@jbrowse/embedded-core 5.0.0-beta.11 → 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 +228 -186
  2. package/esm/EmbeddedSessionThemeMixin.d.ts +118 -94
  3. package/esm/EmbeddedSessionThemeMixin.js +1 -1
  4. package/esm/createEmbeddedRootModel.d.ts +110 -102
  5. package/package.json +7 -7
package/esm/createEmbeddedRootModel.d.ts CHANGED
@@ -96,11 +96,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
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  } & {
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  defaultValue: boolean;
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  };
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- readonly useWorkspaces: {
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- type: "boolean";
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- } & {
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- defaultValue: boolean;
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- };
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  readonly developerMode: {
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  type: "boolean";
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  } & {
@@ -166,13 +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;
@@ -191,7 +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>;
@@ -222,11 +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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  }, {
@@ -247,13 +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;
252
- 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;
256
- 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;
@@ -272,7 +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>;
@@ -303,24 +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;
319
- 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;
@@ -339,7 +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;
341
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  } & {
342
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
339
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
343
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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>;
@@ -370,11 +367,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
370
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  getCanonicalRefName2(refName: string): string;
371
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  isValidRefName(refName: string): boolean;
372
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  } & {
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+ isCircularRefName(refName: string): boolean;
373
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  getRefNamePosition(refName: string): number | undefined;
374
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  getAliasesForRefName(refName: string): string[];
375
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  getRefNameMapForAdapter(adapterConf: {
376
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  [x: string]: unknown;
377
- }, 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>;
378
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
379
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
380
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  has(asmName: string): boolean;
@@ -383,13 +381,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
383
381
  }> & {
384
382
  error: unknown;
385
383
  loadingP: Promise<void> | undefined;
386
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
384
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
387
385
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
388
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
386
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
389
387
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
390
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
391
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  loadedGeneticCodes: Record<string, number> | undefined;
392
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
390
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
393
391
  statusMessage: string | undefined;
394
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  statusProgress: number | undefined;
395
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  statusSource: string | undefined;
@@ -408,7 +406,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
408
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
409
407
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
410
408
  } & {
411
- 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 & {
412
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  regions: import("@jbrowse/core/util").Region[];
413
411
  cytobands: import("@jbrowse/core/util").Feature[];
414
412
  geneticCodes: Record<string, number>;
@@ -439,24 +437,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
439
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  getCanonicalRefName2(refName: string): string;
440
438
  isValidRefName(refName: string): boolean;
441
439
  } & {
440
+ isCircularRefName(refName: string): boolean;
442
441
  getRefNamePosition(refName: string): number | undefined;
443
442
  getAliasesForRefName(refName: string): string[];
444
443
  getRefNameMapForAdapter(adapterConf: {
445
444
  [x: string]: unknown;
446
- }, 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>;
447
446
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
448
447
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
449
448
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
450
449
  }, {
451
450
  error: unknown;
452
451
  loadingP: Promise<void> | undefined;
453
- 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>>;
454
453
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
455
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
454
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
456
455
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
457
456
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
458
457
  loadedGeneticCodes: Record<string, number> | undefined;
459
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
458
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
460
459
  statusMessage: string | undefined;
461
460
  statusProgress: number | undefined;
462
461
  statusSource: string | undefined;
@@ -475,7 +474,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
475
474
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
476
475
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
477
476
  } & {
478
- 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 & {
479
478
  regions: import("@jbrowse/core/util").Region[];
480
479
  cytobands: import("@jbrowse/core/util").Feature[];
481
480
  geneticCodes: Record<string, number>;
@@ -506,11 +505,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
506
505
  getCanonicalRefName2(refName: string): string;
507
506
  isValidRefName(refName: string): boolean;
508
507
  } & {
508
+ isCircularRefName(refName: string): boolean;
509
509
  getRefNamePosition(refName: string): number | undefined;
510
510
  getAliasesForRefName(refName: string): string[];
511
511
  getRefNameMapForAdapter(adapterConf: {
512
512
  [x: string]: unknown;
513
- }, 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>;
514
514
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
515
515
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
516
516
  readonly assemblyNamesList: string[];
@@ -525,13 +525,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
525
525
  }> & {
526
526
  error: unknown;
527
527
  loadingP: Promise<void> | undefined;
528
- 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>>;
529
529
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
530
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
530
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
531
531
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
532
532
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
533
533
  loadedGeneticCodes: Record<string, number> | undefined;
534
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
534
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
535
535
  statusMessage: string | undefined;
536
536
  statusProgress: number | undefined;
537
537
  statusSource: string | undefined;
@@ -550,7 +550,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
550
550
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
551
551
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
552
552
  } & {
553
- 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 & {
554
554
  regions: import("@jbrowse/core/util").Region[];
555
555
  cytobands: import("@jbrowse/core/util").Feature[];
556
556
  geneticCodes: Record<string, number>;
@@ -581,24 +581,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
581
581
  getCanonicalRefName2(refName: string): string;
582
582
  isValidRefName(refName: string): boolean;
583
583
  } & {
584
+ isCircularRefName(refName: string): boolean;
584
585
  getRefNamePosition(refName: string): number | undefined;
585
586
  getAliasesForRefName(refName: string): string[];
586
587
  getRefNameMapForAdapter(adapterConf: {
587
588
  [x: string]: unknown;
588
- }, 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>;
589
590
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
590
591
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
591
592
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
592
593
  }, {
593
594
  error: unknown;
594
595
  loadingP: Promise<void> | undefined;
595
- 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>>;
596
597
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
597
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
598
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
598
599
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
599
600
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
600
601
  loadedGeneticCodes: Record<string, number> | undefined;
601
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
602
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
602
603
  statusMessage: string | undefined;
603
604
  statusProgress: number | undefined;
604
605
  statusSource: string | undefined;
@@ -617,7 +618,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
617
618
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
618
619
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
619
620
  } & {
620
- 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 & {
621
622
  regions: import("@jbrowse/core/util").Region[];
622
623
  cytobands: import("@jbrowse/core/util").Feature[];
623
624
  geneticCodes: Record<string, number>;
@@ -648,11 +649,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
648
649
  getCanonicalRefName2(refName: string): string;
649
650
  isValidRefName(refName: string): boolean;
650
651
  } & {
652
+ isCircularRefName(refName: string): boolean;
651
653
  getRefNamePosition(refName: string): number | undefined;
652
654
  getAliasesForRefName(refName: string): string[];
653
655
  getRefNameMapForAdapter(adapterConf: {
654
656
  [x: string]: unknown;
655
- }, 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>;
656
658
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
657
659
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
658
660
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -660,13 +662,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
660
662
  }> & {
661
663
  error: unknown;
662
664
  loadingP: Promise<void> | undefined;
663
- 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>>;
664
666
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
665
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
667
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
666
668
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
667
669
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
668
670
  loadedGeneticCodes: Record<string, number> | undefined;
669
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
671
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
670
672
  statusMessage: string | undefined;
671
673
  statusProgress: number | undefined;
672
674
  statusSource: string | undefined;
@@ -685,7 +687,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
685
687
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
686
688
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
687
689
  } & {
688
- 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 & {
689
691
  regions: import("@jbrowse/core/util").Region[];
690
692
  cytobands: import("@jbrowse/core/util").Feature[];
691
693
  geneticCodes: Record<string, number>;
@@ -716,24 +718,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
716
718
  getCanonicalRefName2(refName: string): string;
717
719
  isValidRefName(refName: string): boolean;
718
720
  } & {
721
+ isCircularRefName(refName: string): boolean;
719
722
  getRefNamePosition(refName: string): number | undefined;
720
723
  getAliasesForRefName(refName: string): string[];
721
724
  getRefNameMapForAdapter(adapterConf: {
722
725
  [x: string]: unknown;
723
- }, 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>;
724
727
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
725
728
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
726
729
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
727
730
  }, {
728
731
  error: unknown;
729
732
  loadingP: Promise<void> | undefined;
730
- 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>>;
731
734
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
732
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
735
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
733
736
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
734
737
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
735
738
  loadedGeneticCodes: Record<string, number> | undefined;
736
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
739
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
737
740
  statusMessage: string | undefined;
738
741
  statusProgress: number | undefined;
739
742
  statusSource: string | undefined;
@@ -752,7 +755,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
752
755
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
753
756
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
754
757
  } & {
755
- 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 & {
756
759
  regions: import("@jbrowse/core/util").Region[];
757
760
  cytobands: import("@jbrowse/core/util").Feature[];
758
761
  geneticCodes: Record<string, number>;
@@ -783,16 +786,17 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
783
786
  getCanonicalRefName2(refName: string): string;
784
787
  isValidRefName(refName: string): boolean;
785
788
  } & {
789
+ isCircularRefName(refName: string): boolean;
786
790
  getRefNamePosition(refName: string): number | undefined;
787
791
  getAliasesForRefName(refName: string): string[];
788
792
  getRefNameMapForAdapter(adapterConf: {
789
793
  [x: string]: unknown;
790
- }, 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>;
791
795
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
792
796
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
793
797
  getRefNameMapForAdapter(adapterConf: {
794
798
  [x: string]: unknown;
795
- }, 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>;
796
800
  isValidRefName(refName: string, assemblyName: string): boolean;
797
801
  } & {
798
802
  afterAttach(): void;
@@ -919,11 +923,6 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
919
923
  } & {
920
924
  defaultValue: boolean;
921
925
  };
922
- readonly useWorkspaces: {
923
- type: "boolean";
924
- } & {
925
- defaultValue: boolean;
926
- };
927
926
  readonly developerMode: {
928
927
  type: "boolean";
929
928
  } & {
@@ -989,13 +988,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
989
988
  }, {
990
989
  error: unknown;
991
990
  loadingP: Promise<void> | undefined;
992
- 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>>;
993
992
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
994
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
993
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
995
994
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
996
995
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
997
996
  loadedGeneticCodes: Record<string, number> | undefined;
998
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
997
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
999
998
  statusMessage: string | undefined;
1000
999
  statusProgress: number | undefined;
1001
1000
  statusSource: string | undefined;
@@ -1014,7 +1013,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1014
1013
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1015
1014
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1016
1015
  } & {
1017
- 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 & {
1018
1017
  regions: import("@jbrowse/core/util").Region[];
1019
1018
  cytobands: import("@jbrowse/core/util").Feature[];
1020
1019
  geneticCodes: Record<string, number>;
@@ -1045,11 +1044,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1045
1044
  getCanonicalRefName2(refName: string): string;
1046
1045
  isValidRefName(refName: string): boolean;
1047
1046
  } & {
1047
+ isCircularRefName(refName: string): boolean;
1048
1048
  getRefNamePosition(refName: string): number | undefined;
1049
1049
  getAliasesForRefName(refName: string): string[];
1050
1050
  getRefNameMapForAdapter(adapterConf: {
1051
1051
  [x: string]: unknown;
1052
- }, 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>;
1053
1053
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1054
1054
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1055
1055
  }, {
@@ -1070,13 +1070,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1070
1070
  }> & {
1071
1071
  error: unknown;
1072
1072
  loadingP: Promise<void> | undefined;
1073
- 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>>;
1074
1074
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1075
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1075
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1076
1076
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1077
1077
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1078
1078
  loadedGeneticCodes: Record<string, number> | undefined;
1079
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1079
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1080
1080
  statusMessage: string | undefined;
1081
1081
  statusProgress: number | undefined;
1082
1082
  statusSource: string | undefined;
@@ -1095,7 +1095,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1095
1095
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1096
1096
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1097
1097
  } & {
1098
- 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 & {
1099
1099
  regions: import("@jbrowse/core/util").Region[];
1100
1100
  cytobands: import("@jbrowse/core/util").Feature[];
1101
1101
  geneticCodes: Record<string, number>;
@@ -1126,24 +1126,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1126
1126
  getCanonicalRefName2(refName: string): string;
1127
1127
  isValidRefName(refName: string): boolean;
1128
1128
  } & {
1129
+ isCircularRefName(refName: string): boolean;
1129
1130
  getRefNamePosition(refName: string): number | undefined;
1130
1131
  getAliasesForRefName(refName: string): string[];
1131
1132
  getRefNameMapForAdapter(adapterConf: {
1132
1133
  [x: string]: unknown;
1133
- }, 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>;
1134
1135
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1135
1136
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1136
1137
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1137
1138
  }, {
1138
1139
  error: unknown;
1139
1140
  loadingP: Promise<void> | undefined;
1140
- 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>>;
1141
1142
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1142
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1143
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1143
1144
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1144
1145
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1145
1146
  loadedGeneticCodes: Record<string, number> | undefined;
1146
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1147
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1147
1148
  statusMessage: string | undefined;
1148
1149
  statusProgress: number | undefined;
1149
1150
  statusSource: string | undefined;
@@ -1162,7 +1163,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1162
1163
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1163
1164
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1164
1165
  } & {
1165
- 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 & {
1166
1167
  regions: import("@jbrowse/core/util").Region[];
1167
1168
  cytobands: import("@jbrowse/core/util").Feature[];
1168
1169
  geneticCodes: Record<string, number>;
@@ -1193,11 +1194,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1193
1194
  getCanonicalRefName2(refName: string): string;
1194
1195
  isValidRefName(refName: string): boolean;
1195
1196
  } & {
1197
+ isCircularRefName(refName: string): boolean;
1196
1198
  getRefNamePosition(refName: string): number | undefined;
1197
1199
  getAliasesForRefName(refName: string): string[];
1198
1200
  getRefNameMapForAdapter(adapterConf: {
1199
1201
  [x: string]: unknown;
1200
- }, 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>;
1201
1203
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1202
1204
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1203
1205
  has(asmName: string): boolean;
@@ -1206,13 +1208,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1206
1208
  }> & {
1207
1209
  error: unknown;
1208
1210
  loadingP: Promise<void> | undefined;
1209
- 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>>;
1210
1212
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1211
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1213
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1212
1214
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1213
1215
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1214
1216
  loadedGeneticCodes: Record<string, number> | undefined;
1215
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1217
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1216
1218
  statusMessage: string | undefined;
1217
1219
  statusProgress: number | undefined;
1218
1220
  statusSource: string | undefined;
@@ -1231,7 +1233,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1231
1233
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1232
1234
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1233
1235
  } & {
1234
- 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 & {
1235
1237
  regions: import("@jbrowse/core/util").Region[];
1236
1238
  cytobands: import("@jbrowse/core/util").Feature[];
1237
1239
  geneticCodes: Record<string, number>;
@@ -1262,24 +1264,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1262
1264
  getCanonicalRefName2(refName: string): string;
1263
1265
  isValidRefName(refName: string): boolean;
1264
1266
  } & {
1267
+ isCircularRefName(refName: string): boolean;
1265
1268
  getRefNamePosition(refName: string): number | undefined;
1266
1269
  getAliasesForRefName(refName: string): string[];
1267
1270
  getRefNameMapForAdapter(adapterConf: {
1268
1271
  [x: string]: unknown;
1269
- }, 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>;
1270
1273
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1271
1274
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1272
1275
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1273
1276
  }, {
1274
1277
  error: unknown;
1275
1278
  loadingP: Promise<void> | undefined;
1276
- 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>>;
1277
1280
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1278
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1281
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1279
1282
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1280
1283
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1281
1284
  loadedGeneticCodes: Record<string, number> | undefined;
1282
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1285
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1283
1286
  statusMessage: string | undefined;
1284
1287
  statusProgress: number | undefined;
1285
1288
  statusSource: string | undefined;
@@ -1298,7 +1301,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1298
1301
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1299
1302
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1300
1303
  } & {
1301
- 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 & {
1302
1305
  regions: import("@jbrowse/core/util").Region[];
1303
1306
  cytobands: import("@jbrowse/core/util").Feature[];
1304
1307
  geneticCodes: Record<string, number>;
@@ -1329,11 +1332,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1329
1332
  getCanonicalRefName2(refName: string): string;
1330
1333
  isValidRefName(refName: string): boolean;
1331
1334
  } & {
1335
+ isCircularRefName(refName: string): boolean;
1332
1336
  getRefNamePosition(refName: string): number | undefined;
1333
1337
  getAliasesForRefName(refName: string): string[];
1334
1338
  getRefNameMapForAdapter(adapterConf: {
1335
1339
  [x: string]: unknown;
1336
- }, 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>;
1337
1341
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1338
1342
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1339
1343
  readonly assemblyNamesList: string[];
@@ -1348,13 +1352,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1348
1352
  }> & {
1349
1353
  error: unknown;
1350
1354
  loadingP: Promise<void> | undefined;
1351
- 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>>;
1352
1356
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1353
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1357
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1354
1358
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1355
1359
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1356
1360
  loadedGeneticCodes: Record<string, number> | undefined;
1357
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1361
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1358
1362
  statusMessage: string | undefined;
1359
1363
  statusProgress: number | undefined;
1360
1364
  statusSource: string | undefined;
@@ -1373,7 +1377,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1373
1377
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1374
1378
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1375
1379
  } & {
1376
- 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 & {
1377
1381
  regions: import("@jbrowse/core/util").Region[];
1378
1382
  cytobands: import("@jbrowse/core/util").Feature[];
1379
1383
  geneticCodes: Record<string, number>;
@@ -1404,24 +1408,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1404
1408
  getCanonicalRefName2(refName: string): string;
1405
1409
  isValidRefName(refName: string): boolean;
1406
1410
  } & {
1411
+ isCircularRefName(refName: string): boolean;
1407
1412
  getRefNamePosition(refName: string): number | undefined;
1408
1413
  getAliasesForRefName(refName: string): string[];
1409
1414
  getRefNameMapForAdapter(adapterConf: {
1410
1415
  [x: string]: unknown;
1411
- }, 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>;
1412
1417
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1413
1418
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1414
1419
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1415
1420
  }, {
1416
1421
  error: unknown;
1417
1422
  loadingP: Promise<void> | undefined;
1418
- 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>>;
1419
1424
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1420
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1425
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1421
1426
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1422
1427
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1423
1428
  loadedGeneticCodes: Record<string, number> | undefined;
1424
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1429
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1425
1430
  statusMessage: string | undefined;
1426
1431
  statusProgress: number | undefined;
1427
1432
  statusSource: string | undefined;
@@ -1440,7 +1445,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1440
1445
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1441
1446
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1442
1447
  } & {
1443
- 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 & {
1444
1449
  regions: import("@jbrowse/core/util").Region[];
1445
1450
  cytobands: import("@jbrowse/core/util").Feature[];
1446
1451
  geneticCodes: Record<string, number>;
@@ -1471,11 +1476,12 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1471
1476
  getCanonicalRefName2(refName: string): string;
1472
1477
  isValidRefName(refName: string): boolean;
1473
1478
  } & {
1479
+ isCircularRefName(refName: string): boolean;
1474
1480
  getRefNamePosition(refName: string): number | undefined;
1475
1481
  getAliasesForRefName(refName: string): string[];
1476
1482
  getRefNameMapForAdapter(adapterConf: {
1477
1483
  [x: string]: unknown;
1478
- }, 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>;
1479
1485
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1480
1486
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1481
1487
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1483,13 +1489,13 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1483
1489
  }> & {
1484
1490
  error: unknown;
1485
1491
  loadingP: Promise<void> | undefined;
1486
- 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>>;
1487
1493
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1488
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1494
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1489
1495
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1490
1496
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1491
1497
  loadedGeneticCodes: Record<string, number> | undefined;
1492
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1498
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1493
1499
  statusMessage: string | undefined;
1494
1500
  statusProgress: number | undefined;
1495
1501
  statusSource: string | undefined;
@@ -1508,7 +1514,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1508
1514
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1509
1515
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1510
1516
  } & {
1511
- 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 & {
1512
1518
  regions: import("@jbrowse/core/util").Region[];
1513
1519
  cytobands: import("@jbrowse/core/util").Feature[];
1514
1520
  geneticCodes: Record<string, number>;
@@ -1539,24 +1545,25 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1539
1545
  getCanonicalRefName2(refName: string): string;
1540
1546
  isValidRefName(refName: string): boolean;
1541
1547
  } & {
1548
+ isCircularRefName(refName: string): boolean;
1542
1549
  getRefNamePosition(refName: string): number | undefined;
1543
1550
  getAliasesForRefName(refName: string): string[];
1544
1551
  getRefNameMapForAdapter(adapterConf: {
1545
1552
  [x: string]: unknown;
1546
- }, 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>;
1547
1554
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1548
1555
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1549
1556
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1550
1557
  }, {
1551
1558
  error: unknown;
1552
1559
  loadingP: Promise<void> | undefined;
1553
- 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>>;
1554
1561
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1555
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1562
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1556
1563
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1557
1564
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1558
1565
  loadedGeneticCodes: Record<string, number> | undefined;
1559
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1566
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1560
1567
  statusMessage: string | undefined;
1561
1568
  statusProgress: number | undefined;
1562
1569
  statusSource: string | undefined;
@@ -1575,7 +1582,7 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1575
1582
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1576
1583
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1577
1584
  } & {
1578
- 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 & {
1579
1586
  regions: import("@jbrowse/core/util").Region[];
1580
1587
  cytobands: import("@jbrowse/core/util").Feature[];
1581
1588
  geneticCodes: Record<string, number>;
@@ -1606,16 +1613,17 @@ export declare function createEmbeddedRootModel<SESSION extends IAnyModelType &
1606
1613
  getCanonicalRefName2(refName: string): string;
1607
1614
  isValidRefName(refName: string): boolean;
1608
1615
  } & {
1616
+ isCircularRefName(refName: string): boolean;
1609
1617
  getRefNamePosition(refName: string): number | undefined;
1610
1618
  getAliasesForRefName(refName: string): string[];
1611
1619
  getRefNameMapForAdapter(adapterConf: {
1612
1620
  [x: string]: unknown;
1613
- }, 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>;
1614
1622
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1615
1623
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1616
1624
  getRefNameMapForAdapter(adapterConf: {
1617
1625
  [x: string]: unknown;
1618
- }, 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>;
1619
1627
  isValidRefName(refName: string, assemblyName: string): boolean;
1620
1628
  } & {
1621
1629
  afterAttach(): void;