@jbrowse/core 1.5.9 → 1.6.3
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.
- package/BaseFeatureWidget/BaseFeatureDetail.js +91 -78
- package/BaseFeatureWidget/SequenceFeatureDetails.js +64 -56
- package/BaseFeatureWidget/SequenceFeatureDetails.test.js +9 -9
- package/BaseFeatureWidget/index.js +1 -1
- package/BaseFeatureWidget/index.test.js +4 -4
- package/BaseFeatureWidget/util.js +13 -9
- package/CorePlugin.js +32 -20
- package/Plugin.js +13 -11
- package/PluginLoader.js +37 -32
- package/PluginManager.d.ts +8 -5
- package/PluginManager.js +142 -53
- package/ReExports/index.js +4 -4
- package/ReExports/list.js +2 -2
- package/ReExports/material-ui-colors.js +20 -20
- package/ReExports/modules.d.ts +7 -5
- package/ReExports/modules.js +51 -47
- package/TextSearch/BaseResults.js +34 -24
- package/TextSearch/BaseResults.test.js +7 -3
- package/TextSearch/TextSearchManager.js +16 -14
- package/assemblyManager/assembly.js +38 -33
- package/assemblyManager/assemblyConfigSchema.js +2 -2
- package/assemblyManager/assemblyManager.js +19 -15
- package/assemblyManager/index.js +3 -3
- package/babel.config.d.ts +15 -0
- package/babel.config.js +19 -0
- package/configuration/configurationSchema.js +19 -17
- package/configuration/configurationSlot.js +11 -11
- package/configuration/configurationSlot.test.js +5 -5
- package/configuration/index.d.ts +1 -0
- package/configuration/util.js +5 -5
- package/data_adapters/BaseAdapter.d.ts +15 -3
- package/data_adapters/BaseAdapter.js +215 -61
- package/data_adapters/BaseAdapter.test.js +29 -23
- package/data_adapters/CytobandAdapter.d.ts +1 -1
- package/data_adapters/CytobandAdapter.js +24 -18
- package/data_adapters/dataAdapterCache.js +8 -8
- package/package.json +3 -3
- package/pluggableElementTypes/AdapterType.js +30 -21
- package/pluggableElementTypes/ConnectionType.js +28 -18
- package/pluggableElementTypes/DisplayType.js +27 -17
- package/pluggableElementTypes/InternetAccountType.js +24 -14
- package/pluggableElementTypes/PluggableElementBase.js +10 -8
- package/pluggableElementTypes/RpcMethodType.d.ts +1 -1
- package/pluggableElementTypes/RpcMethodType.js +140 -117
- package/pluggableElementTypes/RpcMethodType.test.js +22 -16
- package/pluggableElementTypes/TextSearchAdapterType.js +25 -15
- package/pluggableElementTypes/TrackType.js +25 -15
- package/pluggableElementTypes/ViewType.js +25 -15
- package/pluggableElementTypes/WidgetType.js +27 -17
- package/pluggableElementTypes/index.js +11 -11
- package/pluggableElementTypes/models/BaseConnectionModelFactory.js +5 -5
- package/pluggableElementTypes/models/BaseDisplayModel.js +8 -5
- package/pluggableElementTypes/models/BaseTrackModel.js +11 -8
- package/pluggableElementTypes/models/BaseViewModel.js +3 -3
- package/pluggableElementTypes/models/InternetAccountModel.d.ts +1 -1
- package/pluggableElementTypes/models/InternetAccountModel.js +4 -4
- package/pluggableElementTypes/models/baseConnectionConfig.js +2 -2
- package/pluggableElementTypes/models/baseTrackConfig.js +7 -4
- package/pluggableElementTypes/models/index.js +4 -4
- package/pluggableElementTypes/renderers/BoxRendererType.js +48 -38
- package/pluggableElementTypes/renderers/CircularChordRendererType.js +18 -12
- package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +34 -26
- package/pluggableElementTypes/renderers/FeatureRendererType.js +45 -35
- package/pluggableElementTypes/renderers/RendererType.js +30 -20
- package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +12 -8
- package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +1 -1
- package/pluggableElementTypes/renderers/ServerSideRendererType.js +44 -32
- package/pluggableElementTypes/renderers/index.js +8 -8
- package/pluggableElementTypes/renderers/util/serializableFilterChain.js +10 -8
- package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +2 -2
- package/rpc/BaseRpcDriver.js +42 -37
- package/rpc/BaseRpcDriver.test.js +62 -48
- package/rpc/MainThreadRpcDriver.js +31 -21
- package/rpc/RpcManager.js +18 -16
- package/rpc/WebWorkerRpcDriver.js +37 -27
- package/rpc/configSchema.js +2 -2
- package/rpc/coreRpcMethods.d.ts +16 -0
- package/rpc/coreRpcMethods.js +247 -120
- package/rpc/remoteAbortSignals.js +3 -3
- package/ui/AboutDialog.js +20 -16
- package/ui/App.js +42 -38
- package/ui/AssemblySelector.d.ts +1 -1
- package/ui/AssemblySelector.js +6 -6
- package/ui/Drawer.js +7 -7
- package/ui/DrawerWidget.d.ts +1 -1
- package/ui/DrawerWidget.js +37 -33
- package/ui/DropDownMenu.js +21 -9
- package/ui/EditableTypography.js +30 -19
- package/ui/ErrorMessage.js +5 -5
- package/ui/FactoryResetDialog.js +8 -8
- package/ui/FatalErrorDialog.js +29 -12
- package/ui/FatalErrorDialog.test.js +10 -10
- package/ui/FileSelector/FileSelector.js +42 -32
- package/ui/FileSelector/LocalFileChooser.js +9 -9
- package/ui/FileSelector/UrlChooser.js +4 -4
- package/ui/FileSelector/index.js +4 -4
- package/ui/Icons.js +9 -9
- package/ui/Logo.js +19 -19
- package/ui/Menu.js +46 -35
- package/ui/NewSessionCards.js +29 -19
- package/ui/PrerenderedCanvas.js +27 -10
- package/ui/ResizeHandle.js +17 -10
- package/ui/SanitizedHTML.js +5 -5
- package/ui/SanitizedHTML.test.js +4 -4
- package/ui/Snackbar.js +16 -12
- package/ui/SnackbarModel.js +1 -1
- package/ui/Tooltip.js +11 -7
- package/ui/ViewContainer.d.ts +2 -5
- package/ui/ViewContainer.js +44 -49
- package/ui/index.d.ts +1 -0
- package/ui/index.js +26 -13
- package/ui/theme.js +15 -11
- package/util/Base1DViewModel.d.ts +14 -12
- package/util/Base1DViewModel.js +51 -55
- package/util/Base1DViewModel.test.js +5 -5
- package/util/QuickLRU.js +30 -26
- package/util/aborting.js +25 -15
- package/util/analytics.d.ts +1 -0
- package/util/analytics.js +14 -6
- package/util/blockTypes.js +48 -36
- package/util/calculateDynamicBlocks.js +4 -4
- package/util/calculateDynamicBlocks.test.js +14 -10
- package/util/calculateStaticBlocks.js +1 -1
- package/util/calculateStaticBlocks.test.js +15 -15
- package/util/compositeMap.js +30 -26
- package/util/idMaker.js +4 -4
- package/util/index.d.ts +23 -1
- package/util/index.js +135 -41
- package/util/index.test.js +11 -7
- package/util/io/RemoteFileWithRangeCache.js +40 -28
- package/util/io/index.js +5 -5
- package/util/jexl.js +5 -5
- package/util/jexlStrings.js +2 -2
- package/util/jexlStrings.test.js +2 -2
- package/util/layouts/GranularRectLayout.js +33 -27
- package/util/layouts/GranularRectLayout.test.js +10 -10
- package/util/layouts/MultiLayout.js +19 -13
- package/util/layouts/PrecomputedLayout.js +16 -14
- package/util/layouts/PrecomputedMultiLayout.js +23 -17
- package/util/layouts/SceneGraph.js +18 -12
- package/util/layouts/index.js +6 -6
- package/util/offscreenCanvasPonyfill.js +30 -28
- package/util/offscreenCanvasUtils.js +5 -5
- package/util/range.test.js +20 -20
- package/util/rxjs.js +2 -2
- package/util/simpleFeature.js +23 -18
- package/util/simpleFeature.test.js +3 -3
- package/util/stats.d.ts +1 -1
- package/util/stats.js +10 -6
- package/util/stats.test.js +15 -15
- package/util/tracks.js +1 -3
- package/util/types/index.d.ts +1 -1
- package/util/types/index.js +36 -31
- package/util/types/mst.js +19 -15
- package/util/when.js +5 -5
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} & {
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setFeatures(features: import("../util/simpleFeature").Feature[]): void;
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zoomToDisplayedRegions(leftPx: import("../util/Base1DViewModel").BpOffset | undefined, rightPx: import("../util/Base1DViewModel").BpOffset | undefined): void;
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}, mst._NotCustomized, mst._NotCustomized>;
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// this is all the stuff that the pluginManager re-exports for plugins to use
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@@ -225,7 +229,7 @@ var libs = {
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"use strict";
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var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault")
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value: true
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});
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exports
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exports.default = exports.RefSequenceResult = void 0;
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var
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function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
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|
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function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
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this
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(0, _classCallCheck2.default)(this, BaseResult);
|
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(0, _defineProperty2.default)(this, "renderingComponent", void 0);
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(0, _defineProperty2.default)(this, "matchedAttribute", void 0);
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(0, _defineProperty2.default)(this, "textSearchAdapter", void 0);
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(0, _defineProperty2.default)(this, "relevance", void 0);
|
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(0, _defineProperty2.default)(this, "trackId", void 0);
|
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|
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(0, _defineProperty2.default)(this, "score", void 0);
|
|
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|
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(0, _defineProperty2.default)(this, "locString", void 0);
|
|
31
41
|
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|
|
32
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|
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|
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33
43
|
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|
|
@@ -40,7 +50,7 @@ var BaseResult = /*#__PURE__*/function () {
|
|
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40
50
|
this.score = args.score || 1;
|
|
41
51
|
}
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42
52
|
|
|
43
|
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(0, _createClass2
|
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53
|
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(0, _createClass2.default)(BaseResult, [{
|
|
44
54
|
key: "getLabel",
|
|
45
55
|
value: function getLabel() {
|
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46
56
|
return this.label;
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@@ -85,26 +95,26 @@ var BaseResult = /*#__PURE__*/function () {
|
|
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85
95
|
return BaseResult;
|
|
86
96
|
}();
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|
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exports
|
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|
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exports.default = BaseResult;
|
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89
99
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90
100
|
var RefSequenceResult = /*#__PURE__*/function (_BaseResult) {
|
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|
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(0, _inherits2.default)(RefSequenceResult, _BaseResult);
|
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var _super = (
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var _super = _createSuper(RefSequenceResult);
|
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94
104
|
|
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95
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|
function RefSequenceResult(args) {
|
|
96
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var _args$refName;
|
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97
107
|
|
|
98
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|
var _this;
|
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|
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|
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(0, _classCallCheck2
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(0, _classCallCheck2.default)(this, RefSequenceResult);
|
|
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|
_this = _super.call(this, args);
|
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_this
|
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|
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "refName", void 0);
|
|
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113
|
_this.refName = (_args$refName = args.refName) !== null && _args$refName !== void 0 ? _args$refName : '';
|
|
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114
|
return _this;
|
|
105
115
|
}
|
|
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(0, _createClass2
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(0, _createClass2.default)(RefSequenceResult, [{
|
|
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key: "getLocation",
|
|
109
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value: function getLocation() {
|
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return this.refName;
|
|
@@ -1,18 +1,22 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
|
|
3
|
-
var
|
|
3
|
+
var _typeof = require("@babel/runtime/helpers/typeof");
|
|
4
4
|
|
|
5
5
|
var _BaseResults = _interopRequireWildcard(require("./BaseResults"));
|
|
6
6
|
|
|
7
|
+
function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
|
|
8
|
+
|
|
9
|
+
function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
|
|
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|
+
|
|
7
11
|
test('create BaseResult', function () {
|
|
8
|
-
var baseResult = new _BaseResults
|
|
12
|
+
var baseResult = new _BaseResults.default({
|
|
9
13
|
label: 'chr1'
|
|
10
14
|
});
|
|
11
15
|
expect(baseResult.getLabel()).toEqual('chr1');
|
|
12
16
|
expect(baseResult.getLocation()).toEqual('chr1');
|
|
13
17
|
});
|
|
14
18
|
test('create LocationResult', function () {
|
|
15
|
-
var locationResult = new _BaseResults
|
|
19
|
+
var locationResult = new _BaseResults.default({
|
|
16
20
|
label: 'location result',
|
|
17
21
|
locString: 'chr1:1-900'
|
|
18
22
|
});
|
|
@@ -1,21 +1,23 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
|
|
3
|
-
var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault")
|
|
3
|
+
var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
|
|
4
4
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", {
|
|
6
6
|
value: true
|
|
7
7
|
});
|
|
8
|
-
exports
|
|
8
|
+
exports.default = void 0;
|
|
9
9
|
|
|
10
10
|
var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
|
|
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|
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12
|
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var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/
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|
+
var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
|
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13
|
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|
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var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/
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|
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|
+
var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
|
|
15
15
|
|
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16
|
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var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/
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|
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|
+
var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
|
|
17
17
|
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|
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var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/
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|
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var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
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var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
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var _QuickLRU = _interopRequireDefault(require("../util/QuickLRU"));
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/* text-searching controller */
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var TextSearchManager = /*#__PURE__*/function () {
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function TextSearchManager(pluginManager) {
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(0, _classCallCheck2.default)(this, TextSearchManager);
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this.pluginManager = pluginManager;
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this
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this.adapterCache = new _QuickLRU
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(0, _defineProperty2.default)(this, "adapterCache", void 0);
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this.adapterCache = new _QuickLRU.default({
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maxSize: 15
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});
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}
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*/
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(0, _createClass2.default)(TextSearchManager, [{
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key: "loadTextSearchAdapters",
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value: function loadTextSearchAdapters(searchScope) {
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var _this = this;
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@@ -73,7 +75,7 @@ var TextSearchManager = /*#__PURE__*/function () {
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tracks = _ref.tracks;
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var assemblyName = searchScope.assemblyName;
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return [].concat((0, _toConsumableArray2
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return [].concat((0, _toConsumableArray2.default)(this.getAdaptersWithAssembly(assemblyName, aggregateTextSearchAdapters)), (0, _toConsumableArray2.default)(this.getAdaptersWithAssembly(assemblyName, tracks.map(function (track) {
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return (0, _configuration.readConfObject)(track, ['textSearching', 'textSearchAdapter']);
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}))));
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}
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@@ -95,9 +97,9 @@ var TextSearchManager = /*#__PURE__*/function () {
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}, {
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key: "search",
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value: function () {
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var _search = (0, _asyncToGenerator2
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var _search = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, searchScope, rankFn) {
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var textSearchAdapters, results;
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return _regenerator
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return _regenerator.default.wrap(function _callee$(_context) {
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while (1) {
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switch (_context.prev = _context.next) {
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case 0:
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@@ -146,4 +148,4 @@ var TextSearchManager = /*#__PURE__*/function () {
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return TextSearchManager;
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}();
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exports
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exports.default = TextSearchManager;
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