@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/createEmbeddedRootModel.d.ts CHANGED
@@ -161,13 +161,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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;
@@ -186,7 +186,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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>;
@@ -217,11 +217,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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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  }, {
@@ -242,13 +243,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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;
@@ -267,7 +268,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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>;
@@ -298,24 +299,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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;
@@ -334,7 +336,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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>;
@@ -365,11 +367,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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;
374
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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;
@@ -378,13 +381,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
378
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  }> & {
379
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  error: unknown;
380
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  loadingP: Promise<void> | undefined;
381
- 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;
383
- 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;
@@ -403,7 +406,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
404
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
405
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  } & {
406
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
409
+ 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>;
@@ -434,24 +437,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
436
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  } & {
440
+ isCircularRefName(refName: string): boolean;
437
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  getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
439
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  getRefNameMapForAdapter(adapterConf: {
440
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  [x: string]: unknown;
441
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
445
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
442
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
443
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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>>;
445
449
  }, {
446
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  error: unknown;
447
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  loadingP: Promise<void> | undefined;
448
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
452
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
449
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
450
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
454
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
451
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  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
452
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
453
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  loadedGeneticCodes: Record<string, number> | undefined;
454
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
458
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
457
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  statusSource: string | undefined;
@@ -470,7 +474,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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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;
472
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  } & {
473
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
477
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
474
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  regions: import("@jbrowse/core/util").Region[];
475
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  cytobands: import("@jbrowse/core/util").Feature[];
476
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  geneticCodes: Record<string, number>;
@@ -501,11 +505,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
501
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  getCanonicalRefName2(refName: string): string;
502
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  isValidRefName(refName: string): boolean;
503
507
  } & {
508
+ isCircularRefName(refName: string): boolean;
504
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  getRefNamePosition(refName: string): number | undefined;
505
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  getAliasesForRefName(refName: string): string[];
506
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  getRefNameMapForAdapter(adapterConf: {
507
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  [x: string]: unknown;
508
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
513
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
509
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
510
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
511
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  readonly assemblyNamesList: string[];
@@ -520,13 +525,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
520
525
  }> & {
521
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  error: unknown;
522
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  loadingP: Promise<void> | undefined;
523
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
528
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
524
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
525
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
530
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
526
531
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
527
532
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
528
533
  loadedGeneticCodes: Record<string, number> | undefined;
529
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
534
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
530
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  statusMessage: string | undefined;
531
536
  statusProgress: number | undefined;
532
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  statusSource: string | undefined;
@@ -545,7 +550,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
545
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
546
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
547
552
  } & {
548
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
553
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
549
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  regions: import("@jbrowse/core/util").Region[];
550
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  cytobands: import("@jbrowse/core/util").Feature[];
551
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  geneticCodes: Record<string, number>;
@@ -576,24 +581,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
576
581
  getCanonicalRefName2(refName: string): string;
577
582
  isValidRefName(refName: string): boolean;
578
583
  } & {
584
+ isCircularRefName(refName: string): boolean;
579
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  getRefNamePosition(refName: string): number | undefined;
580
586
  getAliasesForRefName(refName: string): string[];
581
587
  getRefNameMapForAdapter(adapterConf: {
582
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  [x: string]: unknown;
583
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
589
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
584
590
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
585
591
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
586
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  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
587
593
  }, {
588
594
  error: unknown;
589
595
  loadingP: Promise<void> | undefined;
590
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
596
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
591
597
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
592
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
598
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
593
599
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
594
600
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
595
601
  loadedGeneticCodes: Record<string, number> | undefined;
596
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
602
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
597
603
  statusMessage: string | undefined;
598
604
  statusProgress: number | undefined;
599
605
  statusSource: string | undefined;
@@ -612,7 +618,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
612
618
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
613
619
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
614
620
  } & {
615
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
621
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
616
622
  regions: import("@jbrowse/core/util").Region[];
617
623
  cytobands: import("@jbrowse/core/util").Feature[];
618
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  geneticCodes: Record<string, number>;
@@ -643,11 +649,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
643
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  getCanonicalRefName2(refName: string): string;
644
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  isValidRefName(refName: string): boolean;
645
651
  } & {
652
+ isCircularRefName(refName: string): boolean;
646
653
  getRefNamePosition(refName: string): number | undefined;
647
654
  getAliasesForRefName(refName: string): string[];
648
655
  getRefNameMapForAdapter(adapterConf: {
649
656
  [x: string]: unknown;
650
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
657
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
651
658
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
652
659
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
653
660
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -655,13 +662,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
655
662
  }> & {
656
663
  error: unknown;
657
664
  loadingP: Promise<void> | undefined;
658
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
665
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
659
666
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
660
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
667
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
661
668
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
662
669
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
663
670
  loadedGeneticCodes: Record<string, number> | undefined;
664
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
671
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
665
672
  statusMessage: string | undefined;
666
673
  statusProgress: number | undefined;
667
674
  statusSource: string | undefined;
@@ -680,7 +687,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
680
687
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
681
688
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
682
689
  } & {
683
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
690
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
684
691
  regions: import("@jbrowse/core/util").Region[];
685
692
  cytobands: import("@jbrowse/core/util").Feature[];
686
693
  geneticCodes: Record<string, number>;
@@ -711,24 +718,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
711
718
  getCanonicalRefName2(refName: string): string;
712
719
  isValidRefName(refName: string): boolean;
713
720
  } & {
721
+ isCircularRefName(refName: string): boolean;
714
722
  getRefNamePosition(refName: string): number | undefined;
715
723
  getAliasesForRefName(refName: string): string[];
716
724
  getRefNameMapForAdapter(adapterConf: {
717
725
  [x: string]: unknown;
718
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
726
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
719
727
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
720
728
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
721
729
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
722
730
  }, {
723
731
  error: unknown;
724
732
  loadingP: Promise<void> | undefined;
725
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
733
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
726
734
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
727
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
735
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
728
736
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
729
737
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
730
738
  loadedGeneticCodes: Record<string, number> | undefined;
731
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
739
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
732
740
  statusMessage: string | undefined;
733
741
  statusProgress: number | undefined;
734
742
  statusSource: string | undefined;
@@ -747,7 +755,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
747
755
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
748
756
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
749
757
  } & {
750
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
758
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
751
759
  regions: import("@jbrowse/core/util").Region[];
752
760
  cytobands: import("@jbrowse/core/util").Feature[];
753
761
  geneticCodes: Record<string, number>;
@@ -778,16 +786,17 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
778
786
  getCanonicalRefName2(refName: string): string;
779
787
  isValidRefName(refName: string): boolean;
780
788
  } & {
789
+ isCircularRefName(refName: string): boolean;
781
790
  getRefNamePosition(refName: string): number | undefined;
782
791
  getAliasesForRefName(refName: string): string[];
783
792
  getRefNameMapForAdapter(adapterConf: {
784
793
  [x: string]: unknown;
785
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
794
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
786
795
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
787
796
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
788
797
  getRefNameMapForAdapter(adapterConf: {
789
798
  [x: string]: unknown;
790
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
799
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
791
800
  isValidRefName(refName: string, assemblyName: string): boolean;
792
801
  } & {
793
802
  afterAttach(): void;
@@ -979,13 +988,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
979
988
  }, {
980
989
  error: unknown;
981
990
  loadingP: Promise<void> | undefined;
982
- 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>>;
983
992
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
984
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
993
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
985
994
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
986
995
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
987
996
  loadedGeneticCodes: Record<string, number> | undefined;
988
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
997
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
989
998
  statusMessage: string | undefined;
990
999
  statusProgress: number | undefined;
991
1000
  statusSource: string | undefined;
@@ -1004,7 +1013,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1004
1013
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1005
1014
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1006
1015
  } & {
1007
- 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 & {
1008
1017
  regions: import("@jbrowse/core/util").Region[];
1009
1018
  cytobands: import("@jbrowse/core/util").Feature[];
1010
1019
  geneticCodes: Record<string, number>;
@@ -1035,11 +1044,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1035
1044
  getCanonicalRefName2(refName: string): string;
1036
1045
  isValidRefName(refName: string): boolean;
1037
1046
  } & {
1047
+ isCircularRefName(refName: string): boolean;
1038
1048
  getRefNamePosition(refName: string): number | undefined;
1039
1049
  getAliasesForRefName(refName: string): string[];
1040
1050
  getRefNameMapForAdapter(adapterConf: {
1041
1051
  [x: string]: unknown;
1042
- }, 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>;
1043
1053
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1044
1054
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1045
1055
  }, {
@@ -1060,13 +1070,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1060
1070
  }> & {
1061
1071
  error: unknown;
1062
1072
  loadingP: Promise<void> | undefined;
1063
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1073
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1064
1074
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1065
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1075
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1066
1076
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1067
1077
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1068
1078
  loadedGeneticCodes: Record<string, number> | undefined;
1069
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1079
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1070
1080
  statusMessage: string | undefined;
1071
1081
  statusProgress: number | undefined;
1072
1082
  statusSource: string | undefined;
@@ -1085,7 +1095,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1085
1095
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1086
1096
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1087
1097
  } & {
1088
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1098
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1089
1099
  regions: import("@jbrowse/core/util").Region[];
1090
1100
  cytobands: import("@jbrowse/core/util").Feature[];
1091
1101
  geneticCodes: Record<string, number>;
@@ -1116,24 +1126,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1116
1126
  getCanonicalRefName2(refName: string): string;
1117
1127
  isValidRefName(refName: string): boolean;
1118
1128
  } & {
1129
+ isCircularRefName(refName: string): boolean;
1119
1130
  getRefNamePosition(refName: string): number | undefined;
1120
1131
  getAliasesForRefName(refName: string): string[];
1121
1132
  getRefNameMapForAdapter(adapterConf: {
1122
1133
  [x: string]: unknown;
1123
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1134
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1124
1135
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1125
1136
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1126
1137
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1127
1138
  }, {
1128
1139
  error: unknown;
1129
1140
  loadingP: Promise<void> | undefined;
1130
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1141
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1131
1142
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1132
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1143
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1133
1144
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1134
1145
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1135
1146
  loadedGeneticCodes: Record<string, number> | undefined;
1136
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1147
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1137
1148
  statusMessage: string | undefined;
1138
1149
  statusProgress: number | undefined;
1139
1150
  statusSource: string | undefined;
@@ -1152,7 +1163,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1152
1163
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1153
1164
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1154
1165
  } & {
1155
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1166
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1156
1167
  regions: import("@jbrowse/core/util").Region[];
1157
1168
  cytobands: import("@jbrowse/core/util").Feature[];
1158
1169
  geneticCodes: Record<string, number>;
@@ -1183,11 +1194,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1183
1194
  getCanonicalRefName2(refName: string): string;
1184
1195
  isValidRefName(refName: string): boolean;
1185
1196
  } & {
1197
+ isCircularRefName(refName: string): boolean;
1186
1198
  getRefNamePosition(refName: string): number | undefined;
1187
1199
  getAliasesForRefName(refName: string): string[];
1188
1200
  getRefNameMapForAdapter(adapterConf: {
1189
1201
  [x: string]: unknown;
1190
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1202
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1191
1203
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1192
1204
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1193
1205
  has(asmName: string): boolean;
@@ -1196,13 +1208,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1196
1208
  }> & {
1197
1209
  error: unknown;
1198
1210
  loadingP: Promise<void> | undefined;
1199
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1211
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1200
1212
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1201
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1213
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1202
1214
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1203
1215
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1204
1216
  loadedGeneticCodes: Record<string, number> | undefined;
1205
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1217
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1206
1218
  statusMessage: string | undefined;
1207
1219
  statusProgress: number | undefined;
1208
1220
  statusSource: string | undefined;
@@ -1221,7 +1233,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1221
1233
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1222
1234
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1223
1235
  } & {
1224
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1236
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1225
1237
  regions: import("@jbrowse/core/util").Region[];
1226
1238
  cytobands: import("@jbrowse/core/util").Feature[];
1227
1239
  geneticCodes: Record<string, number>;
@@ -1252,24 +1264,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1252
1264
  getCanonicalRefName2(refName: string): string;
1253
1265
  isValidRefName(refName: string): boolean;
1254
1266
  } & {
1267
+ isCircularRefName(refName: string): boolean;
1255
1268
  getRefNamePosition(refName: string): number | undefined;
1256
1269
  getAliasesForRefName(refName: string): string[];
1257
1270
  getRefNameMapForAdapter(adapterConf: {
1258
1271
  [x: string]: unknown;
1259
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1272
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1260
1273
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1261
1274
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1262
1275
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1263
1276
  }, {
1264
1277
  error: unknown;
1265
1278
  loadingP: Promise<void> | undefined;
1266
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1279
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1267
1280
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1268
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1281
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1269
1282
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1270
1283
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1271
1284
  loadedGeneticCodes: Record<string, number> | undefined;
1272
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1285
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1273
1286
  statusMessage: string | undefined;
1274
1287
  statusProgress: number | undefined;
1275
1288
  statusSource: string | undefined;
@@ -1288,7 +1301,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1288
1301
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1289
1302
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1290
1303
  } & {
1291
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1304
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1292
1305
  regions: import("@jbrowse/core/util").Region[];
1293
1306
  cytobands: import("@jbrowse/core/util").Feature[];
1294
1307
  geneticCodes: Record<string, number>;
@@ -1319,11 +1332,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1319
1332
  getCanonicalRefName2(refName: string): string;
1320
1333
  isValidRefName(refName: string): boolean;
1321
1334
  } & {
1335
+ isCircularRefName(refName: string): boolean;
1322
1336
  getRefNamePosition(refName: string): number | undefined;
1323
1337
  getAliasesForRefName(refName: string): string[];
1324
1338
  getRefNameMapForAdapter(adapterConf: {
1325
1339
  [x: string]: unknown;
1326
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1340
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1327
1341
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1328
1342
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1329
1343
  readonly assemblyNamesList: string[];
@@ -1338,13 +1352,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1338
1352
  }> & {
1339
1353
  error: unknown;
1340
1354
  loadingP: Promise<void> | undefined;
1341
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1355
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1342
1356
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1343
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1357
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1344
1358
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1345
1359
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1346
1360
  loadedGeneticCodes: Record<string, number> | undefined;
1347
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1361
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1348
1362
  statusMessage: string | undefined;
1349
1363
  statusProgress: number | undefined;
1350
1364
  statusSource: string | undefined;
@@ -1363,7 +1377,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1363
1377
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1364
1378
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1365
1379
  } & {
1366
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1380
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1367
1381
  regions: import("@jbrowse/core/util").Region[];
1368
1382
  cytobands: import("@jbrowse/core/util").Feature[];
1369
1383
  geneticCodes: Record<string, number>;
@@ -1394,24 +1408,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1394
1408
  getCanonicalRefName2(refName: string): string;
1395
1409
  isValidRefName(refName: string): boolean;
1396
1410
  } & {
1411
+ isCircularRefName(refName: string): boolean;
1397
1412
  getRefNamePosition(refName: string): number | undefined;
1398
1413
  getAliasesForRefName(refName: string): string[];
1399
1414
  getRefNameMapForAdapter(adapterConf: {
1400
1415
  [x: string]: unknown;
1401
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1416
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1402
1417
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1403
1418
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1404
1419
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1405
1420
  }, {
1406
1421
  error: unknown;
1407
1422
  loadingP: Promise<void> | undefined;
1408
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1423
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1409
1424
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1410
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1425
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1411
1426
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1412
1427
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1413
1428
  loadedGeneticCodes: Record<string, number> | undefined;
1414
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1429
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1415
1430
  statusMessage: string | undefined;
1416
1431
  statusProgress: number | undefined;
1417
1432
  statusSource: string | undefined;
@@ -1430,7 +1445,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1430
1445
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1431
1446
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1432
1447
  } & {
1433
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1448
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1434
1449
  regions: import("@jbrowse/core/util").Region[];
1435
1450
  cytobands: import("@jbrowse/core/util").Feature[];
1436
1451
  geneticCodes: Record<string, number>;
@@ -1461,11 +1476,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1461
1476
  getCanonicalRefName2(refName: string): string;
1462
1477
  isValidRefName(refName: string): boolean;
1463
1478
  } & {
1479
+ isCircularRefName(refName: string): boolean;
1464
1480
  getRefNamePosition(refName: string): number | undefined;
1465
1481
  getAliasesForRefName(refName: string): string[];
1466
1482
  getRefNameMapForAdapter(adapterConf: {
1467
1483
  [x: string]: unknown;
1468
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1484
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1469
1485
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1470
1486
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1471
1487
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1473,13 +1489,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1473
1489
  }> & {
1474
1490
  error: unknown;
1475
1491
  loadingP: Promise<void> | undefined;
1476
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1492
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1477
1493
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1478
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1494
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1479
1495
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1480
1496
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1481
1497
  loadedGeneticCodes: Record<string, number> | undefined;
1482
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1498
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1483
1499
  statusMessage: string | undefined;
1484
1500
  statusProgress: number | undefined;
1485
1501
  statusSource: string | undefined;
@@ -1498,7 +1514,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1498
1514
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1499
1515
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1500
1516
  } & {
1501
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1517
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1502
1518
  regions: import("@jbrowse/core/util").Region[];
1503
1519
  cytobands: import("@jbrowse/core/util").Feature[];
1504
1520
  geneticCodes: Record<string, number>;
@@ -1529,24 +1545,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1529
1545
  getCanonicalRefName2(refName: string): string;
1530
1546
  isValidRefName(refName: string): boolean;
1531
1547
  } & {
1548
+ isCircularRefName(refName: string): boolean;
1532
1549
  getRefNamePosition(refName: string): number | undefined;
1533
1550
  getAliasesForRefName(refName: string): string[];
1534
1551
  getRefNameMapForAdapter(adapterConf: {
1535
1552
  [x: string]: unknown;
1536
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1553
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1537
1554
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1538
1555
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1539
1556
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1540
1557
  }, {
1541
1558
  error: unknown;
1542
1559
  loadingP: Promise<void> | undefined;
1543
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1560
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1544
1561
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1545
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1562
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1546
1563
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1547
1564
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1548
1565
  loadedGeneticCodes: Record<string, number> | undefined;
1549
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1566
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1550
1567
  statusMessage: string | undefined;
1551
1568
  statusProgress: number | undefined;
1552
1569
  statusSource: string | undefined;
@@ -1565,7 +1582,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1565
1582
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1566
1583
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1567
1584
  } & {
1568
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1585
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1569
1586
  regions: import("@jbrowse/core/util").Region[];
1570
1587
  cytobands: import("@jbrowse/core/util").Feature[];
1571
1588
  geneticCodes: Record<string, number>;
@@ -1596,16 +1613,17 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1596
1613
  getCanonicalRefName2(refName: string): string;
1597
1614
  isValidRefName(refName: string): boolean;
1598
1615
  } & {
1616
+ isCircularRefName(refName: string): boolean;
1599
1617
  getRefNamePosition(refName: string): number | undefined;
1600
1618
  getAliasesForRefName(refName: string): string[];
1601
1619
  getRefNameMapForAdapter(adapterConf: {
1602
1620
  [x: string]: unknown;
1603
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1621
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1604
1622
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1605
1623
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1606
1624
  getRefNameMapForAdapter(adapterConf: {
1607
1625
  [x: string]: unknown;
1608
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1626
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1609
1627
  isValidRefName(refName: string, assemblyName: string): boolean;
1610
1628
  } & {
1611
1629
  afterAttach(): void;