@jbrowse/product-core 2.14.0 → 2.15.1

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Files changed (11) hide show
  1. package/dist/RootModel/BaseRootModel.d.ts +63 -35
  2. package/dist/Session/MultipleViews.d.ts +204 -112
  3. package/dist/Session/SessionTracks.d.ts +198 -110
  4. package/dist/Session/Tracks.d.ts +198 -110
  5. package/dist/ui/RefNameInfoDialog.js +9 -7
  6. package/esm/RootModel/BaseRootModel.d.ts +63 -35
  7. package/esm/Session/MultipleViews.d.ts +204 -112
  8. package/esm/Session/SessionTracks.d.ts +198 -110
  9. package/esm/Session/Tracks.d.ts +198 -110
  10. package/esm/ui/RefNameInfoDialog.js +11 -9
  11. package/package.json +5 -5
package/dist/Session/MultipleViews.d.ts CHANGED
@@ -44,17 +44,18 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
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  readonly initialized: boolean;
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  readonly name: string;
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- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly" /**
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+ * #action
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+ */).BasicRegion[] | undefined;
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  readonly aliases: string[];
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  readonly displayName: string | undefined;
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  hasName(name: string): boolean;
@@ -71,17 +72,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -110,11 +116,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -137,17 +142,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -178,11 +188,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -205,17 +214,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -244,11 +258,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -271,17 +284,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -312,11 +330,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -339,17 +356,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -378,11 +400,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -405,17 +426,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -449,11 +475,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -476,17 +501,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
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  } & {
479
- setLoaded({ regions, refNameAliases, cytobands, }: {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -515,11 +545,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  refNameAliases: {
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  [x: string]: string;
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  } | undefined;
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- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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- } & {
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- readonly lowerCaseRefNameAliases: {
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- [k: string]: string;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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  } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
@@ -542,17 +571,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameColor(refName: string): string | undefined;
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  isValidRefName(refName: string): boolean;
544
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  } & {
545
- setLoaded({ regions, refNameAliases, cytobands, }: {
574
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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  regions: import("@jbrowse/core/util").Region[];
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  refNameAliases: {
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  [x: string]: string;
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  };
579
+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
581
+ };
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  cytobands: import("@jbrowse/core/util").Feature[];
551
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  }): void;
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  setError(e: unknown): void;
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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  setRefNameAliases(aliases: {
555
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  [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
556
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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  setLoadingP(p?: Promise<void>): void;
@@ -607,17 +641,18 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
607
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  refNameAliases: {
608
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  [x: string]: string;
609
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  } | undefined;
610
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
611
- } & {
612
- readonly lowerCaseRefNameAliases: {
613
- [k: string]: string;
644
+ lowerCaseRefNameAliases: {
645
+ [x: string]: string;
614
646
  } | undefined;
647
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
615
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  } & {
616
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  getConf(arg: string): any;
617
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  } & {
618
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  readonly initialized: boolean;
619
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  readonly name: string;
620
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
653
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly" /**
654
+ * #action
655
+ */).BasicRegion[] | undefined;
621
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  readonly aliases: string[];
622
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  readonly displayName: string | undefined;
623
658
  hasName(name: string): boolean;
@@ -634,17 +669,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
634
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  getRefNameColor(refName: string): string | undefined;
635
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  isValidRefName(refName: string): boolean;
636
671
  } & {
637
- setLoaded({ regions, refNameAliases, cytobands, }: {
672
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
638
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  regions: import("@jbrowse/core/util").Region[];
639
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  refNameAliases: {
640
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  [x: string]: string;
641
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  };
677
+ lowerCaseRefNameAliases: {
678
+ [x: string]: string;
679
+ };
642
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  cytobands: import("@jbrowse/core/util").Feature[];
643
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  }): void;
644
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  setError(e: unknown): void;
645
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
646
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  setRefNameAliases(aliases: {
647
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  [x: string]: string;
686
+ }, lowerCaseAliases: {
687
+ [x: string]: string;
648
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  }): void;
649
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
650
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  setLoadingP(p?: Promise<void>): void;
@@ -675,11 +715,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
675
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  refNameAliases: {
676
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  [x: string]: string;
677
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  } | undefined;
678
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
679
- } & {
680
- readonly lowerCaseRefNameAliases: {
681
- [k: string]: string;
718
+ lowerCaseRefNameAliases: {
719
+ [x: string]: string;
682
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  } | undefined;
721
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
683
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  } & {
684
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  getConf(arg: string): any;
685
724
  } & {
@@ -702,17 +741,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
702
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  getRefNameColor(refName: string): string | undefined;
703
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  isValidRefName(refName: string): boolean;
704
743
  } & {
705
- setLoaded({ regions, refNameAliases, cytobands, }: {
744
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
706
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  regions: import("@jbrowse/core/util").Region[];
707
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  refNameAliases: {
708
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  [x: string]: string;
709
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  };
749
+ lowerCaseRefNameAliases: {
750
+ [x: string]: string;
751
+ };
710
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  cytobands: import("@jbrowse/core/util").Feature[];
711
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  }): void;
712
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  setError(e: unknown): void;
713
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  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
714
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  setRefNameAliases(aliases: {
715
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  [x: string]: string;
758
+ }, lowerCaseAliases: {
759
+ [x: string]: string;
716
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  }): void;
717
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
718
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  setLoadingP(p?: Promise<void>): void;
@@ -741,11 +785,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
741
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  refNameAliases: {
742
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  [x: string]: string;
743
787
  } | undefined;
744
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
745
- } & {
746
- readonly lowerCaseRefNameAliases: {
747
- [k: string]: string;
788
+ lowerCaseRefNameAliases: {
789
+ [x: string]: string;
748
790
  } | undefined;
791
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
749
792
  } & {
750
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  getConf(arg: string): any;
751
794
  } & {
@@ -768,17 +811,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
768
811
  getRefNameColor(refName: string): string | undefined;
769
812
  isValidRefName(refName: string): boolean;
770
813
  } & {
771
- setLoaded({ regions, refNameAliases, cytobands, }: {
814
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
772
815
  regions: import("@jbrowse/core/util").Region[];
773
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  refNameAliases: {
774
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  [x: string]: string;
775
818
  };
819
+ lowerCaseRefNameAliases: {
820
+ [x: string]: string;
821
+ };
776
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  cytobands: import("@jbrowse/core/util").Feature[];
777
823
  }): void;
778
824
  setError(e: unknown): void;
779
825
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
780
826
  setRefNameAliases(aliases: {
781
827
  [x: string]: string;
828
+ }, lowerCaseAliases: {
829
+ [x: string]: string;
782
830
  }): void;
783
831
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
784
832
  setLoadingP(p?: Promise<void>): void;
@@ -809,11 +857,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
809
857
  refNameAliases: {
810
858
  [x: string]: string;
811
859
  } | undefined;
812
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
813
- } & {
814
- readonly lowerCaseRefNameAliases: {
815
- [k: string]: string;
860
+ lowerCaseRefNameAliases: {
861
+ [x: string]: string;
816
862
  } | undefined;
863
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
817
864
  } & {
818
865
  getConf(arg: string): any;
819
866
  } & {
@@ -836,17 +883,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
836
883
  getRefNameColor(refName: string): string | undefined;
837
884
  isValidRefName(refName: string): boolean;
838
885
  } & {
839
- setLoaded({ regions, refNameAliases, cytobands, }: {
886
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
840
887
  regions: import("@jbrowse/core/util").Region[];
841
888
  refNameAliases: {
842
889
  [x: string]: string;
843
890
  };
891
+ lowerCaseRefNameAliases: {
892
+ [x: string]: string;
893
+ };
844
894
  cytobands: import("@jbrowse/core/util").Feature[];
845
895
  }): void;
846
896
  setError(e: unknown): void;
847
897
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
848
898
  setRefNameAliases(aliases: {
849
899
  [x: string]: string;
900
+ }, lowerCaseAliases: {
901
+ [x: string]: string;
850
902
  }): void;
851
903
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
852
904
  setLoadingP(p?: Promise<void>): void;
@@ -875,11 +927,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
875
927
  refNameAliases: {
876
928
  [x: string]: string;
877
929
  } | undefined;
878
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
879
- } & {
880
- readonly lowerCaseRefNameAliases: {
881
- [k: string]: string;
930
+ lowerCaseRefNameAliases: {
931
+ [x: string]: string;
882
932
  } | undefined;
933
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
883
934
  } & {
884
935
  getConf(arg: string): any;
885
936
  } & {
@@ -902,17 +953,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
902
953
  getRefNameColor(refName: string): string | undefined;
903
954
  isValidRefName(refName: string): boolean;
904
955
  } & {
905
- setLoaded({ regions, refNameAliases, cytobands, }: {
956
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
906
957
  regions: import("@jbrowse/core/util").Region[];
907
958
  refNameAliases: {
908
959
  [x: string]: string;
909
960
  };
961
+ lowerCaseRefNameAliases: {
962
+ [x: string]: string;
963
+ };
910
964
  cytobands: import("@jbrowse/core/util").Feature[];
911
965
  }): void;
912
966
  setError(e: unknown): void;
913
967
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
914
968
  setRefNameAliases(aliases: {
915
969
  [x: string]: string;
970
+ }, lowerCaseAliases: {
971
+ [x: string]: string;
916
972
  }): void;
917
973
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
918
974
  setLoadingP(p?: Promise<void>): void;
@@ -946,11 +1002,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
946
1002
  refNameAliases: {
947
1003
  [x: string]: string;
948
1004
  } | undefined;
949
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
950
- } & {
951
- readonly lowerCaseRefNameAliases: {
952
- [k: string]: string;
1005
+ lowerCaseRefNameAliases: {
1006
+ [x: string]: string;
953
1007
  } | undefined;
1008
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
954
1009
  } & {
955
1010
  getConf(arg: string): any;
956
1011
  } & {
@@ -973,17 +1028,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
973
1028
  getRefNameColor(refName: string): string | undefined;
974
1029
  isValidRefName(refName: string): boolean;
975
1030
  } & {
976
- setLoaded({ regions, refNameAliases, cytobands, }: {
1031
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
977
1032
  regions: import("@jbrowse/core/util").Region[];
978
1033
  refNameAliases: {
979
1034
  [x: string]: string;
980
1035
  };
1036
+ lowerCaseRefNameAliases: {
1037
+ [x: string]: string;
1038
+ };
981
1039
  cytobands: import("@jbrowse/core/util").Feature[];
982
1040
  }): void;
983
1041
  setError(e: unknown): void;
984
1042
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
985
1043
  setRefNameAliases(aliases: {
986
1044
  [x: string]: string;
1045
+ }, lowerCaseAliases: {
1046
+ [x: string]: string;
987
1047
  }): void;
988
1048
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
989
1049
  setLoadingP(p?: Promise<void>): void;
@@ -1012,11 +1072,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1012
1072
  refNameAliases: {
1013
1073
  [x: string]: string;
1014
1074
  } | undefined;
1015
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1016
- } & {
1017
- readonly lowerCaseRefNameAliases: {
1018
- [k: string]: string;
1075
+ lowerCaseRefNameAliases: {
1076
+ [x: string]: string;
1019
1077
  } | undefined;
1078
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1020
1079
  } & {
1021
1080
  getConf(arg: string): any;
1022
1081
  } & {
@@ -1039,17 +1098,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1039
1098
  getRefNameColor(refName: string): string | undefined;
1040
1099
  isValidRefName(refName: string): boolean;
1041
1100
  } & {
1042
- setLoaded({ regions, refNameAliases, cytobands, }: {
1101
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1043
1102
  regions: import("@jbrowse/core/util").Region[];
1044
1103
  refNameAliases: {
1045
1104
  [x: string]: string;
1046
1105
  };
1106
+ lowerCaseRefNameAliases: {
1107
+ [x: string]: string;
1108
+ };
1047
1109
  cytobands: import("@jbrowse/core/util").Feature[];
1048
1110
  }): void;
1049
1111
  setError(e: unknown): void;
1050
1112
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1051
1113
  setRefNameAliases(aliases: {
1052
1114
  [x: string]: string;
1115
+ }, lowerCaseAliases: {
1116
+ [x: string]: string;
1053
1117
  }): void;
1054
1118
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1055
1119
  setLoadingP(p?: Promise<void>): void;
@@ -1119,11 +1183,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1119
1183
  refNameAliases: {
1120
1184
  [x: string]: string;
1121
1185
  } | undefined;
1122
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1123
- } & {
1124
- readonly lowerCaseRefNameAliases: {
1125
- [k: string]: string;
1186
+ lowerCaseRefNameAliases: {
1187
+ [x: string]: string;
1126
1188
  } | undefined;
1189
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1127
1190
  } & {
1128
1191
  getConf(arg: string): any;
1129
1192
  } & {
@@ -1146,17 +1209,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1146
1209
  getRefNameColor(refName: string): string | undefined;
1147
1210
  isValidRefName(refName: string): boolean;
1148
1211
  } & {
1149
- setLoaded({ regions, refNameAliases, cytobands, }: {
1212
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1150
1213
  regions: import("@jbrowse/core/util").Region[];
1151
1214
  refNameAliases: {
1152
1215
  [x: string]: string;
1153
1216
  };
1217
+ lowerCaseRefNameAliases: {
1218
+ [x: string]: string;
1219
+ };
1154
1220
  cytobands: import("@jbrowse/core/util").Feature[];
1155
1221
  }): void;
1156
1222
  setError(e: unknown): void;
1157
1223
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1158
1224
  setRefNameAliases(aliases: {
1159
1225
  [x: string]: string;
1226
+ }, lowerCaseAliases: {
1227
+ [x: string]: string;
1160
1228
  }): void;
1161
1229
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1162
1230
  setLoadingP(p?: Promise<void>): void;
@@ -1187,11 +1255,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1187
1255
  refNameAliases: {
1188
1256
  [x: string]: string;
1189
1257
  } | undefined;
1190
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1191
- } & {
1192
- readonly lowerCaseRefNameAliases: {
1193
- [k: string]: string;
1258
+ lowerCaseRefNameAliases: {
1259
+ [x: string]: string;
1194
1260
  } | undefined;
1261
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1195
1262
  } & {
1196
1263
  getConf(arg: string): any;
1197
1264
  } & {
@@ -1214,17 +1281,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1214
1281
  getRefNameColor(refName: string): string | undefined;
1215
1282
  isValidRefName(refName: string): boolean;
1216
1283
  } & {
1217
- setLoaded({ regions, refNameAliases, cytobands, }: {
1284
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1218
1285
  regions: import("@jbrowse/core/util").Region[];
1219
1286
  refNameAliases: {
1220
1287
  [x: string]: string;
1221
1288
  };
1289
+ lowerCaseRefNameAliases: {
1290
+ [x: string]: string;
1291
+ };
1222
1292
  cytobands: import("@jbrowse/core/util").Feature[];
1223
1293
  }): void;
1224
1294
  setError(e: unknown): void;
1225
1295
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1226
1296
  setRefNameAliases(aliases: {
1227
1297
  [x: string]: string;
1298
+ }, lowerCaseAliases: {
1299
+ [x: string]: string;
1228
1300
  }): void;
1229
1301
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1230
1302
  setLoadingP(p?: Promise<void>): void;
@@ -1253,11 +1325,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1253
1325
  refNameAliases: {
1254
1326
  [x: string]: string;
1255
1327
  } | undefined;
1256
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1257
- } & {
1258
- readonly lowerCaseRefNameAliases: {
1259
- [k: string]: string;
1328
+ lowerCaseRefNameAliases: {
1329
+ [x: string]: string;
1260
1330
  } | undefined;
1331
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1261
1332
  } & {
1262
1333
  getConf(arg: string): any;
1263
1334
  } & {
@@ -1280,17 +1351,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1280
1351
  getRefNameColor(refName: string): string | undefined;
1281
1352
  isValidRefName(refName: string): boolean;
1282
1353
  } & {
1283
- setLoaded({ regions, refNameAliases, cytobands, }: {
1354
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1284
1355
  regions: import("@jbrowse/core/util").Region[];
1285
1356
  refNameAliases: {
1286
1357
  [x: string]: string;
1287
1358
  };
1359
+ lowerCaseRefNameAliases: {
1360
+ [x: string]: string;
1361
+ };
1288
1362
  cytobands: import("@jbrowse/core/util").Feature[];
1289
1363
  }): void;
1290
1364
  setError(e: unknown): void;
1291
1365
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1292
1366
  setRefNameAliases(aliases: {
1293
1367
  [x: string]: string;
1368
+ }, lowerCaseAliases: {
1369
+ [x: string]: string;
1294
1370
  }): void;
1295
1371
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1296
1372
  setLoadingP(p?: Promise<void>): void;
@@ -1321,11 +1397,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1321
1397
  refNameAliases: {
1322
1398
  [x: string]: string;
1323
1399
  } | undefined;
1324
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1325
- } & {
1326
- readonly lowerCaseRefNameAliases: {
1327
- [k: string]: string;
1400
+ lowerCaseRefNameAliases: {
1401
+ [x: string]: string;
1328
1402
  } | undefined;
1403
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1329
1404
  } & {
1330
1405
  getConf(arg: string): any;
1331
1406
  } & {
@@ -1348,17 +1423,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1348
1423
  getRefNameColor(refName: string): string | undefined;
1349
1424
  isValidRefName(refName: string): boolean;
1350
1425
  } & {
1351
- setLoaded({ regions, refNameAliases, cytobands, }: {
1426
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1352
1427
  regions: import("@jbrowse/core/util").Region[];
1353
1428
  refNameAliases: {
1354
1429
  [x: string]: string;
1355
1430
  };
1431
+ lowerCaseRefNameAliases: {
1432
+ [x: string]: string;
1433
+ };
1356
1434
  cytobands: import("@jbrowse/core/util").Feature[];
1357
1435
  }): void;
1358
1436
  setError(e: unknown): void;
1359
1437
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1360
1438
  setRefNameAliases(aliases: {
1361
1439
  [x: string]: string;
1440
+ }, lowerCaseAliases: {
1441
+ [x: string]: string;
1362
1442
  }): void;
1363
1443
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1364
1444
  setLoadingP(p?: Promise<void>): void;
@@ -1387,11 +1467,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1387
1467
  refNameAliases: {
1388
1468
  [x: string]: string;
1389
1469
  } | undefined;
1390
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1391
- } & {
1392
- readonly lowerCaseRefNameAliases: {
1393
- [k: string]: string;
1470
+ lowerCaseRefNameAliases: {
1471
+ [x: string]: string;
1394
1472
  } | undefined;
1473
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1395
1474
  } & {
1396
1475
  getConf(arg: string): any;
1397
1476
  } & {
@@ -1414,17 +1493,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1414
1493
  getRefNameColor(refName: string): string | undefined;
1415
1494
  isValidRefName(refName: string): boolean;
1416
1495
  } & {
1417
- setLoaded({ regions, refNameAliases, cytobands, }: {
1496
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1418
1497
  regions: import("@jbrowse/core/util").Region[];
1419
1498
  refNameAliases: {
1420
1499
  [x: string]: string;
1421
1500
  };
1501
+ lowerCaseRefNameAliases: {
1502
+ [x: string]: string;
1503
+ };
1422
1504
  cytobands: import("@jbrowse/core/util").Feature[];
1423
1505
  }): void;
1424
1506
  setError(e: unknown): void;
1425
1507
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1426
1508
  setRefNameAliases(aliases: {
1427
1509
  [x: string]: string;
1510
+ }, lowerCaseAliases: {
1511
+ [x: string]: string;
1428
1512
  }): void;
1429
1513
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1430
1514
  setLoadingP(p?: Promise<void>): void;
@@ -1458,11 +1542,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1458
1542
  refNameAliases: {
1459
1543
  [x: string]: string;
1460
1544
  } | undefined;
1461
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1462
- } & {
1463
- readonly lowerCaseRefNameAliases: {
1464
- [k: string]: string;
1545
+ lowerCaseRefNameAliases: {
1546
+ [x: string]: string;
1465
1547
  } | undefined;
1548
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1466
1549
  } & {
1467
1550
  getConf(arg: string): any;
1468
1551
  } & {
@@ -1485,17 +1568,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1485
1568
  getRefNameColor(refName: string): string | undefined;
1486
1569
  isValidRefName(refName: string): boolean;
1487
1570
  } & {
1488
- setLoaded({ regions, refNameAliases, cytobands, }: {
1571
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1489
1572
  regions: import("@jbrowse/core/util").Region[];
1490
1573
  refNameAliases: {
1491
1574
  [x: string]: string;
1492
1575
  };
1576
+ lowerCaseRefNameAliases: {
1577
+ [x: string]: string;
1578
+ };
1493
1579
  cytobands: import("@jbrowse/core/util").Feature[];
1494
1580
  }): void;
1495
1581
  setError(e: unknown): void;
1496
1582
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1497
1583
  setRefNameAliases(aliases: {
1498
1584
  [x: string]: string;
1585
+ }, lowerCaseAliases: {
1586
+ [x: string]: string;
1499
1587
  }): void;
1500
1588
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1501
1589
  setLoadingP(p?: Promise<void>): void;
@@ -1524,11 +1612,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1524
1612
  refNameAliases: {
1525
1613
  [x: string]: string;
1526
1614
  } | undefined;
1527
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1528
- } & {
1529
- readonly lowerCaseRefNameAliases: {
1530
- [k: string]: string;
1615
+ lowerCaseRefNameAliases: {
1616
+ [x: string]: string;
1531
1617
  } | undefined;
1618
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1532
1619
  } & {
1533
1620
  getConf(arg: string): any;
1534
1621
  } & {
@@ -1551,17 +1638,22 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1551
1638
  getRefNameColor(refName: string): string | undefined;
1552
1639
  isValidRefName(refName: string): boolean;
1553
1640
  } & {
1554
- setLoaded({ regions, refNameAliases, cytobands, }: {
1641
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1555
1642
  regions: import("@jbrowse/core/util").Region[];
1556
1643
  refNameAliases: {
1557
1644
  [x: string]: string;
1558
1645
  };
1646
+ lowerCaseRefNameAliases: {
1647
+ [x: string]: string;
1648
+ };
1559
1649
  cytobands: import("@jbrowse/core/util").Feature[];
1560
1650
  }): void;
1561
1651
  setError(e: unknown): void;
1562
1652
  setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1563
1653
  setRefNameAliases(aliases: {
1564
1654
  [x: string]: string;
1655
+ }, lowerCaseAliases: {
1656
+ [x: string]: string;
1565
1657
  }): void;
1566
1658
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1567
1659
  setLoadingP(p?: Promise<void>): void;