@jbrowse/app-core 5.0.0-beta.8 → 5.0.0-beta.9

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 (26) hide show
  1. package/esm/AppSession/AppSessionMixin.d.ts +2 -8
  2. package/esm/Assemblies/AssembliesMixin.d.ts +170 -92
  3. package/esm/JBrowseConfig/RootConfiguration.d.ts +78 -126
  4. package/esm/JBrowseConfig/RootConfiguration.js +5 -11
  5. package/esm/JBrowseConfig/defaultShareUrl.d.ts +1 -0
  6. package/esm/JBrowseConfig/defaultShareUrl.js +5 -0
  7. package/esm/JBrowseConfig/index.d.ts +79 -79
  8. package/esm/JBrowseConfig/index.js +1 -1
  9. package/esm/JBrowseModel/index.d.ts +79 -82
  10. package/esm/JBrowseModel/index.js +19 -10
  11. package/esm/JbApi/jbApi.d.ts +1069 -33
  12. package/esm/JbApi/jbApi.js +508 -138
  13. package/esm/SessionSpec/index.d.ts +1 -1
  14. package/esm/SessionSpec/index.js +1 -1
  15. package/esm/SessionSpec/loadSessionSpec.d.ts +58 -2
  16. package/esm/SessionSpec/loadSessionSpec.js +173 -93
  17. package/esm/SessionSpec/types.d.ts +6 -0
  18. package/esm/WorkspaceLayout/model.d.ts +8 -8
  19. package/esm/WorkspaceLayout/model.js +8 -8
  20. package/esm/ui/App/App.js +1 -2
  21. package/esm/ui/App/ViewStack.js +7 -1
  22. package/esm/ui/App/index.d.ts +1 -1
  23. package/esm/ui/App/index.js +1 -1
  24. package/package.json +4 -4
  25. package/esm/ui/App/AppReadyMarker.d.ts +0 -43
  26. package/esm/ui/App/AppReadyMarker.js +0 -78
package/esm/AppSession/AppSessionMixin.d.ts CHANGED
@@ -524,10 +524,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
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  readonly assemblyNamesList: string[];
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  readonly configuredAssemblyNames: Set<string>;
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- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
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- setSubschema(slotName: string, data: Record<string, unknown>): any;
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- setSlot(slotName: string, value: unknown): void;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
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+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
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  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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  } & {
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  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1299,10 +1296,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
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  readonly assemblyNamesList: string[];
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  readonly configuredAssemblyNames: Set<string>;
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- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
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- setSubschema(slotName: string, data: Record<string, unknown>): any;
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- setSlot(slotName: string, value: unknown): void;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
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+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
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  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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  } & {
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  settleAssemblyResolution(assemblyName: string): Promise<void>;
package/esm/Assemblies/AssembliesMixin.d.ts CHANGED
@@ -14,81 +14,85 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
14
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  */
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  sessionAssemblies: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly aliases: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "Other possible names for the assembly";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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  readonly refNameColors: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly geneticCodes: {
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- readonly type: "frozen";
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- readonly defaultValue: {};
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- readonly description: "Map of reference sequence name to NCBI genetic-code (translation table) id for sequences not using the standard code, e.g. { \"chrM\": 2 }";
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+ type: "frozen";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly geneticCodesLocation: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "";
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- readonly locationType: "UriLocation";
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- };
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- readonly description: "Optional TSV file of refName<TAB>geneticCodeId, an alternative to inlining the geneticCodes map";
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  readonly displayName: {
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- readonly type: "string";
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- readonly defaultValue: "";
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- readonly description: "A human readable display name for the assembly e.g. \"Homo sapiens (hg38)\" while the assembly name may just be \"hg38\"";
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>, [undefined]>;
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+ name: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>, [undefined]>;
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  /**
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  * #property
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  */
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  temporaryAssemblies: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly aliases: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "Other possible names for the assembly";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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  readonly refNameColors: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly geneticCodes: {
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- readonly type: "frozen";
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- readonly defaultValue: {};
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- readonly description: "Map of reference sequence name to NCBI genetic-code (translation table) id for sequences not using the standard code, e.g. { \"chrM\": 2 }";
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+ type: "frozen";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly geneticCodesLocation: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "";
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- readonly locationType: "UriLocation";
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- };
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- readonly description: "Optional TSV file of refName<TAB>geneticCodeId, an alternative to inlining the geneticCodes map";
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  readonly displayName: {
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- readonly type: "string";
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- readonly defaultValue: "";
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- readonly description: "A human readable display name for the assembly e.g. \"Homo sapiens (hg38)\" while the assembly name may just be \"hg38\"";
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ name: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>, [undefined]>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>, [undefined]>;
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  }, {
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  /**
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  * #method
@@ -108,46 +112,83 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
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  /**
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  * #action
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  */
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- addSessionAssembly(conf: AnyConfiguration): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
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- setSubschema(slotName: string, data: Record<string, unknown>): any;
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- setSlot(slotName: string, value: unknown): void;
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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+ addSessionAssembly(conf: AnyConfiguration): (import("@jbrowse/core/configuration").ConfigNodeProps<{
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+ readonly aliases: {
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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+ readonly refNameColors: {
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ readonly geneticCodes: {
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+ type: "frozen";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ readonly geneticCodesLocation: {
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
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+ };
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+ readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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+ readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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+ readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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+ readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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+ readonly displayName: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ name: {
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+ type: "string";
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+ } & {
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+ defaultValue: string;
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+ };
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+ }> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly aliases: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "Other possible names for the assembly";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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  readonly refNameColors: {
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- readonly type: "stringArray";
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- readonly defaultValue: readonly [];
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- readonly description: "Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.";
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+ type: "stringArray";
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+ } & {
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+ defaultValue: unknown;
125
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  };
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  readonly geneticCodes: {
127
- readonly type: "frozen";
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- readonly defaultValue: {};
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- readonly description: "Map of reference sequence name to NCBI genetic-code (translation table) id for sequences not using the standard code, e.g. { \"chrM\": 2 }";
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+ type: "frozen";
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+ } & {
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+ defaultValue: unknown;
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  };
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  readonly geneticCodesLocation: {
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- readonly type: "fileLocation";
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- readonly defaultValue: {
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- readonly uri: "";
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- readonly locationType: "UriLocation";
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- };
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- readonly description: "Optional TSV file of refName<TAB>geneticCodeId, an alternative to inlining the geneticCodes map";
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+ type: "fileLocation";
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+ } & {
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+ defaultValue: unknown;
138
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  };
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  readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
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  readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
145
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  readonly displayName: {
146
- readonly type: "string";
147
- readonly defaultValue: "";
148
- readonly description: "A human readable display name for the assembly e.g. \"Homo sapiens (hg38)\" while the assembly name may just be \"hg38\"";
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+ type: "string";
183
+ } & {
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+ defaultValue: string;
149
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  };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>) | undefined;
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+ name: {
187
+ type: "string";
188
+ } & {
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+ defaultValue: string;
190
+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>) | undefined;
151
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  /**
152
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  * #action
153
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  */
@@ -164,46 +205,83 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
164
205
  * #action
165
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  * used for read vs ref type assemblies.
166
207
  */
167
- addTemporaryAssembly(conf: AnyConfiguration): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
168
- setSubschema(slotName: string, data: Record<string, unknown>): any;
169
- setSlot(slotName: string, value: unknown): void;
170
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
208
+ addTemporaryAssembly(conf: AnyConfiguration): (import("@jbrowse/core/configuration").ConfigNodeProps<{
209
+ readonly aliases: {
210
+ type: "stringArray";
211
+ } & {
212
+ defaultValue: unknown;
213
+ };
214
+ readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
215
+ readonly refNameColors: {
216
+ type: "stringArray";
217
+ } & {
218
+ defaultValue: unknown;
219
+ };
220
+ readonly geneticCodes: {
221
+ type: "frozen";
222
+ } & {
223
+ defaultValue: unknown;
224
+ };
225
+ readonly geneticCodesLocation: {
226
+ type: "fileLocation";
227
+ } & {
228
+ defaultValue: unknown;
229
+ };
230
+ readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
231
+ readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
232
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
233
+ readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
234
+ readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
235
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
236
+ readonly displayName: {
237
+ type: "string";
238
+ } & {
239
+ defaultValue: string;
240
+ };
241
+ name: {
242
+ type: "string";
243
+ } & {
244
+ defaultValue: string;
245
+ };
246
+ }> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
171
247
  readonly aliases: {
172
- readonly type: "stringArray";
173
- readonly defaultValue: readonly [];
174
- readonly description: "Other possible names for the assembly";
248
+ type: "stringArray";
249
+ } & {
250
+ defaultValue: unknown;
175
251
  };
176
252
  readonly sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
177
253
  readonly refNameColors: {
178
- readonly type: "stringArray";
179
- readonly defaultValue: readonly [];
180
- readonly description: "Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.";
254
+ type: "stringArray";
255
+ } & {
256
+ defaultValue: unknown;
181
257
  };
182
258
  readonly geneticCodes: {
183
- readonly type: "frozen";
184
- readonly defaultValue: {};
185
- readonly description: "Map of reference sequence name to NCBI genetic-code (translation table) id for sequences not using the standard code, e.g. { \"chrM\": 2 }";
259
+ type: "frozen";
260
+ } & {
261
+ defaultValue: unknown;
186
262
  };
187
263
  readonly geneticCodesLocation: {
188
- readonly type: "fileLocation";
189
- readonly defaultValue: {
190
- readonly uri: "";
191
- readonly locationType: "UriLocation";
192
- };
193
- readonly description: "Optional TSV file of refName<TAB>geneticCodeId, an alternative to inlining the geneticCodes map";
264
+ type: "fileLocation";
265
+ } & {
266
+ defaultValue: unknown;
194
267
  };
195
268
  readonly refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
196
269
  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
197
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
270
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
198
271
  readonly cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
199
272
  readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
200
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
273
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
201
274
  readonly displayName: {
202
- readonly type: "string";
203
- readonly defaultValue: "";
204
- readonly description: "A human readable display name for the assembly e.g. \"Homo sapiens (hg38)\" while the assembly name may just be \"hg38\"";
275
+ type: "string";
276
+ } & {
277
+ defaultValue: string;
278
+ };
279
+ name: {
280
+ type: "string";
281
+ } & {
282
+ defaultValue: string;
205
283
  };
206
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>) | undefined;
284
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>) | undefined;
207
285
  /**
208
286
  * #action
209
287
  */