
2483
  statusProgress: number | undefined;
2447
2484
  statusSource: string | undefined;
@@ -2460,7 +2497,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2460
2497
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2461
2498
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2462
2499
  } & {
2463
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2500
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2464
2501
  regions: import("@jbrowse/core/util").Region[];
2465
2502
  cytobands: import("@jbrowse/core/util").Feature[];
2466
2503
  geneticCodes: Record<string, number>;
@@ -2491,11 +2528,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2491
2528
  getCanonicalRefName2(refName: string): string;
2492
2529
  isValidRefName(refName: string): boolean;
2493
2530
  } & {
2531
+ isCircularRefName(refName: string): boolean;
2494
2532
  getRefNamePosition(refName: string): number | undefined;
2495
2533
  getAliasesForRefName(refName: string): string[];
2496
2534
  getRefNameMapForAdapter(adapterConf: {
2497
2535
  [x: string]: unknown;
2498
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2536
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2499
2537
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2500
2538
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
2501
2539
  readonly assemblyNamesList: string[];
@@ -2510,13 +2548,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2510
2548
  }> & {
2511
2549
  error: unknown;
2512
2550
  loadingP: Promise<void> | undefined;
2513
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2551
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2514
2552
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2515
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2553
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2516
2554
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2517
2555
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2518
2556
  loadedGeneticCodes: Record<string, number> | undefined;
2519
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2557
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2520
2558
  statusMessage: string | undefined;
2521
2559
  statusProgress: number | undefined;
2522
2560
  statusSource: string | undefined;
@@ -2535,7 +2573,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2535
2573
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2536
2574
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2537
2575
  } & {
2538
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2576
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2539
2577
  regions: import("@jbrowse/core/util").Region[];
2540
2578
  cytobands: import("@jbrowse/core/util").Feature[];
2541
2579
  geneticCodes: Record<string, number>;
@@ -2566,24 +2604,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2566
2604
  getCanonicalRefName2(refName: string): string;
2567
2605
  isValidRefName(refName: string): boolean;
2568
2606
  } & {
2607
+ isCircularRefName(refName: string): boolean;
2569
2608
  getRefNamePosition(refName: string): number | undefined;
2570
2609
  getAliasesForRefName(refName: string): string[];
2571
2610
  getRefNameMapForAdapter(adapterConf: {
2572
2611
  [x: string]: unknown;
2573
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2612
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2574
2613
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2575
2614
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2576
2615
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2577
2616
  }, {
2578
2617
  error: unknown;
2579
2618
  loadingP: Promise<void> | undefined;
2580
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2619
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2581
2620
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2582
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2621
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2583
2622
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2584
2623
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2585
2624
  loadedGeneticCodes: Record<string, number> | undefined;
2586
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2625
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2587
2626
  statusMessage: string | undefined;
2588
2627
  statusProgress: number | undefined;
2589
2628
  statusSource: string | undefined;
@@ -2602,7 +2641,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2602
2641
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2603
2642
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2604
2643
  } & {
2605
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2644
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2606
2645
  regions: import("@jbrowse/core/util").Region[];
2607
2646
  cytobands: import("@jbrowse/core/util").Feature[];
2608
2647
  geneticCodes: Record<string, number>;
@@ -2633,11 +2672,12 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2633
2672
  getCanonicalRefName2(refName: string): string;
2634
2673
  isValidRefName(refName: string): boolean;
2635
2674
  } & {
2675
+ isCircularRefName(refName: string): boolean;
2636
2676
  getRefNamePosition(refName: string): number | undefined;
2637
2677
  getAliasesForRefName(refName: string): string[];
2638
2678
  getRefNameMapForAdapter(adapterConf: {
2639
2679
  [x: string]: unknown;
2640
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2680
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2641
2681
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2642
2682
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
2643
2683
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -2645,13 +2685,13 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2645
2685
  }> & {
2646
2686
  error: unknown;
2647
2687
  loadingP: Promise<void> | undefined;
2648
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2688
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2649
2689
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2650
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2690
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2651
2691
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2652
2692
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2653
2693
  loadedGeneticCodes: Record<string, number> | undefined;
2654
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2694
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2655
2695
  statusMessage: string | undefined;
2656
2696
  statusProgress: number | undefined;
2657
2697
  statusSource: string | undefined;
@@ -2670,7 +2710,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2670
2710
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2671
2711
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2672
2712
  } & {
2673
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2713
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2674
2714
  regions: import("@jbrowse/core/util").Region[];
2675
2715
  cytobands: import("@jbrowse/core/util").Feature[];
2676
2716
  geneticCodes: Record<string, number>;
@@ -2701,24 +2741,25 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2701
2741
  getCanonicalRefName2(refName: string): string;
2702
2742
  isValidRefName(refName: string): boolean;
2703
2743
  } & {
2744
+ isCircularRefName(refName: string): boolean;
2704
2745
  getRefNamePosition(refName: string): number | undefined;
2705
2746
  getAliasesForRefName(refName: string): string[];
2706
2747
  getRefNameMapForAdapter(adapterConf: {
2707
2748
  [x: string]: unknown;
2708
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2749
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2709
2750
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2710
2751
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
2711
2752
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
2712
2753
  }, {
2713
2754
  error: unknown;
2714
2755
  loadingP: Promise<void> | undefined;
2715
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
2756
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
2716
2757
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2717
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2758
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2718
2759
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
2719
2760
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2720
2761
  loadedGeneticCodes: Record<string, number> | undefined;
2721
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
2762
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
2722
2763
  statusMessage: string | undefined;
2723
2764
  statusProgress: number | undefined;
2724
2765
  statusSource: string | undefined;
@@ -2737,7 +2778,7 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2737
2778
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
2738
2779
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
2739
2780
  } & {
2740
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
2781
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
2741
2782
  regions: import("@jbrowse/core/util").Region[];
2742
2783
  cytobands: import("@jbrowse/core/util").Feature[];
2743
2784
  geneticCodes: Record<string, number>;
@@ -2768,16 +2809,17 @@ export declare function EmbeddedSessionMixin(pluginManager: PluginManager): impo
2768
2809
  getCanonicalRefName2(refName: string): string;
2769
2810
  isValidRefName(refName: string): boolean;
2770
2811
  } & {
2812
+ isCircularRefName(refName: string): boolean;
2771
2813
  getRefNamePosition(refName: string): number | undefined;
2772
2814
  getAliasesForRefName(refName: string): string[];
2773
2815
  getRefNameMapForAdapter(adapterConf: {
2774
2816
  [x: string]: unknown;
2775
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2817
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2776
2818
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
2777
2819
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
2778
2820
  getRefNameMapForAdapter(adapterConf: {
2779
2821
  [x: string]: unknown;
2780
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
2822
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
2781
2823
  isValidRefName(refName: string, assemblyName: string): boolean;
2782
2824
  } & {
2783
2825
  afterAttach(): void;