@jbrowse/core 2.12.0 → 2.12.1

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 (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 +2 -2
  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 +2 -2
  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
@@ -3,6 +3,7 @@ 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.default = ArrayValue;
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  const react_1 = __importDefault(require("react"));
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  const is_object_1 = __importDefault(require("is-object"));
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  const mui_1 = require("tss-react/mui");
@@ -41,4 +42,3 @@ function ArrayValue({ name, value, description, prefix = [], }) {
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  react_1.default.createElement(BasicValue_1.default, { value: val }))))));
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  }
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  }
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- exports.default = ArrayValue;
@@ -3,6 +3,7 @@ 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.default = Attributes;
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  const react_1 = __importDefault(require("react"));
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  const is_object_1 = __importDefault(require("is-object"));
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  // locals
@@ -49,4 +50,3 @@ function Attributes(props) {
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  }
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  })));
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  }
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- exports.default = Attributes;
@@ -3,6 +3,7 @@ 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.default = BasicValue;
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  const react_1 = __importDefault(require("react"));
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  const mui_1 = require("tss-react/mui");
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  const is_object_1 = __importDefault(require("is-object"));
@@ -23,4 +24,3 @@ function BasicValue({ value }) {
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  const isLink = `${value}`.match(/^https?:\/\//);
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  return (react_1.default.createElement("div", { className: classes.fieldValue }, react_1.default.isValidElement(value) ? (value) : isLink ? (react_1.default.createElement(material_1.Link, { href: `${value}` }, `${value}`)) : (react_1.default.createElement(ui_1.SanitizedHTML, { html: (0, is_object_1.default)(value) ? JSON.stringify(value) : String(value) }))));
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  }
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- exports.default = BasicValue;
@@ -26,6 +26,7 @@ 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.default = DataGridDetails;
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  const react_1 = __importStar(require("react"));
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  const mui_1 = require("tss-react/mui");
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  const x_data_grid_1 = require("@mui/x-data-grid");
@@ -96,4 +97,3 @@ function DataGridDetails({ value, prefix, name, }) {
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  }
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  return null;
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  }
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- exports.default = DataGridDetails;
@@ -3,6 +3,7 @@ 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.default = FieldName;
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  const react_1 = __importDefault(require("react"));
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  const material_1 = require("@mui/material");
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  const mui_1 = require("tss-react/mui");
@@ -28,4 +29,3 @@ function FieldName({ description, name, width, prefix = [], }) {
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  return description ? (react_1.default.createElement(material_1.Tooltip, { title: description, placement: "left" },
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  react_1.default.createElement("div", { className: cx(classes.fieldDescription, classes.fieldName) }, val))) : (react_1.default.createElement("div", { className: classes.fieldName, style: { width: width } }, val));
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  }
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- exports.default = FieldName;
@@ -3,6 +3,7 @@ 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.default = SimpleField;
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  const react_1 = __importDefault(require("react"));
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  const mui_1 = require("tss-react/mui");
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  const FieldName_1 = __importDefault(require("./FieldName"));
@@ -19,4 +20,3 @@ function SimpleField({ name, value, description, prefix, width, }) {
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  react_1.default.createElement(FieldName_1.default, { prefix: prefix, description: description, name: name, width: width }),
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  react_1.default.createElement(BasicValue_1.default, { value: value }))) : null;
21
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  }
22
- exports.default = SimpleField;
@@ -3,6 +3,7 @@ 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.default = UriField;
6
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  const react_1 = __importDefault(require("react"));
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  const FieldName_1 = __importDefault(require("./FieldName"));
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  const mui_1 = require("tss-react/mui");
@@ -27,4 +28,3 @@ function UriField({ value, prefix, name, }) {
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  react_1.default.createElement(FieldName_1.default, { prefix: prefix, name: name }),
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  react_1.default.createElement(BasicValue_1.default, { value: href })));
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  }
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- exports.default = UriField;
@@ -26,7 +26,9 @@ 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 });
29
- exports.Attributes = exports.FeatureDetails = exports.BaseAttributes = exports.BaseCoreDetails = exports.BaseCard = void 0;
29
+ exports.Attributes = exports.BaseAttributes = exports.BaseCoreDetails = void 0;
30
+ exports.BaseCard = BaseCard;
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+ exports.FeatureDetails = FeatureDetails;
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  /* eslint-disable @typescript-eslint/no-explicit-any */
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  const react_1 = __importStar(require("react"));
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  const react_error_boundary_1 = require("react-error-boundary");
@@ -72,7 +74,6 @@ function BaseCard({ children, title, defaultExpanded = true, }) {
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  react_1.default.createElement(material_1.Typography, { variant: "button" }, title)),
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  react_1.default.createElement(material_1.AccordionDetails, { className: classes.expansionPanelDetails }, children)));
74
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  }
75
- exports.BaseCard = BaseCard;
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  function Position(props) {
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  const { feature } = props;
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  const strand = feature.strand;
@@ -158,7 +159,6 @@ function FeatureDetails(props) {
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  react_1.default.createElement(ExtraPanel.Component, { ...props })))) : null,
159
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  depth < maxDepth && (subfeatures === null || subfeatures === void 0 ? void 0 : subfeatures.length) ? (react_1.default.createElement(BaseCard, { title: "Subfeatures", defaultExpanded: depth < 1 }, subfeatures.map((sub, idx) => (react_1.default.createElement(FeatureDetails, { key: JSON.stringify(sub), feature: { ...sub, uniqueId: `${uniqueId}_${idx}` }, model: model, depth: depth + 1 }))))) : null));
160
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  }
161
- exports.FeatureDetails = FeatureDetails;
162
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  const BaseFeatureDetail = (0, mobx_react_1.observer)(function ({ model }) {
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  const { error, featureData } = model;
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  if (error) {
@@ -3,24 +3,24 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.accessNested = exports.generateMaxWidth = exports.generateTitle = exports.isEmpty = void 0;
6
+ exports.isEmpty = isEmpty;
7
+ exports.generateTitle = generateTitle;
8
+ exports.generateMaxWidth = generateMaxWidth;
9
+ exports.accessNested = accessNested;
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  const is_object_1 = __importDefault(require("is-object"));
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  const util_1 = require("../../util");
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  const util_2 = require("../util");
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  function isEmpty(obj) {
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  return Object.keys(obj).length === 0;
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  }
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- exports.isEmpty = isEmpty;
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  function generateTitle(name, id, type) {
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  return [(0, util_2.ellipses)(`${name}` || `${id}`), `${type}`]
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  .filter(f => !!f)
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  .join(' - ');
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  }
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- exports.generateTitle = generateTitle;
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  function generateMaxWidth(array, prefix) {
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  return (Math.ceil((0, util_1.max)(array.map(key => (0, util_1.measureText)([...prefix, key[0]].join('.'), 12)))) + 10);
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  }
23
- exports.generateMaxWidth = generateMaxWidth;
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  // pick using a path from an object, similar to _.get from lodash with special
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  // logic for Descriptions from e.g. VCF headers
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  //
@@ -39,4 +39,3 @@ function accessNested(arr, obj = {}) {
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  ? obj2.Description
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  : undefined;
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  }
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- exports.accessNested = accessNested;
@@ -3,6 +3,7 @@ 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.default = HelpDialog;
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  const react_1 = __importDefault(require("react"));
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  const material_1 = require("@mui/material");
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  const ui_1 = require("@jbrowse/core/ui");
@@ -29,4 +30,3 @@ function HelpDialog({ handleClose, }) {
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  react_1.default.createElement(material_1.DialogActions, null,
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  react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), autoFocus: true, variant: "contained" }, "Close"))));
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  }
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- exports.default = HelpDialog;
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.useFeatureSequence = void 0;
3
+ exports.useFeatureSequence = useFeatureSequence;
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  const react_1 = require("react");
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  const util_1 = require("../../util");
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  const configuration_1 = require("../../configuration");
@@ -64,4 +64,3 @@ function useFeatureSequence(model, feature, upDownBp, forceLoad) {
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  }, [feature, model, upDownBp, forceLoad]);
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  return { sequence, error };
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  }
67
- exports.useFeatureSequence = useFeatureSequence;
@@ -28,7 +28,7 @@ export declare function SequenceFeatureDetailsF(): import("mobx-state-tree").IMo
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  /**
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  * #action
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  */
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- setShowCoordinates(f: 'none' | 'relative' | 'genomic'): void;
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+ setShowCoordinates(f: "none" | "relative" | "genomic"): void;
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  /**
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  * #action
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  */
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.SequenceFeatureDetailsF = void 0;
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+ exports.SequenceFeatureDetailsF = SequenceFeatureDetailsF;
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const mobx_1 = require("mobx");
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  // locals
@@ -111,4 +111,3 @@ function SequenceFeatureDetailsF() {
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  },
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  }));
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  }
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- exports.SequenceFeatureDetailsF = SequenceFeatureDetailsF;
@@ -1,6 +1,7 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.splitString = exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
3
+ exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
4
+ exports.splitString = splitString;
4
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  // note that these are currently put into the style section instead of being
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  // defined in classes to aid copy and paste to an external document e.g. word
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  exports.intronColor = undefined;
@@ -50,4 +51,3 @@ function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0
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  charactersPerRow,
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  };
52
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  }
53
- exports.splitString = splitString;
@@ -62,9 +62,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  } & {
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  setFeature(f: import("../util").SimpleFeatureSerialized): void;
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  setUpDownBp(f: number): void;
65
- setIntronBp(f: number): void; /**
66
- * #property
67
- */
65
+ setIntronBp(f: number): void;
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  setUpperCaseCDS(f: boolean): void;
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  setShowCoordinates(f: "none" | "relative" | "genomic"): void;
70
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  setMode(mode: string): void;
@@ -157,9 +155,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  } & {
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  setFeature(f: import("../util").SimpleFeatureSerialized): void;
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  setUpDownBp(f: number): void;
160
- setIntronBp(f: number): void; /**
161
- * #property
162
- */
158
+ setIntronBp(f: number): void;
163
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  setUpperCaseCDS(f: boolean): void;
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  setShowCoordinates(f: "none" | "relative" | "genomic"): void;
165
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  setMode(mode: string): void;
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
4
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.stateModelFactory = void 0;
6
+ exports.stateModelFactory = stateModelFactory;
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  const mobx_state_tree_1 = require("mobx-state-tree");
8
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  const mobx_1 = require("mobx");
9
9
  const clone_1 = __importDefault(require("clone"));
@@ -170,4 +170,3 @@ function stateModelFactory(pluginManager) {
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  };
171
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  });
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  }
173
- exports.stateModelFactory = stateModelFactory;
@@ -25,16 +25,16 @@ export declare function dedupe(list: Feat[]): Feat[];
25
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  export declare function revlist(list: Feat[], seqlen: number): {
26
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  start: number;
27
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  end: number;
28
- type?: string | undefined;
29
- name?: string | undefined;
30
- id?: string | undefined;
28
+ type?: string;
29
+ name?: string;
30
+ id?: string;
31
31
  }[];
32
32
  export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
33
33
  type: string;
34
34
  start: number;
35
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  end: number;
36
- name?: string | undefined;
37
- id?: string | undefined;
36
+ name?: string;
37
+ id?: string;
38
38
  }[];
39
39
  export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
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  type: string;
@@ -1,10 +1,14 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.ellipses = exports.calculateUTRs2 = exports.calculateUTRs = exports.revlist = exports.dedupe = exports.stitch = void 0;
3
+ exports.stitch = stitch;
4
+ exports.dedupe = dedupe;
5
+ exports.revlist = revlist;
6
+ exports.calculateUTRs = calculateUTRs;
7
+ exports.calculateUTRs2 = calculateUTRs2;
8
+ exports.ellipses = ellipses;
4
9
  function stitch(subfeats, sequence) {
5
10
  return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
6
11
  }
7
- exports.stitch = stitch;
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  // filter items if they have the same "ID" or location
9
13
  function getItemId(feat) {
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14
  return `${feat.start}-${feat.end}`;
@@ -13,7 +17,6 @@ function getItemId(feat) {
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17
  function dedupe(list) {
14
18
  return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
15
19
  }
16
- exports.dedupe = dedupe;
17
20
  function revlist(list, seqlen) {
18
21
  return list
19
22
  .map(sub => ({
@@ -23,7 +26,6 @@ function revlist(list, seqlen) {
23
26
  }))
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  .sort((a, b) => a.start - b.start);
25
28
  }
26
- exports.revlist = revlist;
27
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  function calculateUTRs(cds, exons) {
28
30
  // checking length ensures the .at below are valid
29
31
  if (!cds.length) {
@@ -45,7 +47,6 @@ function calculateUTRs(cds, exons) {
45
47
  ].map(elt => ({ ...elt, type: 'three_prime_UTR' }));
46
48
  return [...fiveUTRs, ...threeUTRs];
47
49
  }
48
- exports.calculateUTRs = calculateUTRs;
49
50
  // calculates UTRs using impliedUTRs logic, but there are no exon subfeatures
50
51
  function calculateUTRs2(cds, parentFeat) {
51
52
  if (!cds.length) {
@@ -60,8 +61,6 @@ function calculateUTRs2(cds, parentFeat) {
60
61
  }));
61
62
  return [...fiveUTRs, ...threeUTRs];
62
63
  }
63
- exports.calculateUTRs2 = calculateUTRs2;
64
64
  function ellipses(slug) {
65
65
  return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;
66
66
  }
67
- exports.ellipses = ellipses;
package/PluginLoader.js CHANGED
@@ -3,7 +3,10 @@ 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.pluginDescriptionString = exports.isCJSPluginDefinition = exports.isESMPluginDefinition = exports.isUMDPluginDefinition = void 0;
6
+ exports.isUMDPluginDefinition = isUMDPluginDefinition;
7
+ exports.isESMPluginDefinition = isESMPluginDefinition;
8
+ exports.isCJSPluginDefinition = isCJSPluginDefinition;
9
+ exports.pluginDescriptionString = pluginDescriptionString;
7
10
  const load_script_1 = __importDefault(require("load-script"));
8
11
  // locals
9
12
  const Plugin_1 = __importDefault(require("./Plugin"));
@@ -15,12 +18,10 @@ function isUMDPluginDefinition(def) {
15
18
  def.umdLoc !== undefined) &&
16
19
  def.name !== undefined);
17
20
  }
18
- exports.isUMDPluginDefinition = isUMDPluginDefinition;
19
21
  function isESMPluginDefinition(def) {
20
22
  return (def.esmUrl !== undefined ||
21
23
  def.esmLoc !== undefined);
22
24
  }
23
- exports.isESMPluginDefinition = isESMPluginDefinition;
24
25
  function promisifiedLoadScript(src) {
25
26
  return new Promise((resolve, reject) => {
26
27
  (0, load_script_1.default)(src, (err, script) => {
@@ -48,7 +49,6 @@ async function loadScript(scriptUrl) {
48
49
  function isCJSPluginDefinition(def) {
49
50
  return def.cjsUrl !== undefined;
50
51
  }
51
- exports.isCJSPluginDefinition = isCJSPluginDefinition;
52
52
  function pluginDescriptionString(pluginDefinition) {
53
53
  var _a;
54
54
  if (isUMDPluginDefinition(pluginDefinition)) {
@@ -63,7 +63,6 @@ function pluginDescriptionString(pluginDefinition) {
63
63
  }
64
64
  return 'unknown plugin';
65
65
  }
66
- exports.pluginDescriptionString = pluginDescriptionString;
67
66
  function isInWebWorker() {
68
67
  return Boolean('WorkerGlobalScope' in globalThis);
69
68
  }
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { IAnyType, IAnyModelType } from 'mobx-state-tree';
3
2
  import PluggableElementBase from './pluggableElementTypes/PluggableElementBase';
4
3
  import RendererType from './pluggableElementTypes/renderers/RendererType';
@@ -71,8 +70,8 @@ export default class PluginManager {
71
70
  [key: string]: (value: any, ...args: any[]) => any;
72
71
  }) => void;
73
72
  getFunction: (name: string) => (value: any, ...args: any[]) => any;
74
- eval: (expression: string, context?: import("jexl/Expression").Context | undefined) => Promise<any>;
75
- evalSync: (expression: string, context?: import("jexl/Expression").Context | undefined) => any;
73
+ eval: (expression: string, context?: import("jexl/Expression").Context) => Promise<any>;
74
+ evalSync: (expression: string, context?: import("jexl/Expression").Context) => any;
76
75
  compile: (expression: string) => import("jexl/Expression").default;
77
76
  createExpression: (expression: string) => import("jexl/Expression").default;
78
77
  removeOp: (operator: string) => void;
@@ -157,7 +156,7 @@ export default class PluginManager {
157
156
  interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
158
157
  minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
159
158
  }, {
160
- features: import("./util").Feature[] | undefined;
159
+ features: undefined | import("./util").Feature[];
161
160
  volatileWidth: number;
162
161
  } & {
163
162
  setDisplayedRegions(regions: import("./util").Region[]): void;
@@ -184,12 +183,12 @@ export default class PluginManager {
184
183
  offset: number;
185
184
  start: number;
186
185
  end: number;
187
- reversed?: boolean | undefined;
186
+ reversed?: boolean;
188
187
  };
189
188
  bpToPx({ refName, coord, regionNumber, }: {
190
189
  refName: string;
191
190
  coord: number;
192
- regionNumber?: number | undefined;
191
+ regionNumber?: number;
193
192
  }): number | undefined;
194
193
  } & {
195
194
  setFeatures(features: import("./util").Feature[]): void;
@@ -201,7 +200,7 @@ export default class PluginManager {
201
200
  centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
202
201
  scroll(distance: number): number;
203
202
  } & {
204
- moveTo(start?: import("./util/Base1DUtils").BpOffset | undefined, end?: import("./util/Base1DUtils").BpOffset | undefined): void;
203
+ moveTo(start?: import("./util/Base1DUtils").BpOffset, end?: import("./util/Base1DUtils").BpOffset): void;
205
204
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
206
205
  '@jbrowse/core/util/io': typeof import("./util/io");
207
206
  '@jbrowse/core/util/mst-reflection': typeof import("./util/mst-reflection");
@@ -65,7 +65,7 @@ declare const libs: {
65
65
  interRegionPaddingWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
66
66
  minimumBlockWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
67
67
  }, {
68
- features: coreUtil.Feature[] | undefined;
68
+ features: undefined | coreUtil.Feature[];
69
69
  volatileWidth: number;
70
70
  } & {
71
71
  setDisplayedRegions(regions: coreUtil.Region[]): void;
@@ -92,12 +92,12 @@ declare const libs: {
92
92
  offset: number;
93
93
  start: number;
94
94
  end: number;
95
- reversed?: boolean | undefined;
95
+ reversed?: boolean;
96
96
  };
97
97
  bpToPx({ refName, coord, regionNumber, }: {
98
98
  refName: string;
99
99
  coord: number;
100
- regionNumber?: number | undefined;
100
+ regionNumber?: number;
101
101
  }): number | undefined;
102
102
  } & {
103
103
  setFeatures(features: coreUtil.Feature[]): void;
@@ -109,7 +109,7 @@ declare const libs: {
109
109
  centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
110
110
  scroll(distance: number): number;
111
111
  } & {
112
- moveTo(start?: import("../util/Base1DUtils").BpOffset | undefined, end?: import("../util/Base1DUtils").BpOffset | undefined): void;
112
+ moveTo(start?: import("../util/Base1DUtils").BpOffset, end?: import("../util/Base1DUtils").BpOffset): void;
113
113
  }, mst._NotCustomized, mst._NotCustomized>;
114
114
  '@jbrowse/core/util/io': typeof coreIo;
115
115
  '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;
@@ -137,12 +137,12 @@ declare const libs: {
137
137
  makeStyles: <Params = void, RuleNameSubsetReferencableInNestedSelectors extends string = never>(params?: {
138
138
  name?: string | Record<string, unknown> | undefined;
139
139
  uniqId?: string | undefined;
140
- } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, muiStyleOverridesParams?: {
140
+ } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material/styles").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, muiStyleOverridesParams?: {
141
141
  props: Record<string, unknown>;
142
142
  ownerState?: Record<string, unknown> | undefined;
143
143
  } | undefined) => {
144
144
  classes: Record<RuleName, string>;
145
- theme: MUIStyles.Theme;
145
+ theme: import("@mui/material/styles").Theme;
146
146
  css: import("tss-react").Css;
147
147
  cx: import("tss-react").Cx;
148
148
  };
@@ -16,13 +16,17 @@ export default class TextSearchManager {
16
16
  relevantAdapters(searchScope: SearchScope): ({
17
17
  [x: string]: any;
18
18
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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 & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
20
22
  } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
21
23
  getAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): AnyConfigurationModel[];
22
24
  getTrackAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): ({
23
25
  [x: string]: any;
24
26
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
25
- setSubschema(slotName: string, data: unknown): any;
27
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
28
+ [x: string]: any;
29
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
26
30
  } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
27
31
  /**
28
32
  * Returns list of relevant results given a search query and options
@@ -3,6 +3,7 @@ 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.default = assemblyFactory;
6
7
  const mobx_state_tree_1 = require("mobx-state-tree");
7
8
  const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
8
9
  // locals
@@ -375,7 +376,6 @@ function assemblyFactory(assemblyConfigType, pm) {
375
376
  },
376
377
  }));
377
378
  }
378
- exports.default = assemblyFactory;
379
379
  async function getRefNameAliases(config, pm, signal) {
380
380
  const type = pm.getAdapterType(config.type);
381
381
  const CLASS = await type.getAdapterClass();