@jbrowse/core 2.12.0 → 2.12.2

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Files changed (91) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +1 -1
  2. package/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +1 -1
  3. package/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +1 -1
  4. package/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +1 -1
  5. package/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +1 -1
  6. package/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +1 -1
  7. package/BaseFeatureWidget/BaseFeatureDetail/UriField.js +1 -1
  8. package/BaseFeatureWidget/BaseFeatureDetail/index.js +3 -3
  9. package/BaseFeatureWidget/BaseFeatureDetail/util.js +4 -5
  10. package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +1 -1
  11. package/BaseFeatureWidget/SequenceFeatureDetails/hooks.js +1 -2
  12. package/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +1 -1
  13. package/BaseFeatureWidget/SequenceFeatureDetails/model.js +1 -2
  14. package/BaseFeatureWidget/SequenceFeatureDetails/util.js +2 -2
  15. package/BaseFeatureWidget/stateModelFactory.d.ts +2 -6
  16. package/BaseFeatureWidget/stateModelFactory.js +1 -2
  17. package/BaseFeatureWidget/util.d.ts +5 -5
  18. package/BaseFeatureWidget/util.js +6 -7
  19. package/PluginLoader.js +4 -5
  20. package/PluginManager.d.ts +6 -7
  21. package/ReExports/modules.d.ts +6 -6
  22. package/TextSearch/TextSearchManager.d.ts +6 -2
  23. package/assemblyManager/assembly.js +1 -1
  24. package/assemblyManager/assemblyManager.d.ts +9 -82
  25. package/configuration/configurationSchema.d.ts +7 -1
  26. package/configuration/configurationSchema.js +2 -3
  27. package/configuration/configurationSlot.js +1 -1
  28. package/configuration/util.d.ts +1 -1
  29. package/configuration/util.js +7 -8
  30. package/data_adapters/BaseAdapter/util.js +5 -6
  31. package/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +0 -1
  32. package/data_adapters/CytobandAdapter/CytobandAdapter.js +1 -2
  33. package/data_adapters/CytobandAdapter/index.js +1 -1
  34. package/data_adapters/dataAdapterCache.js +4 -5
  35. package/package.json +3 -3
  36. package/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +1 -3
  37. package/pluggableElementTypes/models/BaseDisplayModel.d.ts +3 -3
  38. package/pluggableElementTypes/models/BaseTrackModel.d.ts +6 -2
  39. package/pluggableElementTypes/models/BaseTrackModel.js +2 -3
  40. package/pluggableElementTypes/models/InternetAccountModel.d.ts +13 -13
  41. package/pluggableElementTypes/models/baseTrackConfig.js +1 -2
  42. package/rpc/BaseRpcDriver.js +1 -2
  43. package/rpc/methods/util.js +1 -2
  44. package/rpc/remoteAbortSignals.js +5 -6
  45. package/stories/examples/WithSequencePanel.js +5 -6
  46. package/tsconfig.build.tsbuildinfo +1 -1
  47. package/ui/ColorPicker.js +3 -3
  48. package/ui/ErrorMessageStackTraceDialog.js +1 -1
  49. package/ui/FactoryResetDialog.js +1 -1
  50. package/ui/FatalErrorDialog.js +1 -1
  51. package/ui/Icons.js +9 -10
  52. package/ui/LoadingEllipses.js +1 -1
  53. package/ui/Logo.js +2 -3
  54. package/ui/Menu.js +1 -2
  55. package/ui/RedErrorMessageBox.js +1 -1
  56. package/ui/SanitizedHTML.js +1 -1
  57. package/ui/SnackbarModel.js +1 -1
  58. package/ui/theme.js +3 -3
  59. package/util/Base1DUtils.js +4 -5
  60. package/util/Base1DViewModel.d.ts +2 -2
  61. package/util/aborting.js +5 -6
  62. package/util/analytics.js +3 -4
  63. package/util/blobToDataURL.js +1 -2
  64. package/util/calculateDynamicBlocks.js +1 -1
  65. package/util/calculateStaticBlocks.js +1 -1
  66. package/util/color/cssColorsLevel4.js +2 -3
  67. package/util/color/index.js +4 -4
  68. package/util/dedupe.js +1 -2
  69. package/util/formatFastaStrings.js +2 -3
  70. package/util/idMaker.js +1 -1
  71. package/util/index.d.ts +2 -2
  72. package/util/index.js +70 -71
  73. package/util/io/RemoteFileWithRangeCache.d.ts +0 -1
  74. package/util/io/RemoteFileWithRangeCache.js +3 -3
  75. package/util/io/index.js +4 -4
  76. package/util/jexl.js +1 -1
  77. package/util/jexlStrings.js +1 -2
  78. package/util/map-obj.js +1 -1
  79. package/util/mst-reflection.js +6 -7
  80. package/util/offscreenCanvasPonyfill.js +2 -2
  81. package/util/offscreenCanvasUtils.js +3 -4
  82. package/util/range.js +3 -4
  83. package/util/rxjs.js +1 -2
  84. package/util/simpleFeature.js +1 -2
  85. package/util/stats.js +5 -6
  86. package/util/tracks.js +17 -17
  87. package/util/types/index.js +23 -23
  88. package/util/types/mst.d.ts +0 -1
  89. package/util/useMeasure.d.ts +2 -3
  90. package/util/useMeasure.js +1 -1
  91. package/util/when.js +2 -3
@@ -1,4 +1,5 @@
1
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  import { IAnyType } from 'mobx-state-tree';
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+ import { AnyConfigurationModel } from '../configuration';
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  import { Assembly } from './assembly';
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  import PluginManager from '../PluginManager';
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  import RpcManager from '../rpc/RpcManager';
@@ -33,16 +34,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  readonly initialized: boolean;
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  readonly name: string;
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  readonly regions: import("./assembly").BasicRegion[] | undefined;
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- /**
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- * #action
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- * private: you would generally want to add to manipulate
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- * jbrowse.assemblies, session.sessionAssemblies, or
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- * session.temporaryAssemblies instead of using this directly
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- *
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- * this can take an active instance of an assembly, in which case it is
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- * referred to, or it can take an identifier e.g. assembly name, which is
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- * used as a reference. snapshots cannot be used
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- */
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  readonly aliases: string[];
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  readonly displayName: string | undefined;
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  hasName(name: string): boolean;
@@ -68,7 +59,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  [x: string]: string | undefined;
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  }): void;
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  setCytobands(cytobands: import("../util").Feature[]): void;
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- setLoadingP(p?: Promise<void> | undefined): void;
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+ setLoadingP(p?: Promise<void>): void;
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  load(): Promise<void>;
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  loadPre(): Promise<void>;
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  } & {
@@ -107,16 +98,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  readonly initialized: boolean;
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  readonly name: string;
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  readonly regions: import("./assembly").BasicRegion[] | undefined;
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- /**
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- * #action
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- * private: you would generally want to add to manipulate
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- * jbrowse.assemblies, session.sessionAssemblies, or
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- * session.temporaryAssemblies instead of using this directly
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- *
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- * this can take an active instance of an assembly, in which case it is
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- * referred to, or it can take an identifier e.g. assembly name, which is
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- * used as a reference. snapshots cannot be used
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- */
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  readonly aliases: string[];
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  readonly displayName: string | undefined;
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  hasName(name: string): boolean;
@@ -142,7 +123,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  [x: string]: string | undefined;
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  }): void;
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  setCytobands(cytobands: import("../util").Feature[]): void;
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- setLoadingP(p?: Promise<void> | undefined): void;
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+ setLoadingP(p?: Promise<void>): void;
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  load(): Promise<void>;
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  loadPre(): Promise<void>;
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  } & {
@@ -179,16 +160,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  readonly initialized: boolean;
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  readonly name: string;
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  readonly regions: import("./assembly").BasicRegion[] | undefined;
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- /**
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- * #action
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- * private: you would generally want to add to manipulate
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- * jbrowse.assemblies, session.sessionAssemblies, or
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- * session.temporaryAssemblies instead of using this directly
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- *
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- * this can take an active instance of an assembly, in which case it is
189
- * referred to, or it can take an identifier e.g. assembly name, which is
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- * used as a reference. snapshots cannot be used
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- */
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  readonly aliases: string[];
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  readonly displayName: string | undefined;
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  hasName(name: string): boolean;
@@ -214,7 +185,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  [x: string]: string | undefined;
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  }): void;
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  setCytobands(cytobands: import("../util").Feature[]): void;
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- setLoadingP(p?: Promise<void> | undefined): void;
188
+ setLoadingP(p?: Promise<void>): void;
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  load(): Promise<void>;
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  loadPre(): Promise<void>;
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  } & {
@@ -256,16 +227,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
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  readonly initialized: boolean;
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  readonly name: string;
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  readonly regions: import("./assembly").BasicRegion[] | undefined;
259
- /**
260
- * #action
261
- * private: you would generally want to add to manipulate
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- * jbrowse.assemblies, session.sessionAssemblies, or
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- * session.temporaryAssemblies instead of using this directly
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- *
265
- * this can take an active instance of an assembly, in which case it is
266
- * referred to, or it can take an identifier e.g. assembly name, which is
267
- * used as a reference. snapshots cannot be used
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- */
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  readonly aliases: string[];
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  readonly displayName: string | undefined;
271
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  hasName(name: string): boolean;
@@ -291,7 +252,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
291
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  [x: string]: string | undefined;
292
253
  }): void;
293
254
  setCytobands(cytobands: import("../util").Feature[]): void;
294
- setLoadingP(p?: Promise<void> | undefined): void;
255
+ setLoadingP(p?: Promise<void>): void;
295
256
  load(): Promise<void>;
296
257
  loadPre(): Promise<void>;
297
258
  } & {
@@ -328,16 +289,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
328
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  readonly initialized: boolean;
329
290
  readonly name: string;
330
291
  readonly regions: import("./assembly").BasicRegion[] | undefined;
331
- /**
332
- * #action
333
- * private: you would generally want to add to manipulate
334
- * jbrowse.assemblies, session.sessionAssemblies, or
335
- * session.temporaryAssemblies instead of using this directly
336
- *
337
- * this can take an active instance of an assembly, in which case it is
338
- * referred to, or it can take an identifier e.g. assembly name, which is
339
- * used as a reference. snapshots cannot be used
340
- */
341
292
  readonly aliases: string[];
342
293
  readonly displayName: string | undefined;
343
294
  hasName(name: string): boolean;
@@ -363,7 +314,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
363
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  [x: string]: string | undefined;
364
315
  }): void;
365
316
  setCytobands(cytobands: import("../util").Feature[]): void;
366
- setLoadingP(p?: Promise<void> | undefined): void;
317
+ setLoadingP(p?: Promise<void>): void;
367
318
  load(): Promise<void>;
368
319
  loadPre(): Promise<void>;
369
320
  } & {
@@ -390,11 +341,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
390
341
  * looks at jbrowse.assemblies, session.sessionAssemblies, and
391
342
  * session.temporaryAssemblies to load from
392
343
  */
393
- readonly assemblyList: ({
394
- [x: string]: any;
395
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
396
- setSubschema(slotName: string, data: unknown): any;
397
- } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
344
+ readonly assemblyList: AnyConfigurationModel[];
398
345
  readonly rpcManager: RpcManager;
399
346
  } & {
400
347
  /**
@@ -422,16 +369,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
422
369
  readonly initialized: boolean;
423
370
  readonly name: string;
424
371
  readonly regions: import("./assembly").BasicRegion[] | undefined;
425
- /**
426
- * #action
427
- * private: you would generally want to add to manipulate
428
- * jbrowse.assemblies, session.sessionAssemblies, or
429
- * session.temporaryAssemblies instead of using this directly
430
- *
431
- * this can take an active instance of an assembly, in which case it is
432
- * referred to, or it can take an identifier e.g. assembly name, which is
433
- * used as a reference. snapshots cannot be used
434
- */
435
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  readonly aliases: string[];
436
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  readonly displayName: string | undefined;
437
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  hasName(name: string): boolean;
@@ -457,7 +394,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
457
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  [x: string]: string | undefined;
458
395
  }): void;
459
396
  setCytobands(cytobands: import("../util").Feature[]): void;
460
- setLoadingP(p?: Promise<void> | undefined): void;
397
+ setLoadingP(p?: Promise<void>): void;
461
398
  load(): Promise<void>;
462
399
  loadPre(): Promise<void>;
463
400
  } & {
@@ -494,16 +431,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
494
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  readonly initialized: boolean;
495
432
  readonly name: string;
496
433
  readonly regions: import("./assembly").BasicRegion[] | undefined;
497
- /**
498
- * #action
499
- * private: you would generally want to add to manipulate
500
- * jbrowse.assemblies, session.sessionAssemblies, or
501
- * session.temporaryAssemblies instead of using this directly
502
- *
503
- * this can take an active instance of an assembly, in which case it is
504
- * referred to, or it can take an identifier e.g. assembly name, which is
505
- * used as a reference. snapshots cannot be used
506
- */
507
434
  readonly aliases: string[];
508
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  readonly displayName: string | undefined;
509
436
  hasName(name: string): boolean;
@@ -529,7 +456,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
529
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  [x: string]: string | undefined;
530
457
  }): void;
531
458
  setCytobands(cytobands: import("../util").Feature[]): void;
532
- setLoadingP(p?: Promise<void> | undefined): void;
459
+ setLoadingP(p?: Promise<void>): void;
533
460
  load(): Promise<void>;
534
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  loadPre(): Promise<void>;
535
462
  } & {
@@ -16,7 +16,13 @@ export interface ConfigurationSchemaOptions<BASE_SCHEMA extends AnyConfiguration
16
16
  preProcessSnapshot?: (snapshot: {}) => {};
17
17
  }
18
18
  declare function makeConfigurationSchemaModel<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<any, any>>(modelName: string, schemaDefinition: DEFINITION, options: OPTIONS): import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<Record<string, any>, {
19
- setSubschema(slotName: string, data: unknown): any;
19
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
20
+ [x: string]: any;
21
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
22
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
23
+ [x: string]: any;
24
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
25
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
20
26
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
21
27
  export interface ConfigurationSchemaType<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<any, any>> extends ReturnType<typeof makeConfigurationSchemaModel<DEFINITION, OPTIONS>> {
22
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  isJBrowseConfigurationSchema: boolean;
@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.ConfigurationReference = exports.ConfigurationSchema = void 0;
6
+ exports.ConfigurationSchema = ConfigurationSchema;
7
+ exports.ConfigurationReference = ConfigurationReference;
7
8
  /* eslint-disable @typescript-eslint/no-explicit-any */
8
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  const mobx_state_tree_1 = require("mobx-state-tree");
9
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  const mst_1 = require("../util/types/mst");
@@ -178,11 +179,9 @@ function ConfigurationSchema(modelName, inputSchemaDefinition, inputOptions) {
178
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  schemaType.jbrowseSchemaOptions = options;
179
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  return schemaType;
180
181
  }
181
- exports.ConfigurationSchema = ConfigurationSchema;
182
182
  function ConfigurationReference(schemaType) {
183
183
  // we cast this to SCHEMATYPE, because the reference *should* behave just
184
184
  // like the object it points to. It won't be undefined (this is a
185
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  // `reference`, not a `safeReference`)
186
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  return mobx_state_tree_1.types.union(mobx_state_tree_1.types.reference(schemaType), schemaType);
187
187
  }
188
- exports.ConfigurationReference = ConfigurationReference;
@@ -1,5 +1,6 @@
1
1
  "use strict";
2
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  Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.default = ConfigSlot;
3
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  /* eslint-disable @typescript-eslint/no-explicit-any */
4
5
  const mobx_state_tree_1 = require("mobx-state-tree");
5
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  const jexlStrings_1 = require("../util/jexlStrings");
@@ -269,4 +270,3 @@ function ConfigSlot(slotName, { description = '', model, type, defaultValue, con
269
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  Object.defineProperty(m, 'isJBrowseConfigurationSlot', { value: true });
270
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  return m;
271
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  }
272
- exports.default = ConfigSlot;
@@ -31,4 +31,4 @@ export declare function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType: unk
31
31
  export declare function isBareConfigurationSchemaType(thing: unknown): thing is AnyConfigurationSchemaType;
32
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  export declare function isConfigurationSchemaType(thing: unknown): thing is AnyConfigurationSchemaType;
33
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  export declare function isConfigurationModel(thing: unknown): thing is AnyConfigurationModel;
34
- export declare function isConfigurationSlotType(thing: unknown): boolean;
34
+ export declare function isConfigurationSlotType(thing: unknown): thing is object & Record<"isJBrowseConfigurationSlot", unknown>;
@@ -1,6 +1,12 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.isConfigurationSlotType = exports.isConfigurationModel = exports.isConfigurationSchemaType = exports.isBareConfigurationSchemaType = exports.getTypeNamesFromExplicitlyTypedUnion = exports.getConf = exports.readConfObject = void 0;
3
+ exports.readConfObject = readConfObject;
4
+ exports.getConf = getConf;
5
+ exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
6
+ exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
7
+ exports.isConfigurationSchemaType = isConfigurationSchemaType;
8
+ exports.isConfigurationModel = isConfigurationModel;
9
+ exports.isConfigurationSlotType = isConfigurationSlotType;
4
10
  /* eslint-disable @typescript-eslint/no-explicit-any */
5
11
  const mobx_state_tree_1 = require("mobx-state-tree");
6
12
  const mst_reflection_1 = require("../util/mst-reflection");
@@ -63,7 +69,6 @@ function readConfObject(confObject, slotPath, args = {}) {
63
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  }
64
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  throw new TypeError('slotPath must be a string or array');
65
71
  }
66
- exports.readConfObject = readConfObject;
67
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  /**
68
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  * helper method for readConfObject, reads the config from a mst model
69
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  *
@@ -82,7 +87,6 @@ function getConf(model, slotPath, args) {
82
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  }
83
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  throw new TypeError('cannot getConf on this model, it has no configuration');
84
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  }
85
- exports.getConf = getConf;
86
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  /**
87
91
  * given a union of explicitly typed configuration schema types,
88
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  * extract an array of the type names contained in the union
@@ -114,7 +118,6 @@ function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
114
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  }
115
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  return [];
116
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  }
117
- exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
118
121
  function isBareConfigurationSchemaType(thing) {
119
122
  if ((0, mobx_state_tree_1.isType)(thing)) {
120
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  if ((0, mobx_state_tree_1.isModelType)(thing) &&
@@ -129,7 +132,6 @@ function isBareConfigurationSchemaType(thing) {
129
132
  }
130
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  return false;
131
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  }
132
- exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
133
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  function isConfigurationSchemaType(thing) {
134
136
  if (!(0, mobx_state_tree_1.isType)(thing)) {
135
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  return false;
@@ -155,14 +157,11 @@ function isConfigurationSchemaType(thing) {
155
157
  }
156
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  return false;
157
159
  }
158
- exports.isConfigurationSchemaType = isConfigurationSchemaType;
159
160
  function isConfigurationModel(thing) {
160
161
  return (0, mobx_state_tree_1.isStateTreeNode)(thing) && isConfigurationSchemaType((0, mobx_state_tree_1.getType)(thing));
161
162
  }
162
- exports.isConfigurationModel = isConfigurationModel;
163
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  function isConfigurationSlotType(thing) {
164
164
  return (typeof thing === 'object' &&
165
165
  thing !== null &&
166
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  'isJBrowseConfigurationSlot' in thing);
167
167
  }
168
- exports.isConfigurationSlotType = isConfigurationSlotType;
@@ -1,23 +1,22 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.isTextSearchAdapter = exports.isRefNameAliasAdapter = exports.isFeatureAdapter = exports.isRegionsAdapter = exports.isSequenceAdapter = void 0;
3
+ exports.isSequenceAdapter = isSequenceAdapter;
4
+ exports.isRegionsAdapter = isRegionsAdapter;
5
+ exports.isFeatureAdapter = isFeatureAdapter;
6
+ exports.isRefNameAliasAdapter = isRefNameAliasAdapter;
7
+ exports.isTextSearchAdapter = isTextSearchAdapter;
4
8
  function isSequenceAdapter(t) {
5
9
  return 'getRegions' in t && 'getFeatures' in t;
6
10
  }
7
- exports.isSequenceAdapter = isSequenceAdapter;
8
11
  function isRegionsAdapter(t) {
9
12
  return 'getRegions' in t;
10
13
  }
11
- exports.isRegionsAdapter = isRegionsAdapter;
12
14
  function isFeatureAdapter(t) {
13
15
  return 'getFeatures' in t;
14
16
  }
15
- exports.isFeatureAdapter = isFeatureAdapter;
16
17
  function isRefNameAliasAdapter(t) {
17
18
  return 'getRefNameAliases' in t;
18
19
  }
19
- exports.isRefNameAliasAdapter = isRefNameAliasAdapter;
20
20
  function isTextSearchAdapter(t) {
21
21
  return 'searchIndex' in t;
22
22
  }
23
- exports.isTextSearchAdapter = isTextSearchAdapter;
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  import { SimpleFeature } from '../../util';
3
2
  import { BaseAdapter } from '../BaseAdapter';
4
3
  export declare function isGzip(buf: Buffer): boolean;
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.isGzip = void 0;
3
+ exports.isGzip = isGzip;
4
4
  const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
5
5
  // locals
6
6
  const util_1 = require("../../util");
@@ -9,7 +9,6 @@ const BaseAdapter_1 = require("../BaseAdapter");
9
9
  function isGzip(buf) {
10
10
  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
11
11
  }
12
- exports.isGzip = isGzip;
13
12
  class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
14
13
  async getData() {
15
14
  const pm = this.pluginManager;
@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
26
26
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
27
  };
28
28
  Object.defineProperty(exports, "__esModule", { value: true });
29
+ exports.default = CytobandAdapterF;
29
30
  const pluggableElementTypes_1 = require("../../pluggableElementTypes");
30
31
  const configSchema_1 = __importDefault(require("./configSchema"));
31
32
  function CytobandAdapterF(pluginManager) {
@@ -35,4 +36,3 @@ function CytobandAdapterF(pluginManager) {
35
36
  getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CytobandAdapter'))).then(f => f.default),
36
37
  }));
37
38
  }
38
- exports.default = CytobandAdapterF;
@@ -3,12 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.clearAdapterCache = exports.freeAdapterResources = exports.getAdapter = exports.adapterConfigCacheKey = void 0;
6
+ exports.adapterConfigCacheKey = adapterConfigCacheKey;
7
+ exports.getAdapter = getAdapter;
8
+ exports.freeAdapterResources = freeAdapterResources;
9
+ exports.clearAdapterCache = clearAdapterCache;
7
10
  const idMaker_1 = __importDefault(require("../util/idMaker"));
8
11
  function adapterConfigCacheKey(conf = {}) {
9
12
  return `${(0, idMaker_1.default)(conf)}`;
10
13
  }
11
- exports.adapterConfigCacheKey = adapterConfigCacheKey;
12
14
  let adapterCache = {};
13
15
  /**
14
16
  * instantiate a data adapter, or return an already-instantiated one if we have one with the same
@@ -55,7 +57,6 @@ async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
55
57
  cacheEntry.sessionIds.add(sessionId);
56
58
  return cacheEntry;
57
59
  }
58
- exports.getAdapter = getAdapter;
59
60
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
60
61
  function freeAdapterResources(specification) {
61
62
  let deleteCount = 0;
@@ -91,8 +92,6 @@ function freeAdapterResources(specification) {
91
92
  }
92
93
  return deleteCount;
93
94
  }
94
- exports.freeAdapterResources = freeAdapterResources;
95
95
  function clearAdapterCache() {
96
96
  adapterCache = {};
97
97
  }
98
- exports.clearAdapterCache = clearAdapterCache;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/core",
3
- "version": "2.12.0",
3
+ "version": "2.12.2",
4
4
  "description": "JBrowse 2 core libraries used by plugins",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -32,6 +32,7 @@
32
32
  "dependencies": {
33
33
  "@babel/runtime": "^7.17.9",
34
34
  "@gmod/bgzf-filehandle": "^1.4.3",
35
+ "@gmod/http-range-fetcher": "^3.0.0",
35
36
  "@mui/icons-material": "^5.0.1",
36
37
  "@mui/x-data-grid": "^7.0.0",
37
38
  "@types/clone": "^2.0.0",
@@ -47,7 +48,6 @@
47
48
  "escape-html": "^1.0.3",
48
49
  "fast-deep-equal": "^3.1.3",
49
50
  "generic-filehandle": "^3.0.0",
50
- "http-range-fetcher": "^2.0.0",
51
51
  "is-object": "^1.0.1",
52
52
  "jexl": "^2.3.0",
53
53
  "librpc-web-mod": "^1.1.5",
@@ -74,5 +74,5 @@
74
74
  "access": "public",
75
75
  "directory": "dist"
76
76
  },
77
- "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
77
+ "gitHead": "1ec66736ce048a1637f52b7a7ef2eb02d956b771"
78
78
  }
@@ -20,9 +20,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
20
20
  type: string;
21
21
  defaultValue: string;
22
22
  description: string;
23
- }; /**
24
- * #property
25
- */
23
+ };
26
24
  assemblyNames: {
27
25
  type: string;
28
26
  defaultValue: never[];
@@ -49,8 +49,8 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
49
49
  error: unknown;
50
50
  message: string | undefined;
51
51
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
52
- onHorizontalScroll?: Function | undefined;
53
- blockState?: Record<string, any> | undefined;
52
+ onHorizontalScroll?: Function;
53
+ blockState?: Record<string, any>;
54
54
  }>;
55
55
  /**
56
56
  * #getter
@@ -108,7 +108,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
108
108
  * if a display-level message should be displayed instead,
109
109
  * make this return a react component
110
110
  */
111
- readonly DisplayMessageComponent: React.FC<any> | undefined;
111
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
112
112
  /**
113
113
  * #method
114
114
  */
@@ -5,7 +5,9 @@ import { MenuItem } from '../../ui';
5
5
  export declare function getCompatibleDisplays(self: IAnyStateTreeNode): ({
6
6
  [x: string]: any;
7
7
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
8
- setSubschema(slotName: string, data: unknown): any;
8
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
9
+ [x: string]: any;
10
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
9
11
  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>)[];
10
12
  /**
11
13
  * #stateModel BaseTrackModel
@@ -49,7 +51,9 @@ export declare function createBaseTrackModel(pm: PluginManager, trackType: strin
49
51
  readonly canConfigure: boolean | ({
50
52
  [x: string]: any;
51
53
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
52
- setSubschema(slotName: string, data: unknown): any;
54
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
55
+ [x: string]: any;
56
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
53
57
  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>) | undefined;
54
58
  } & {
55
59
  /**
@@ -1,6 +1,7 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.createBaseTrackModel = exports.getCompatibleDisplays = void 0;
3
+ exports.getCompatibleDisplays = getCompatibleDisplays;
4
+ exports.createBaseTrackModel = createBaseTrackModel;
4
5
  const mobx_1 = require("mobx");
5
6
  const mobx_state_tree_1 = require("mobx-state-tree");
6
7
  // locals
@@ -16,7 +17,6 @@ function getCompatibleDisplays(self) {
16
17
  const displays = self.configuration.displays;
17
18
  return displays.filter(d => compatTypes.has(d.type));
18
19
  }
19
- exports.getCompatibleDisplays = getCompatibleDisplays;
20
20
  /**
21
21
  * #stateModel BaseTrackModel
22
22
  * #category track
@@ -184,4 +184,3 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
184
184
  },
185
185
  }));
186
186
  }
187
- exports.createBaseTrackModel = createBaseTrackModel;
@@ -149,19 +149,19 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
149
149
  */
150
150
  addAuthHeaderToInit(init: RequestInit | undefined, token: string): {
151
151
  headers: Headers;
152
- body?: BodyInit | null | undefined;
153
- cache?: RequestCache | undefined;
154
- credentials?: RequestCredentials | undefined;
155
- integrity?: string | undefined;
156
- keepalive?: boolean | undefined;
157
- method?: string | undefined;
158
- mode?: RequestMode | undefined;
159
- priority?: RequestPriority | undefined;
160
- redirect?: RequestRedirect | undefined;
161
- referrer?: string | undefined;
162
- referrerPolicy?: ReferrerPolicy | undefined;
163
- signal?: AbortSignal | null | undefined;
164
- window?: null | undefined;
152
+ body?: BodyInit | null;
153
+ cache?: RequestCache;
154
+ credentials?: RequestCredentials;
155
+ integrity?: string;
156
+ keepalive?: boolean;
157
+ method?: string;
158
+ mode?: RequestMode;
159
+ priority?: RequestPriority;
160
+ redirect?: RequestRedirect;
161
+ referrer?: string;
162
+ referrerPolicy?: ReferrerPolicy;
163
+ signal?: AbortSignal | null;
164
+ window?: null;
165
165
  };
166
166
  /**
167
167
  * #action
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.createBaseTrackConfig = void 0;
3
+ exports.createBaseTrackConfig = createBaseTrackConfig;
4
4
  const mobx_state_tree_1 = require("mobx-state-tree");
5
5
  const configuration_1 = require("../../configuration");
6
6
  /**
@@ -176,4 +176,3 @@ function createBaseTrackConfig(pluginManager) {
176
176
  }),
177
177
  });
178
178
  }
179
- exports.createBaseTrackConfig = createBaseTrackConfig;
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.watchWorker = void 0;
3
+ exports.watchWorker = watchWorker;
4
4
  const mobx_state_tree_1 = require("mobx-state-tree");
5
5
  const util_1 = require("../util");
6
6
  const remoteAbortSignals_1 = require("./remoteAbortSignals");
@@ -21,7 +21,6 @@ async function watchWorker(worker, pingTime, rpcDriverClassName) {
21
21
  await new Promise(resolve => setTimeout(resolve, pingTime));
22
22
  }
23
23
  }
24
- exports.watchWorker = watchWorker;
25
24
  function detectHardwareConcurrency() {
26
25
  const mainThread = typeof window !== 'undefined';
27
26
  const canDetect = mainThread && 'hardwareConcurrency' in window.navigator;
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.validateRendererType = void 0;
3
+ exports.validateRendererType = validateRendererType;
4
4
  function validateRendererType(rendererType, RendererType) {
5
5
  if (!RendererType) {
6
6
  throw new Error(`renderer "${rendererType}" not found`);
@@ -11,4 +11,3 @@ function validateRendererType(rendererType, RendererType) {
11
11
  }
12
12
  return RendererType;
13
13
  }
14
- exports.validateRendererType = validateRendererType;
@@ -1,7 +1,11 @@
1
1
  "use strict";
2
2
  /* ---------------- for the RPC client ----------------- */
3
3
  Object.defineProperty(exports, "__esModule", { value: true });
4
- exports.remoteAbortRpcHandler = exports.remoteAbort = exports.deserializeAbortSignal = exports.isRemoteAbortSignal = exports.serializeAbortSignal = void 0;
4
+ exports.serializeAbortSignal = serializeAbortSignal;
5
+ exports.isRemoteAbortSignal = isRemoteAbortSignal;
6
+ exports.deserializeAbortSignal = deserializeAbortSignal;
7
+ exports.remoteAbort = remoteAbort;
8
+ exports.remoteAbortRpcHandler = remoteAbortRpcHandler;
5
9
  let abortSignalCounter = 0;
6
10
  const abortSignalIds = new WeakMap(); // map of abortsignal => numerical ID
7
11
  /**
@@ -27,7 +31,6 @@ function serializeAbortSignal(signal, callfunc) {
27
31
  }
28
32
  return { abortSignalId };
29
33
  }
30
- exports.serializeAbortSignal = serializeAbortSignal;
31
34
  /* ---------------- for the RPC server ----------------- */
32
35
  /**
33
36
  * test whether a given object
@@ -40,7 +43,6 @@ function isRemoteAbortSignal(thing) {
40
43
  'abortSignalId' in thing &&
41
44
  typeof thing.abortSignalId === 'number');
42
45
  }
43
- exports.isRemoteAbortSignal = isRemoteAbortSignal;
44
46
  // the server side keeps a set of surrogate abort controllers that can be
45
47
  // aborted based on ID
46
48
  const surrogateAbortControllers = new Map(); // numerical ID => surrogate abort controller
@@ -58,7 +60,6 @@ function deserializeAbortSignal({ abortSignalId, }) {
58
60
  }
59
61
  return surrogateAbortController.signal;
60
62
  }
61
- exports.deserializeAbortSignal = deserializeAbortSignal;
62
63
  /**
63
64
  * fire an abort signal from a remote abort signal ID
64
65
  *
@@ -71,10 +72,8 @@ function remoteAbort(props) {
71
72
  surrogateAbortController.abort();
72
73
  }
73
74
  }
74
- exports.remoteAbort = remoteAbort;
75
75
  function remoteAbortRpcHandler() {
76
76
  return {
77
77
  signalAbort: remoteAbort,
78
78
  };
79
79
  }
80
- exports.remoteAbortRpcHandler = remoteAbortRpcHandler;