@jbrowse/core 2.3.4 → 2.4.1

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Files changed (116) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +18 -19
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +76 -69
  3. package/BaseFeatureWidget/SequenceBox.js +9 -3
  4. package/BaseFeatureWidget/SequenceFeatureDetails.js +70 -52
  5. package/BaseFeatureWidget/SequencePanel.d.ts +3 -3
  6. package/BaseFeatureWidget/SequencePanel.js +8 -5
  7. package/BaseFeatureWidget/index.js +2 -2
  8. package/CorePlugin.js +2 -7
  9. package/PluginLoader.d.ts +1 -1
  10. package/PluginLoader.js +20 -24
  11. package/PluginManager.d.ts +1 -1
  12. package/PluginManager.js +2 -3
  13. package/ReExports/Attributes.d.ts +1 -2
  14. package/ReExports/Attributes.js +4 -3
  15. package/ReExports/BaseCard.d.ts +1 -2
  16. package/ReExports/BaseCard.js +4 -3
  17. package/ReExports/DataGrid.d.ts +1 -2
  18. package/ReExports/DataGrid.js +2 -2
  19. package/ReExports/FeatureDetails.d.ts +1 -2
  20. package/ReExports/FeatureDetails.js +4 -3
  21. package/ReExports/index.d.ts +1 -2
  22. package/ReExports/index.js +3 -2
  23. package/ReExports/modules.d.ts +1 -1
  24. package/ReExports/modules.js +2 -2
  25. package/assemblyManager/assembly.js +5 -5
  26. package/assemblyManager/assemblyConfigSchema.js +2 -2
  27. package/configuration/configurationSchema.js +1 -1
  28. package/configuration/util.js +1 -1
  29. package/data_adapters/BaseAdapter.js +1 -1
  30. package/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +8 -0
  31. package/data_adapters/CytobandAdapter/CytobandAdapter.js +40 -0
  32. package/data_adapters/CytobandAdapter/configSchema.d.ts +2 -0
  33. package/data_adapters/CytobandAdapter/configSchema.js +17 -0
  34. package/data_adapters/CytobandAdapter/index.d.ts +3 -0
  35. package/data_adapters/CytobandAdapter/index.js +37 -0
  36. package/data_adapters/dataAdapterCache.d.ts +3 -2
  37. package/data_adapters/dataAdapterCache.js +2 -3
  38. package/package.json +5 -4
  39. package/pluggableElementTypes/PluggableElementBase.d.ts +1 -1
  40. package/pluggableElementTypes/PluggableElementBase.js +1 -2
  41. package/pluggableElementTypes/RpcMethodType.d.ts +5 -8
  42. package/pluggableElementTypes/RpcMethodType.js +23 -34
  43. package/pluggableElementTypes/index.d.ts +11 -1
  44. package/pluggableElementTypes/index.js +23 -23
  45. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +2 -2
  46. package/pluggableElementTypes/models/BaseTrackModel.js +8 -13
  47. package/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +13 -2
  48. package/pluggableElementTypes/renderers/CircularChordRendererType.js +10 -2
  49. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.d.ts +8 -2
  50. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +10 -4
  51. package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +1 -1
  52. package/pluggableElementTypes/renderers/ServerSideRendererType.js +2 -34
  53. package/pluggableElementTypes/renderers/index.d.ts +7 -9
  54. package/pluggableElementTypes/renderers/index.js +15 -15
  55. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +1 -1
  56. package/rpc/BaseRpcDriver.js +7 -8
  57. package/rpc/WebWorkerRpcDriver.js +18 -12
  58. package/rpc/coreRpcMethods.d.ts +9 -11
  59. package/rpc/coreRpcMethods.js +17 -17
  60. package/rpc/methods/CoreGetFeatureDetails.js +1 -1
  61. package/rpc/methods/util.d.ts +2 -2
  62. package/rpc/methods/util.js +2 -2
  63. package/rpc/remoteAbortSignals.js +0 -1
  64. package/tsconfig.build.tsbuildinfo +1 -1
  65. package/ui/App.js +3 -18
  66. package/ui/AppLogo.js +1 -6
  67. package/ui/ColorPicker.js +1 -1
  68. package/ui/Dialog.js +1 -1
  69. package/ui/DrawerWidget.js +4 -4
  70. package/ui/EditableTypography.js +1 -1
  71. package/ui/FileSelector/FileSelector.d.ts +2 -2
  72. package/ui/FileSelector/FileSelector.js +24 -35
  73. package/ui/FileSelector/index.d.ts +1 -2
  74. package/ui/FileSelector/index.js +3 -2
  75. package/ui/LoadingEllipses.js +2 -2
  76. package/ui/Menu.js +45 -32
  77. package/ui/ResizeBar.js +10 -6
  78. package/ui/ResizeHandle.js +3 -6
  79. package/ui/SanitizedHTML.js +2 -0
  80. package/ui/ViewContainer.js +7 -44
  81. package/ui/ViewMenu.d.ts +9 -0
  82. package/ui/ViewMenu.js +69 -0
  83. package/ui/ViewPanel.d.ts +19 -0
  84. package/ui/ViewPanel.js +49 -0
  85. package/ui/theme.d.ts +10 -166
  86. package/ui/theme.js +260 -48
  87. package/util/Base1DUtils.js +16 -14
  88. package/util/Base1DViewModel.d.ts +1 -1
  89. package/util/Base1DViewModel.js +9 -8
  90. package/util/aborting.js +1 -1
  91. package/util/analytics.js +1 -1
  92. package/util/blockTypes.js +10 -10
  93. package/util/color/index.d.ts +1 -2
  94. package/util/color/index.js +4 -3
  95. package/util/idMaker.js +5 -8
  96. package/util/index.d.ts +9 -9
  97. package/util/index.js +35 -52
  98. package/util/io/RemoteFileWithRangeCache.js +2 -2
  99. package/util/io/index.d.ts +1 -2
  100. package/util/io/index.js +6 -6
  101. package/util/jexl.js +3 -1
  102. package/util/layouts/GranularRectLayout.js +10 -4
  103. package/util/layouts/MultiLayout.js +1 -1
  104. package/util/layouts/SceneGraph.js +3 -7
  105. package/util/map-obj.d.ts +3 -0
  106. package/util/map-obj.js +33 -0
  107. package/util/offscreenCanvasPonyfill.js +4 -3
  108. package/util/offscreenCanvasUtils.d.ts +18 -4
  109. package/util/offscreenCanvasUtils.js +49 -7
  110. package/util/tracks.d.ts +1 -1
  111. package/util/tracks.js +0 -1
  112. package/util/types/index.d.ts +1 -1
  113. package/util/types/index.js +3 -3
  114. package/util/types/mst.js +3 -3
  115. package/data_adapters/CytobandAdapter.d.ts +0 -8
  116. package/data_adapters/CytobandAdapter.js +0 -49
package/rpc/coreRpcMethods.js CHANGED
@@ -3,20 +3,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.CoreEstimateRegionStats = exports.CoreFreeResources = exports.CoreGetFeatureDetails = exports.CoreRender = exports.CoreGetFeatures = exports.CoreGetMetadata = exports.CoreGetFileInfo = exports.CoreGetRefNames = void 0;
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- const CoreGetRefNames_1 = __importDefault(require("./methods/CoreGetRefNames"));
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- exports.CoreGetRefNames = CoreGetRefNames_1.default;
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- const CoreGetMetadata_1 = __importDefault(require("./methods/CoreGetMetadata"));
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- exports.CoreGetMetadata = CoreGetMetadata_1.default;
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- const CoreGetFeatureDetails_1 = __importDefault(require("./methods/CoreGetFeatureDetails"));
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- exports.CoreGetFeatureDetails = CoreGetFeatureDetails_1.default;
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- const CoreGetFeatures_1 = __importDefault(require("./methods/CoreGetFeatures"));
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- exports.CoreGetFeatures = CoreGetFeatures_1.default;
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- const CoreGetFileInfo_1 = __importDefault(require("./methods/CoreGetFileInfo"));
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- exports.CoreGetFileInfo = CoreGetFileInfo_1.default;
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- const CoreFreeResources_1 = __importDefault(require("./methods/CoreFreeResources"));
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- exports.CoreFreeResources = CoreFreeResources_1.default;
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- const CoreRender_1 = __importDefault(require("./methods/CoreRender"));
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- exports.CoreRender = CoreRender_1.default;
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- const CoreEstimateRegionStats_1 = __importDefault(require("./methods/CoreEstimateRegionStats"));
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- exports.CoreEstimateRegionStats = CoreEstimateRegionStats_1.default;
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+ exports.CoreEstimateRegionStats = exports.CoreFreeResources = exports.CoreRender = exports.CoreGetFeatures = exports.CoreGetFileInfo = exports.CoreGetMetadata = exports.CoreGetFeatureDetails = exports.CoreGetRefNames = void 0;
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+ var CoreGetRefNames_1 = require("./methods/CoreGetRefNames");
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+ Object.defineProperty(exports, "CoreGetRefNames", { enumerable: true, get: function () { return __importDefault(CoreGetRefNames_1).default; } });
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+ var CoreGetFeatureDetails_1 = require("./methods/CoreGetFeatureDetails");
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+ Object.defineProperty(exports, "CoreGetFeatureDetails", { enumerable: true, get: function () { return __importDefault(CoreGetFeatureDetails_1).default; } });
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+ var CoreGetMetadata_1 = require("./methods/CoreGetMetadata");
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+ Object.defineProperty(exports, "CoreGetMetadata", { enumerable: true, get: function () { return __importDefault(CoreGetMetadata_1).default; } });
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+ var CoreGetFileInfo_1 = require("./methods/CoreGetFileInfo");
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+ Object.defineProperty(exports, "CoreGetFileInfo", { enumerable: true, get: function () { return __importDefault(CoreGetFileInfo_1).default; } });
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+ var CoreGetFeatures_1 = require("./methods/CoreGetFeatures");
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+ Object.defineProperty(exports, "CoreGetFeatures", { enumerable: true, get: function () { return __importDefault(CoreGetFeatures_1).default; } });
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+ var CoreRender_1 = require("./methods/CoreRender");
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+ Object.defineProperty(exports, "CoreRender", { enumerable: true, get: function () { return __importDefault(CoreRender_1).default; } });
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+ var CoreFreeResources_1 = require("./methods/CoreFreeResources");
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+ Object.defineProperty(exports, "CoreFreeResources", { enumerable: true, get: function () { return __importDefault(CoreFreeResources_1).default; } });
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+ var CoreEstimateRegionStats_1 = require("./methods/CoreEstimateRegionStats");
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+ Object.defineProperty(exports, "CoreEstimateRegionStats", { enumerable: true, get: function () { return __importDefault(CoreEstimateRegionStats_1).default; } });
package/rpc/methods/CoreGetFeatureDetails.js CHANGED
@@ -34,7 +34,7 @@ class CoreGetFeatureDetails extends RpcMethodType_1.default {
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  }
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  const { rendererType, featureId } = deserializedArgs;
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  const RendererType = (0, util_2.validateRendererType)(rendererType, this.pluginManager.getRendererType(rendererType));
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- // @ts-ignore
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+ // @ts-expect-error
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  const sess = RendererType.sessions[(0, util_1.getLayoutId)(args)];
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  const { layout } = sess.cachedLayout;
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  const xref = layout.getDataByID(featureId);
package/rpc/methods/util.d.ts CHANGED
@@ -1,4 +1,4 @@
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- import ServerSideRendererType, { RenderArgs as ServerSideRenderArgs, RenderArgsSerialized as ServerSideRenderArgsSerialized, RenderResults, ResultsSerialized } from '../../pluggableElementTypes/renderers/ServerSideRendererType';
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+ import ServerSideRendererType, { RenderArgs as ServerSideRenderArgs, RenderArgsSerialized as ServerSideRenderArgsSerialized } from '../../pluggableElementTypes/renderers/ServerSideRendererType';
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  import { Region } from '../../util';
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  export interface RenderArgs extends ServerSideRenderArgs {
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  adapterConfig: {};
@@ -10,5 +10,5 @@ export interface RenderArgsSerialized extends ServerSideRenderArgsSerialized {
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  adapterConfig: {};
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  rendererType: string;
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  }
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- export type { RenderResults, ResultsSerialized };
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  export declare function validateRendererType<T>(rendererType: string, RendererType: T): T & ServerSideRendererType;
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+ export { type RenderResults, type ResultsSerialized, } from '../../pluggableElementTypes/renderers/ServerSideRendererType';
package/rpc/methods/util.js CHANGED
@@ -9,12 +9,12 @@ function validateRendererType(rendererType, RendererType) {
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  if (!RendererType) {
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  throw new Error(`renderer "${rendererType}" not found`);
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  }
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- // @ts-ignore
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+ // @ts-expect-error
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  if (!RendererType.ReactComponent) {
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  throw new Error(`renderer ${rendererType} has no ReactComponent, it may not be completely implemented yet`);
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  }
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  if (!(RendererType instanceof ServerSideRendererType_1.default)) {
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- throw new Error('CoreRender requires a renderer that is a subclass of ServerSideRendererType');
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+ throw new TypeError('CoreRender requires a renderer that is a subclass of ServerSideRendererType');
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  }
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  return RendererType;
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  }
package/rpc/remoteAbortSignals.js CHANGED
@@ -38,7 +38,6 @@ function isRemoteAbortSignal(thing) {
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  return (typeof thing === 'object' &&
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  thing !== null &&
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  'abortSignalId' in thing &&
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- // @ts-ignore
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  typeof thing.abortSignalId === 'number');
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  }
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  exports.isRemoteAbortSignal = isRemoteAbortSignal;