@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/EmbeddedSessionThemeMixin.d.ts CHANGED
@@ -33,13 +33,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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;
@@ -58,7 +58,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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>;
@@ -89,11 +89,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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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  }, {
@@ -114,13 +115,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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;
@@ -139,7 +140,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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>;
@@ -170,24 +171,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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;
@@ -206,7 +208,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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>;
@@ -237,11 +239,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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;
246
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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;
@@ -250,13 +253,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
250
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  }> & {
251
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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;
@@ -275,7 +278,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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>;
@@ -306,24 +309,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
308
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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;
315
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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;
320
- 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;
322
- 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;
324
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
325
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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;
@@ -342,7 +346,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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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;
344
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  } & {
345
- 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[];
347
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -373,11 +377,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
373
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
375
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  } & {
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+ isCircularRefName(refName: string): boolean;
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  getRefNamePosition(refName: string): number | undefined;
377
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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>;
385
+ }, 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;
382
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
383
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  readonly assemblyNamesList: string[];
@@ -392,13 +397,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
392
397
  }> & {
393
398
  error: unknown;
394
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  loadingP: Promise<void> | undefined;
395
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
400
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
396
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
397
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
402
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
398
403
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
399
404
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
400
405
  loadedGeneticCodes: Record<string, number> | undefined;
401
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
406
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
402
407
  statusMessage: string | undefined;
403
408
  statusProgress: number | undefined;
404
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  statusSource: string | undefined;
@@ -417,7 +422,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
417
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
418
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
419
424
  } & {
420
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
425
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
421
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  regions: import("@jbrowse/core/util").Region[];
422
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  cytobands: import("@jbrowse/core/util").Feature[];
423
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  geneticCodes: Record<string, number>;
@@ -448,24 +453,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
448
453
  getCanonicalRefName2(refName: string): string;
449
454
  isValidRefName(refName: string): boolean;
450
455
  } & {
456
+ isCircularRefName(refName: string): boolean;
451
457
  getRefNamePosition(refName: string): number | undefined;
452
458
  getAliasesForRefName(refName: string): string[];
453
459
  getRefNameMapForAdapter(adapterConf: {
454
460
  [x: string]: unknown;
455
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
461
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
456
462
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
457
463
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
458
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  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
459
465
  }, {
460
466
  error: unknown;
461
467
  loadingP: Promise<void> | undefined;
462
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
468
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
463
469
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
464
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
470
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
465
471
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
466
472
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
467
473
  loadedGeneticCodes: Record<string, number> | undefined;
468
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
474
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
469
475
  statusMessage: string | undefined;
470
476
  statusProgress: number | undefined;
471
477
  statusSource: string | undefined;
@@ -484,7 +490,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
484
490
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
485
491
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
486
492
  } & {
487
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
493
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
488
494
  regions: import("@jbrowse/core/util").Region[];
489
495
  cytobands: import("@jbrowse/core/util").Feature[];
490
496
  geneticCodes: Record<string, number>;
@@ -515,11 +521,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
515
521
  getCanonicalRefName2(refName: string): string;
516
522
  isValidRefName(refName: string): boolean;
517
523
  } & {
524
+ isCircularRefName(refName: string): boolean;
518
525
  getRefNamePosition(refName: string): number | undefined;
519
526
  getAliasesForRefName(refName: string): string[];
520
527
  getRefNameMapForAdapter(adapterConf: {
521
528
  [x: string]: unknown;
522
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
529
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
523
530
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
524
531
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
525
532
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -527,13 +534,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
527
534
  }> & {
528
535
  error: unknown;
529
536
  loadingP: Promise<void> | undefined;
530
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
537
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
531
538
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
532
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
539
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
533
540
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
534
541
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
535
542
  loadedGeneticCodes: Record<string, number> | undefined;
536
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
543
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
537
544
  statusMessage: string | undefined;
538
545
  statusProgress: number | undefined;
539
546
  statusSource: string | undefined;
@@ -552,7 +559,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
552
559
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
553
560
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
554
561
  } & {
555
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
562
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
556
563
  regions: import("@jbrowse/core/util").Region[];
557
564
  cytobands: import("@jbrowse/core/util").Feature[];
558
565
  geneticCodes: Record<string, number>;
@@ -583,24 +590,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
583
590
  getCanonicalRefName2(refName: string): string;
584
591
  isValidRefName(refName: string): boolean;
585
592
  } & {
593
+ isCircularRefName(refName: string): boolean;
586
594
  getRefNamePosition(refName: string): number | undefined;
587
595
  getAliasesForRefName(refName: string): string[];
588
596
  getRefNameMapForAdapter(adapterConf: {
589
597
  [x: string]: unknown;
590
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
598
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
591
599
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
592
600
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
593
601
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
594
602
  }, {
595
603
  error: unknown;
596
604
  loadingP: Promise<void> | undefined;
597
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
605
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
598
606
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
599
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
607
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
600
608
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
601
609
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
602
610
  loadedGeneticCodes: Record<string, number> | undefined;
603
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
611
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
604
612
  statusMessage: string | undefined;
605
613
  statusProgress: number | undefined;
606
614
  statusSource: string | undefined;
@@ -619,7 +627,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
619
627
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
620
628
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
621
629
  } & {
622
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
630
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
623
631
  regions: import("@jbrowse/core/util").Region[];
624
632
  cytobands: import("@jbrowse/core/util").Feature[];
625
633
  geneticCodes: Record<string, number>;
@@ -650,16 +658,17 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
650
658
  getCanonicalRefName2(refName: string): string;
651
659
  isValidRefName(refName: string): boolean;
652
660
  } & {
661
+ isCircularRefName(refName: string): boolean;
653
662
  getRefNamePosition(refName: string): number | undefined;
654
663
  getAliasesForRefName(refName: string): string[];
655
664
  getRefNameMapForAdapter(adapterConf: {
656
665
  [x: string]: unknown;
657
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
666
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
658
667
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
659
668
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
660
669
  getRefNameMapForAdapter(adapterConf: {
661
670
  [x: string]: unknown;
662
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
671
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
663
672
  isValidRefName(refName: string, assemblyName: string): boolean;
664
673
  } & {
665
674
  afterAttach(): void;
@@ -672,8 +681,11 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
672
681
  error: unknown;
673
682
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
674
683
  pluginManager: PluginManager;
684
+ detachDisposers: (() => void)[];
675
685
  } & {
676
686
  setError(error: unknown): void;
687
+ addDetachDisposer(disposer: () => void): void;
688
+ detach(): void;
677
689
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
678
690
  setDefaultSession(): void;
679
691
  setSessionPath(path: string): void;
@@ -688,13 +700,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
688
700
  }, {
689
701
  error: unknown;
690
702
  loadingP: Promise<void> | undefined;
691
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
703
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
692
704
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
693
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
705
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
694
706
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
695
707
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
696
708
  loadedGeneticCodes: Record<string, number> | undefined;
697
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
709
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
698
710
  statusMessage: string | undefined;
699
711
  statusProgress: number | undefined;
700
712
  statusSource: string | undefined;
@@ -713,7 +725,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
713
725
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
714
726
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
715
727
  } & {
716
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
728
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
717
729
  regions: import("@jbrowse/core/util").Region[];
718
730
  cytobands: import("@jbrowse/core/util").Feature[];
719
731
  geneticCodes: Record<string, number>;
@@ -744,11 +756,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
744
756
  getCanonicalRefName2(refName: string): string;
745
757
  isValidRefName(refName: string): boolean;
746
758
  } & {
759
+ isCircularRefName(refName: string): boolean;
747
760
  getRefNamePosition(refName: string): number | undefined;
748
761
  getAliasesForRefName(refName: string): string[];
749
762
  getRefNameMapForAdapter(adapterConf: {
750
763
  [x: string]: unknown;
751
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
764
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
752
765
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
753
766
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
754
767
  }, {
@@ -769,13 +782,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
769
782
  }> & {
770
783
  error: unknown;
771
784
  loadingP: Promise<void> | undefined;
772
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
785
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
773
786
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
774
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
787
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
775
788
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
776
789
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
777
790
  loadedGeneticCodes: Record<string, number> | undefined;
778
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
791
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
779
792
  statusMessage: string | undefined;
780
793
  statusProgress: number | undefined;
781
794
  statusSource: string | undefined;
@@ -794,7 +807,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
794
807
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
795
808
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
796
809
  } & {
797
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
810
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
798
811
  regions: import("@jbrowse/core/util").Region[];
799
812
  cytobands: import("@jbrowse/core/util").Feature[];
800
813
  geneticCodes: Record<string, number>;
@@ -825,24 +838,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
825
838
  getCanonicalRefName2(refName: string): string;
826
839
  isValidRefName(refName: string): boolean;
827
840
  } & {
841
+ isCircularRefName(refName: string): boolean;
828
842
  getRefNamePosition(refName: string): number | undefined;
829
843
  getAliasesForRefName(refName: string): string[];
830
844
  getRefNameMapForAdapter(adapterConf: {
831
845
  [x: string]: unknown;
832
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
846
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
833
847
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
834
848
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
835
849
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
836
850
  }, {
837
851
  error: unknown;
838
852
  loadingP: Promise<void> | undefined;
839
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
853
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
840
854
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
841
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
855
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
842
856
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
843
857
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
844
858
  loadedGeneticCodes: Record<string, number> | undefined;
845
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
859
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
846
860
  statusMessage: string | undefined;
847
861
  statusProgress: number | undefined;
848
862
  statusSource: string | undefined;
@@ -861,7 +875,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
861
875
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
862
876
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
863
877
  } & {
864
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
878
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
865
879
  regions: import("@jbrowse/core/util").Region[];
866
880
  cytobands: import("@jbrowse/core/util").Feature[];
867
881
  geneticCodes: Record<string, number>;
@@ -892,11 +906,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
892
906
  getCanonicalRefName2(refName: string): string;
893
907
  isValidRefName(refName: string): boolean;
894
908
  } & {
909
+ isCircularRefName(refName: string): boolean;
895
910
  getRefNamePosition(refName: string): number | undefined;
896
911
  getAliasesForRefName(refName: string): string[];
897
912
  getRefNameMapForAdapter(adapterConf: {
898
913
  [x: string]: unknown;
899
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
914
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
900
915
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
901
916
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
902
917
  has(asmName: string): boolean;
@@ -905,13 +920,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
905
920
  }> & {
906
921
  error: unknown;
907
922
  loadingP: Promise<void> | undefined;
908
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
923
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
909
924
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
910
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
925
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
911
926
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
912
927
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
913
928
  loadedGeneticCodes: Record<string, number> | undefined;
914
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
929
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
915
930
  statusMessage: string | undefined;
916
931
  statusProgress: number | undefined;
917
932
  statusSource: string | undefined;
@@ -930,7 +945,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
930
945
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
931
946
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
932
947
  } & {
933
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
948
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
934
949
  regions: import("@jbrowse/core/util").Region[];
935
950
  cytobands: import("@jbrowse/core/util").Feature[];
936
951
  geneticCodes: Record<string, number>;
@@ -961,24 +976,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
961
976
  getCanonicalRefName2(refName: string): string;
962
977
  isValidRefName(refName: string): boolean;
963
978
  } & {
979
+ isCircularRefName(refName: string): boolean;
964
980
  getRefNamePosition(refName: string): number | undefined;
965
981
  getAliasesForRefName(refName: string): string[];
966
982
  getRefNameMapForAdapter(adapterConf: {
967
983
  [x: string]: unknown;
968
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
984
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
969
985
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
970
986
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
971
987
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
972
988
  }, {
973
989
  error: unknown;
974
990
  loadingP: Promise<void> | undefined;
975
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
991
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
976
992
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
977
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
993
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
978
994
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
979
995
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
980
996
  loadedGeneticCodes: Record<string, number> | undefined;
981
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
997
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
982
998
  statusMessage: string | undefined;
983
999
  statusProgress: number | undefined;
984
1000
  statusSource: string | undefined;
@@ -997,7 +1013,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
997
1013
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
998
1014
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
999
1015
  } & {
1000
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1016
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1001
1017
  regions: import("@jbrowse/core/util").Region[];
1002
1018
  cytobands: import("@jbrowse/core/util").Feature[];
1003
1019
  geneticCodes: Record<string, number>;
@@ -1028,11 +1044,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1028
1044
  getCanonicalRefName2(refName: string): string;
1029
1045
  isValidRefName(refName: string): boolean;
1030
1046
  } & {
1047
+ isCircularRefName(refName: string): boolean;
1031
1048
  getRefNamePosition(refName: string): number | undefined;
1032
1049
  getAliasesForRefName(refName: string): string[];
1033
1050
  getRefNameMapForAdapter(adapterConf: {
1034
1051
  [x: string]: unknown;
1035
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1052
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1036
1053
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1037
1054
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1038
1055
  readonly assemblyNamesList: string[];
@@ -1047,13 +1064,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1047
1064
  }> & {
1048
1065
  error: unknown;
1049
1066
  loadingP: Promise<void> | undefined;
1050
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1067
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1051
1068
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1052
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1069
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1053
1070
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1054
1071
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1055
1072
  loadedGeneticCodes: Record<string, number> | undefined;
1056
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1073
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1057
1074
  statusMessage: string | undefined;
1058
1075
  statusProgress: number | undefined;
1059
1076
  statusSource: string | undefined;
@@ -1072,7 +1089,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1072
1089
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1073
1090
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1074
1091
  } & {
1075
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1092
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1076
1093
  regions: import("@jbrowse/core/util").Region[];
1077
1094
  cytobands: import("@jbrowse/core/util").Feature[];
1078
1095
  geneticCodes: Record<string, number>;
@@ -1103,24 +1120,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1103
1120
  getCanonicalRefName2(refName: string): string;
1104
1121
  isValidRefName(refName: string): boolean;
1105
1122
  } & {
1123
+ isCircularRefName(refName: string): boolean;
1106
1124
  getRefNamePosition(refName: string): number | undefined;
1107
1125
  getAliasesForRefName(refName: string): string[];
1108
1126
  getRefNameMapForAdapter(adapterConf: {
1109
1127
  [x: string]: unknown;
1110
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1128
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1111
1129
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1112
1130
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1113
1131
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1114
1132
  }, {
1115
1133
  error: unknown;
1116
1134
  loadingP: Promise<void> | undefined;
1117
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1135
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1118
1136
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1119
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1137
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1120
1138
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1121
1139
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1122
1140
  loadedGeneticCodes: Record<string, number> | undefined;
1123
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1141
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1124
1142
  statusMessage: string | undefined;
1125
1143
  statusProgress: number | undefined;
1126
1144
  statusSource: string | undefined;
@@ -1139,7 +1157,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1139
1157
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1140
1158
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1141
1159
  } & {
1142
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1160
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1143
1161
  regions: import("@jbrowse/core/util").Region[];
1144
1162
  cytobands: import("@jbrowse/core/util").Feature[];
1145
1163
  geneticCodes: Record<string, number>;
@@ -1170,11 +1188,12 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1170
1188
  getCanonicalRefName2(refName: string): string;
1171
1189
  isValidRefName(refName: string): boolean;
1172
1190
  } & {
1191
+ isCircularRefName(refName: string): boolean;
1173
1192
  getRefNamePosition(refName: string): number | undefined;
1174
1193
  getAliasesForRefName(refName: string): string[];
1175
1194
  getRefNameMapForAdapter(adapterConf: {
1176
1195
  [x: string]: unknown;
1177
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1196
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1178
1197
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1179
1198
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1180
1199
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1182,13 +1201,13 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1182
1201
  }> & {
1183
1202
  error: unknown;
1184
1203
  loadingP: Promise<void> | undefined;
1185
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1204
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1186
1205
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1187
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1206
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1188
1207
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1189
1208
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1190
1209
  loadedGeneticCodes: Record<string, number> | undefined;
1191
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1210
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1192
1211
  statusMessage: string | undefined;
1193
1212
  statusProgress: number | undefined;
1194
1213
  statusSource: string | undefined;
@@ -1207,7 +1226,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1207
1226
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1208
1227
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1209
1228
  } & {
1210
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1229
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1211
1230
  regions: import("@jbrowse/core/util").Region[];
1212
1231
  cytobands: import("@jbrowse/core/util").Feature[];
1213
1232
  geneticCodes: Record<string, number>;
@@ -1238,24 +1257,25 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1238
1257
  getCanonicalRefName2(refName: string): string;
1239
1258
  isValidRefName(refName: string): boolean;
1240
1259
  } & {
1260
+ isCircularRefName(refName: string): boolean;
1241
1261
  getRefNamePosition(refName: string): number | undefined;
1242
1262
  getAliasesForRefName(refName: string): string[];
1243
1263
  getRefNameMapForAdapter(adapterConf: {
1244
1264
  [x: string]: unknown;
1245
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1265
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1246
1266
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1247
1267
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1248
1268
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1249
1269
  }, {
1250
1270
  error: unknown;
1251
1271
  loadingP: Promise<void> | undefined;
1252
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1272
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1253
1273
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1254
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1274
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1255
1275
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1256
1276
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1257
1277
  loadedGeneticCodes: Record<string, number> | undefined;
1258
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1278
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1259
1279
  statusMessage: string | undefined;
1260
1280
  statusProgress: number | undefined;
1261
1281
  statusSource: string | undefined;
@@ -1274,7 +1294,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1274
1294
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1275
1295
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1276
1296
  } & {
1277
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1297
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1278
1298
  regions: import("@jbrowse/core/util").Region[];
1279
1299
  cytobands: import("@jbrowse/core/util").Feature[];
1280
1300
  geneticCodes: Record<string, number>;
@@ -1305,16 +1325,17 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1305
1325
  getCanonicalRefName2(refName: string): string;
1306
1326
  isValidRefName(refName: string): boolean;
1307
1327
  } & {
1328
+ isCircularRefName(refName: string): boolean;
1308
1329
  getRefNamePosition(refName: string): number | undefined;
1309
1330
  getAliasesForRefName(refName: string): string[];
1310
1331
  getRefNameMapForAdapter(adapterConf: {
1311
1332
  [x: string]: unknown;
1312
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1333
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1313
1334
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1314
1335
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1315
1336
  getRefNameMapForAdapter(adapterConf: {
1316
1337
  [x: string]: unknown;
1317
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1338
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1318
1339
  isValidRefName(refName: string, assemblyName: string): boolean;
1319
1340
  } & {
1320
1341
  afterAttach(): void;
@@ -1327,8 +1348,11 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1327
1348
  error: unknown;
1328
1349
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1329
1350
  pluginManager: PluginManager;
1351
+ detachDisposers: (() => void)[];
1330
1352
  } & {
1331
1353
  setError(error: unknown): void;
1354
+ addDetachDisposer(disposer: () => void): void;
1355
+ detach(): void;
1332
1356
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1333
1357
  setDefaultSession(): void;
1334
1358
  setSessionPath(path: string): void;
@@ -1370,7 +1394,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1370
1394
  setName(str: string): void;
1371
1395
  setFocusedViewId(viewId: string | undefined): void;
1372
1396
  removeActiveDialog(): void;
1373
- queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1397
+ queueDialog<T extends import("@jbrowse/core/util").DialogComponentType>(callback: (doneCallback: () => void) => [T, React.ComponentProps<T>]): void;
1374
1398
  removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1375
1399
  } & {
1376
1400
  snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
@@ -1433,7 +1457,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1433
1457
  /**
1434
1458
  * #action
1435
1459
  * Switch the session to light or dark, leaving the host's configured
1436
- * colours alone. `themeOptions` carries the mode to the renderer, so
1460
+ * colors alone. `themeOptions` carries the mode to the renderer, so
1437
1461
  * labels drawn in the worker follow it, and `palette` is derived from
1438
1462
  * the same args, so React-drawn elements follow it too. An embedder who
1439
1463
  * sets only a React-side palette leaves the worker-drawn labels in the