@jbrowse/core 1.5.4 → 1.5.8
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 +78 -91
- package/BaseFeatureWidget/SequenceFeatureDetails.js +57 -65
- package/BaseFeatureWidget/SequenceFeatureDetails.test.js +9 -9
- package/BaseFeatureWidget/index.js +1 -1
- package/BaseFeatureWidget/index.test.js +3 -3
- package/BaseFeatureWidget/types.js +5 -1
- package/BaseFeatureWidget/util.js +9 -13
- package/CorePlugin.js +19 -31
- package/Plugin.js +11 -13
- package/PluginLoader.js +33 -38
- package/PluginManager.js +55 -56
- package/ReExports/index.js +4 -4
- package/ReExports/list.js +2 -2
- package/ReExports/material-ui-colors.js +20 -20
- package/ReExports/modules.js +47 -51
- package/TextSearch/BaseResults.js +24 -34
- package/TextSearch/BaseResults.test.js +3 -7
- package/TextSearch/TextSearchManager.js +16 -17
- package/assemblyManager/assembly.js +34 -39
- package/assemblyManager/assemblyConfigSchema.js +2 -2
- package/assemblyManager/assemblyManager.js +16 -20
- package/assemblyManager/index.js +3 -3
- package/configuration/configurationSchema.js +17 -19
- package/configuration/configurationSlot.js +11 -11
- package/configuration/configurationSlot.test.js +5 -5
- package/configuration/util.js +5 -5
- package/data_adapters/BaseAdapter.js +38 -40
- package/data_adapters/BaseAdapter.test.js +24 -30
- package/data_adapters/CytobandAdapter.js +16 -22
- package/data_adapters/dataAdapterCache.js +9 -9
- package/package.json +3 -4
- package/pluggableElementTypes/AdapterType.js +22 -31
- package/pluggableElementTypes/ConnectionType.js +18 -28
- package/pluggableElementTypes/DisplayType.js +17 -27
- package/pluggableElementTypes/InternetAccountType.js +14 -24
- package/pluggableElementTypes/PluggableElementBase.js +8 -10
- package/pluggableElementTypes/RpcMethodType.js +41 -55
- package/pluggableElementTypes/RpcMethodType.test.js +17 -23
- package/pluggableElementTypes/TextSearchAdapterType.js +15 -25
- package/pluggableElementTypes/TrackType.js +15 -25
- package/pluggableElementTypes/ViewType.js +15 -25
- package/pluggableElementTypes/WidgetType.js +17 -27
- package/pluggableElementTypes/index.js +11 -11
- package/pluggableElementTypes/models/BaseConnectionModelFactory.js +5 -5
- package/pluggableElementTypes/models/BaseDisplayModel.js +5 -8
- package/pluggableElementTypes/models/BaseTrackModel.js +8 -11
- package/pluggableElementTypes/models/BaseViewModel.js +3 -3
- package/pluggableElementTypes/models/InternetAccountModel.js +5 -5
- package/pluggableElementTypes/models/baseConnectionConfig.js +2 -2
- package/pluggableElementTypes/models/baseTrackConfig.js +4 -7
- package/pluggableElementTypes/models/index.js +4 -4
- package/pluggableElementTypes/renderers/BoxRendererType.js +39 -49
- package/pluggableElementTypes/renderers/CircularChordRendererType.js +12 -18
- package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +27 -35
- package/pluggableElementTypes/renderers/FeatureRendererType.js +36 -46
- package/pluggableElementTypes/renderers/RendererType.js +21 -31
- package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +8 -12
- package/pluggableElementTypes/renderers/ServerSideRendererType.js +31 -44
- package/pluggableElementTypes/renderers/index.js +8 -8
- package/pluggableElementTypes/renderers/util/serializableFilterChain.js +8 -10
- package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +2 -2
- package/rpc/BaseRpcDriver.js +38 -41
- package/rpc/BaseRpcDriver.test.js +49 -63
- package/rpc/MainThreadRpcDriver.js +22 -32
- package/rpc/RpcManager.js +20 -19
- package/rpc/WebWorkerRpcDriver.js +29 -38
- package/rpc/configSchema.js +2 -2
- package/rpc/coreRpcMethods.js +72 -82
- package/rpc/remoteAbortSignals.js +3 -3
- package/ui/AboutDialog.js +17 -21
- package/ui/App.js +38 -42
- package/ui/AssemblySelector.js +5 -5
- package/ui/Drawer.js +7 -7
- package/ui/DrawerWidget.js +33 -37
- package/ui/DropDownMenu.js +9 -21
- package/ui/EditableTypography.js +19 -30
- package/ui/ErrorMessage.js +5 -5
- package/ui/FactoryResetDialog.js +8 -8
- package/ui/FatalErrorDialog.js +12 -29
- package/ui/FatalErrorDialog.test.js +11 -11
- package/ui/FileSelector/FileSelector.js +32 -42
- 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 +35 -46
- package/ui/NewSessionCards.js +19 -29
- package/ui/PrerenderedCanvas.js +10 -27
- package/ui/ResizeHandle.js +10 -17
- package/ui/SanitizedHTML.js +5 -5
- package/ui/SanitizedHTML.test.js +4 -4
- package/ui/Snackbar.js +12 -16
- package/ui/SnackbarModel.js +1 -1
- package/ui/Tooltip.js +7 -11
- package/ui/ViewContainer.js +20 -30
- package/ui/index.js +13 -17
- package/ui/theme.js +11 -15
- package/util/Base1DViewModel.js +10 -14
- package/util/Base1DViewModel.test.js +5 -5
- package/util/QuickLRU.js +27 -31
- package/util/aborting.js +16 -26
- package/util/analytics.js +7 -7
- package/util/blockTypes.js +39 -49
- package/util/calculateDynamicBlocks.js +4 -4
- package/util/calculateDynamicBlocks.test.js +10 -14
- package/util/calculateStaticBlocks.js +1 -1
- package/util/calculateStaticBlocks.test.js +15 -15
- package/util/compositeMap.js +28 -31
- package/util/idMaker.js +4 -4
- package/util/index.js +35 -48
- package/util/index.test.js +7 -11
- package/util/io/RemoteFileWithRangeCache.js +29 -41
- package/util/io/index.js +6 -6
- package/util/jexl.js +8 -5
- package/util/jexlStrings.js +2 -2
- package/util/jexlStrings.test.js +2 -2
- package/util/layouts/BaseLayout.js +5 -1
- package/util/layouts/GranularRectLayout.js +27 -33
- package/util/layouts/GranularRectLayout.test.js +10 -10
- package/util/layouts/MultiLayout.js +14 -19
- package/util/layouts/PrecomputedLayout.js +14 -16
- package/util/layouts/PrecomputedMultiLayout.js +17 -23
- package/util/layouts/SceneGraph.js +18 -18
- package/util/layouts/index.js +6 -6
- package/util/offscreenCanvasPonyfill.js +29 -31
- package/util/offscreenCanvasUtils.js +6 -6
- package/util/range.test.js +20 -20
- package/util/rxjs.js +2 -2
- package/util/simpleFeature.js +19 -24
- package/util/simpleFeature.test.js +3 -3
- package/util/stats.js +7 -11
- package/util/stats.test.js +15 -15
- package/util/types/index.js +32 -34
- package/util/types/mst.js +15 -19
- package/util/types/util.js +5 -1
- package/util/when.js +6 -6
- package/babel.config.d.ts +0 -15
- package/babel.config.js +0 -19
package/util/compositeMap.js
CHANGED
|
@@ -1,35 +1,32 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
|
|
3
|
-
var _interopRequireDefault = require("
|
|
3
|
+
var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
|
|
4
4
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", {
|
|
6
6
|
value: true
|
|
7
7
|
});
|
|
8
|
-
exports
|
|
8
|
+
exports["default"] = void 0;
|
|
9
9
|
|
|
10
|
-
var
|
|
10
|
+
var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
|
|
11
11
|
|
|
12
|
-
var
|
|
12
|
+
var _createForOfIteratorHelper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
|
|
13
13
|
|
|
14
|
-
var
|
|
14
|
+
var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
|
|
15
15
|
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
|
|
19
|
-
|
|
20
|
-
function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
|
|
16
|
+
var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
|
|
21
17
|
|
|
22
18
|
// takes an array or Map or Set (anything iterable with values()) of Maps
|
|
23
19
|
// and lets you query them as one Map
|
|
24
20
|
var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
25
21
|
function CompositeMap(submaps) {
|
|
26
|
-
(0, _classCallCheck2
|
|
22
|
+
(0, _classCallCheck2["default"])(this, CompositeMap);
|
|
23
|
+
this.submaps = submaps;
|
|
27
24
|
}
|
|
28
25
|
|
|
29
|
-
(0, _createClass2
|
|
26
|
+
(0, _createClass2["default"])(CompositeMap, [{
|
|
30
27
|
key: "has",
|
|
31
28
|
value: function has(id) {
|
|
32
|
-
var _iterator =
|
|
29
|
+
var _iterator = (0, _createForOfIteratorHelper2["default"])(this.submaps.values()),
|
|
33
30
|
_step;
|
|
34
31
|
|
|
35
32
|
try {
|
|
@@ -51,7 +48,7 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
51
48
|
}, {
|
|
52
49
|
key: "get",
|
|
53
50
|
value: function get(id) {
|
|
54
|
-
var _iterator2 =
|
|
51
|
+
var _iterator2 = (0, _createForOfIteratorHelper2["default"])(this.submaps.values()),
|
|
55
52
|
_step2;
|
|
56
53
|
|
|
57
54
|
try {
|
|
@@ -72,14 +69,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
72
69
|
}
|
|
73
70
|
}, {
|
|
74
71
|
key: "values",
|
|
75
|
-
value: /*#__PURE__*/
|
|
72
|
+
value: /*#__PURE__*/_index["default"].mark(function values() {
|
|
76
73
|
var _iterator3, _step3, key;
|
|
77
74
|
|
|
78
|
-
return
|
|
75
|
+
return _index["default"].wrap(function values$(_context) {
|
|
79
76
|
while (1) {
|
|
80
77
|
switch (_context.prev = _context.next) {
|
|
81
78
|
case 0:
|
|
82
|
-
_iterator3 =
|
|
79
|
+
_iterator3 = (0, _createForOfIteratorHelper2["default"])(this.keys());
|
|
83
80
|
_context.prev = 1;
|
|
84
81
|
|
|
85
82
|
_iterator3.s();
|
|
@@ -124,20 +121,20 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
124
121
|
})
|
|
125
122
|
}, {
|
|
126
123
|
key: "keys",
|
|
127
|
-
value: /*#__PURE__*/
|
|
124
|
+
value: /*#__PURE__*/_index["default"].mark(function keys() {
|
|
128
125
|
var keys, _iterator4, _step4, submap, _iterator6, _step6, key, _iterator5, _step5, _key;
|
|
129
126
|
|
|
130
|
-
return
|
|
127
|
+
return _index["default"].wrap(function keys$(_context2) {
|
|
131
128
|
while (1) {
|
|
132
129
|
switch (_context2.prev = _context2.next) {
|
|
133
130
|
case 0:
|
|
134
131
|
keys = new Set();
|
|
135
|
-
_iterator4 =
|
|
132
|
+
_iterator4 = (0, _createForOfIteratorHelper2["default"])(this.submaps.values());
|
|
136
133
|
|
|
137
134
|
try {
|
|
138
135
|
for (_iterator4.s(); !(_step4 = _iterator4.n()).done;) {
|
|
139
136
|
submap = _step4.value;
|
|
140
|
-
_iterator6 =
|
|
137
|
+
_iterator6 = (0, _createForOfIteratorHelper2["default"])(submap.keys());
|
|
141
138
|
|
|
142
139
|
try {
|
|
143
140
|
for (_iterator6.s(); !(_step6 = _iterator6.n()).done;) {
|
|
@@ -156,7 +153,7 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
156
153
|
_iterator4.f();
|
|
157
154
|
}
|
|
158
155
|
|
|
159
|
-
_iterator5 =
|
|
156
|
+
_iterator5 = (0, _createForOfIteratorHelper2["default"])(keys);
|
|
160
157
|
_context2.prev = 4;
|
|
161
158
|
|
|
162
159
|
_iterator5.s();
|
|
@@ -202,14 +199,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
202
199
|
}, {
|
|
203
200
|
key: "find",
|
|
204
201
|
value: function find(f) {
|
|
205
|
-
var _iterator7 =
|
|
202
|
+
var _iterator7 = (0, _createForOfIteratorHelper2["default"])(this.submaps.values()),
|
|
206
203
|
_step7;
|
|
207
204
|
|
|
208
205
|
try {
|
|
209
206
|
for (_iterator7.s(); !(_step7 = _iterator7.n()).done;) {
|
|
210
207
|
var submap = _step7.value;
|
|
211
208
|
|
|
212
|
-
var _iterator8 =
|
|
209
|
+
var _iterator8 = (0, _createForOfIteratorHelper2["default"])(submap.values()),
|
|
213
210
|
_step8;
|
|
214
211
|
|
|
215
212
|
try {
|
|
@@ -237,14 +234,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
237
234
|
}
|
|
238
235
|
}, {
|
|
239
236
|
key: _Symbol$iterator,
|
|
240
|
-
value: /*#__PURE__*/
|
|
237
|
+
value: /*#__PURE__*/_index["default"].mark(function value() {
|
|
241
238
|
var _iterator9, _step9, key;
|
|
242
239
|
|
|
243
|
-
return
|
|
240
|
+
return _index["default"].wrap(function value$(_context3) {
|
|
244
241
|
while (1) {
|
|
245
242
|
switch (_context3.prev = _context3.next) {
|
|
246
243
|
case 0:
|
|
247
|
-
_iterator9 =
|
|
244
|
+
_iterator9 = (0, _createForOfIteratorHelper2["default"])(this.keys());
|
|
248
245
|
_context3.prev = 1;
|
|
249
246
|
|
|
250
247
|
_iterator9.s();
|
|
@@ -289,14 +286,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
289
286
|
})
|
|
290
287
|
}, {
|
|
291
288
|
key: "entries",
|
|
292
|
-
value: /*#__PURE__*/
|
|
289
|
+
value: /*#__PURE__*/_index["default"].mark(function entries() {
|
|
293
290
|
var _iterator10, _step10, k;
|
|
294
291
|
|
|
295
|
-
return
|
|
292
|
+
return _index["default"].wrap(function entries$(_context4) {
|
|
296
293
|
while (1) {
|
|
297
294
|
switch (_context4.prev = _context4.next) {
|
|
298
295
|
case 0:
|
|
299
|
-
_iterator10 =
|
|
296
|
+
_iterator10 = (0, _createForOfIteratorHelper2["default"])(this.keys());
|
|
300
297
|
_context4.prev = 1;
|
|
301
298
|
|
|
302
299
|
_iterator10.s();
|
|
@@ -343,4 +340,4 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
|
|
|
343
340
|
return CompositeMap;
|
|
344
341
|
}(Symbol.iterator);
|
|
345
342
|
|
|
346
|
-
exports
|
|
343
|
+
exports["default"] = CompositeMap;
|
package/util/idMaker.js
CHANGED
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
|
|
3
|
-
var _interopRequireDefault = require("
|
|
3
|
+
var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
|
|
4
4
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", {
|
|
6
6
|
value: true
|
|
7
7
|
});
|
|
8
|
-
exports
|
|
8
|
+
exports["default"] = idMaker;
|
|
9
9
|
|
|
10
|
-
var _typeof2 = _interopRequireDefault(require("
|
|
10
|
+
var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
|
|
11
11
|
|
|
12
12
|
var _ = require("./");
|
|
13
13
|
|
|
@@ -26,7 +26,7 @@ function idMaker(args) {
|
|
|
26
26
|
break;
|
|
27
27
|
}
|
|
28
28
|
|
|
29
|
-
if ((0, _typeof2
|
|
29
|
+
if ((0, _typeof2["default"])(args[key]) === 'object' && args[key]) {
|
|
30
30
|
id += idMaker(args[key], id);
|
|
31
31
|
} else {
|
|
32
32
|
id += "".concat(key, "-").concat(args[key], ";");
|
package/util/index.js
CHANGED
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
|
|
3
|
-
var
|
|
3
|
+
var _interopRequireWildcard = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireWildcard.js")["default"];
|
|
4
4
|
|
|
5
|
-
var
|
|
5
|
+
var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
|
|
6
6
|
|
|
7
7
|
Object.defineProperty(exports, "__esModule", {
|
|
8
8
|
value: true
|
|
@@ -60,7 +60,7 @@ var _exportNames = {
|
|
|
60
60
|
Object.defineProperty(exports, "SimpleFeature", {
|
|
61
61
|
enumerable: true,
|
|
62
62
|
get: function get() {
|
|
63
|
-
return _simpleFeature
|
|
63
|
+
return _simpleFeature["default"];
|
|
64
64
|
}
|
|
65
65
|
});
|
|
66
66
|
exports.assembleLocString = assembleLocString;
|
|
@@ -111,17 +111,19 @@ exports.updateStatus = updateStatus;
|
|
|
111
111
|
exports.useDebounce = useDebounce;
|
|
112
112
|
exports.useDebouncedCallback = useDebouncedCallback;
|
|
113
113
|
|
|
114
|
-
var
|
|
114
|
+
var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
|
|
115
115
|
|
|
116
|
-
var
|
|
116
|
+
var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
|
|
117
117
|
|
|
118
|
-
var _asyncToGenerator2 = _interopRequireDefault(require("
|
|
118
|
+
var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
|
|
119
119
|
|
|
120
|
-
var
|
|
120
|
+
var _createForOfIteratorHelper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
|
|
121
121
|
|
|
122
|
-
var
|
|
122
|
+
var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
|
|
123
123
|
|
|
124
|
-
var
|
|
124
|
+
var _slicedToArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
|
|
125
|
+
|
|
126
|
+
var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
|
|
125
127
|
|
|
126
128
|
var _mobxStateTree = require("mobx-state-tree");
|
|
127
129
|
|
|
@@ -219,33 +221,20 @@ Object.keys(_offscreenCanvasUtils).forEach(function (key) {
|
|
|
219
221
|
});
|
|
220
222
|
});
|
|
221
223
|
|
|
222
|
-
|
|
223
|
-
|
|
224
|
-
function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof3(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; }
|
|
225
|
-
|
|
226
|
-
function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
|
|
227
|
-
|
|
228
|
-
function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
|
|
229
|
-
|
|
230
|
-
function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
|
|
231
|
-
|
|
232
|
-
function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
|
|
233
|
-
|
|
234
|
-
function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
|
|
235
|
-
|
|
224
|
+
/* eslint-disable @typescript-eslint/no-explicit-any */
|
|
236
225
|
if (!Object.fromEntries) {
|
|
237
226
|
// @ts-ignore
|
|
238
|
-
_object
|
|
227
|
+
_object["default"].shim();
|
|
239
228
|
}
|
|
240
229
|
|
|
241
|
-
var inDevelopment = (typeof process === "undefined" ? "undefined" : (0, _typeof2
|
|
230
|
+
var inDevelopment = (typeof process === "undefined" ? "undefined" : (0, _typeof2["default"])(process)) === 'object' && process.env && process.env.NODE_ENV === 'development';
|
|
242
231
|
exports.inDevelopment = inDevelopment;
|
|
243
232
|
var inProduction = !inDevelopment;
|
|
244
233
|
exports.inProduction = inProduction;
|
|
245
234
|
|
|
246
235
|
function useDebounce(value, delay) {
|
|
247
236
|
var _useState = (0, _react.useState)(value),
|
|
248
|
-
_useState2 = (0, _slicedToArray2
|
|
237
|
+
_useState2 = (0, _slicedToArray2["default"])(_useState, 2),
|
|
249
238
|
debouncedValue = _useState2[0],
|
|
250
239
|
setDebouncedValue = _useState2[1];
|
|
251
240
|
|
|
@@ -289,7 +278,7 @@ function useDebouncedCallback(callback) {
|
|
|
289
278
|
|
|
290
279
|
timeout.current = setTimeout(function () {
|
|
291
280
|
if (argsRef.current) {
|
|
292
|
-
callback.apply(void 0, (0, _toConsumableArray2
|
|
281
|
+
callback.apply(void 0, (0, _toConsumableArray2["default"])(argsRef.current));
|
|
293
282
|
}
|
|
294
283
|
}, wait);
|
|
295
284
|
};
|
|
@@ -503,7 +492,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
|
|
|
503
492
|
throw new Error("invalid location string: \"".concat(locString, "\""));
|
|
504
493
|
}
|
|
505
494
|
|
|
506
|
-
var _assemblyMatch = (0, _slicedToArray2
|
|
495
|
+
var _assemblyMatch = (0, _slicedToArray2["default"])(assemblyMatch, 4),
|
|
507
496
|
assemblyName = _assemblyMatch[2],
|
|
508
497
|
location = _assemblyMatch[3];
|
|
509
498
|
|
|
@@ -537,7 +526,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
|
|
|
537
526
|
var singleMatch = suffix.match(/^(-?(\d+|\d{1,3}(,\d{3})*))(\.\.|-)?$/);
|
|
538
527
|
|
|
539
528
|
if (rangeMatch) {
|
|
540
|
-
var _rangeMatch = (0, _slicedToArray2
|
|
529
|
+
var _rangeMatch = (0, _slicedToArray2["default"])(rangeMatch, 6),
|
|
541
530
|
start = _rangeMatch[1],
|
|
542
531
|
end = _rangeMatch[5];
|
|
543
532
|
|
|
@@ -550,7 +539,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
|
|
|
550
539
|
};
|
|
551
540
|
}
|
|
552
541
|
} else if (singleMatch) {
|
|
553
|
-
var _singleMatch = (0, _slicedToArray2
|
|
542
|
+
var _singleMatch = (0, _slicedToArray2["default"])(singleMatch, 5),
|
|
554
543
|
_start = _singleMatch[1],
|
|
555
544
|
separator = _singleMatch[4];
|
|
556
545
|
|
|
@@ -763,7 +752,7 @@ function iterMap(iterable, func, sizeHint) {
|
|
|
763
752
|
var results = sizeHint ? new Array(sizeHint) : [];
|
|
764
753
|
var counter = 0;
|
|
765
754
|
|
|
766
|
-
var _iterator =
|
|
755
|
+
var _iterator = (0, _createForOfIteratorHelper2["default"])(iterable),
|
|
767
756
|
_step;
|
|
768
757
|
|
|
769
758
|
try {
|
|
@@ -783,7 +772,7 @@ function iterMap(iterable, func, sizeHint) {
|
|
|
783
772
|
|
|
784
773
|
// similar to electron.js
|
|
785
774
|
function mergeConfigs(A, B) {
|
|
786
|
-
var merged = (0, _deepmerge
|
|
775
|
+
var merged = (0, _deepmerge["default"])(A, B);
|
|
787
776
|
|
|
788
777
|
if (B.defaultSession) {
|
|
789
778
|
merged.defaultSession = B.defaultSession;
|
|
@@ -856,9 +845,9 @@ function makeAbortableReaction(self, dataFunction, asyncReactionFunction, reacti
|
|
|
856
845
|
return undefined;
|
|
857
846
|
}
|
|
858
847
|
}, /*#__PURE__*/function () {
|
|
859
|
-
var _ref = (0, _asyncToGenerator2
|
|
848
|
+
var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(data, mobxReactionHandle) {
|
|
860
849
|
var thisInProgress, result;
|
|
861
|
-
return
|
|
850
|
+
return _index["default"].wrap(function _callee$(_context) {
|
|
862
851
|
while (1) {
|
|
863
852
|
switch (_context.prev = _context.next) {
|
|
864
853
|
case 0:
|
|
@@ -930,16 +919,16 @@ function renameRegionIfNeeded(refNameMap, region) {
|
|
|
930
919
|
if (region && refNameMap && refNameMap[region.refName]) {
|
|
931
920
|
// clone the region so we don't modify it
|
|
932
921
|
if ((0, _mobxStateTree.isStateTreeNode)(region)) {
|
|
933
|
-
region =
|
|
922
|
+
region = (0, _objectSpread2["default"])({}, (0, _mobxStateTree.getSnapshot)(region));
|
|
934
923
|
} else {
|
|
935
|
-
region =
|
|
924
|
+
region = (0, _objectSpread2["default"])({}, region);
|
|
936
925
|
} // modify it directly in the container
|
|
937
926
|
|
|
938
927
|
|
|
939
928
|
var newRef = refNameMap[region.refName];
|
|
940
929
|
|
|
941
930
|
if (newRef) {
|
|
942
|
-
return
|
|
931
|
+
return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, region), {}, {
|
|
943
932
|
refName: newRef,
|
|
944
933
|
originalRefName: region.refName
|
|
945
934
|
});
|
|
@@ -954,10 +943,10 @@ function renameRegionsIfNeeded(_x3, _x4) {
|
|
|
954
943
|
}
|
|
955
944
|
|
|
956
945
|
function _renameRegionsIfNeeded() {
|
|
957
|
-
_renameRegionsIfNeeded = (0, _asyncToGenerator2
|
|
946
|
+
_renameRegionsIfNeeded = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3(assemblyManager, args) {
|
|
958
947
|
var _args$regions, regions, adapterConfig, assemblyNames, assemblyMaps;
|
|
959
948
|
|
|
960
|
-
return
|
|
949
|
+
return _index["default"].wrap(function _callee3$(_context3) {
|
|
961
950
|
while (1) {
|
|
962
951
|
switch (_context3.prev = _context3.next) {
|
|
963
952
|
case 0:
|
|
@@ -977,8 +966,8 @@ function _renameRegionsIfNeeded() {
|
|
|
977
966
|
_context3.t0 = Object;
|
|
978
967
|
_context3.next = 7;
|
|
979
968
|
return Promise.all(assemblyNames.map( /*#__PURE__*/function () {
|
|
980
|
-
var _ref3 = (0, _asyncToGenerator2
|
|
981
|
-
return
|
|
969
|
+
var _ref3 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(assemblyName) {
|
|
970
|
+
return _index["default"].wrap(function _callee2$(_context2) {
|
|
982
971
|
while (1) {
|
|
983
972
|
switch (_context2.prev = _context2.next) {
|
|
984
973
|
case 0:
|
|
@@ -1006,7 +995,7 @@ function _renameRegionsIfNeeded() {
|
|
|
1006
995
|
case 7:
|
|
1007
996
|
_context3.t1 = _context3.sent;
|
|
1008
997
|
assemblyMaps = _context3.t0.fromEntries.call(_context3.t0, _context3.t1);
|
|
1009
|
-
return _context3.abrupt("return",
|
|
998
|
+
return _context3.abrupt("return", (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, args), {}, {
|
|
1010
999
|
regions: regions.map(function (region) {
|
|
1011
1000
|
return renameRegionIfNeeded(assemblyMaps[region.assemblyName], region);
|
|
1012
1001
|
})
|
|
@@ -1247,9 +1236,9 @@ function updateStatus(_x5, _x6, _x7) {
|
|
|
1247
1236
|
}
|
|
1248
1237
|
|
|
1249
1238
|
function _updateStatus() {
|
|
1250
|
-
_updateStatus = (0, _asyncToGenerator2
|
|
1239
|
+
_updateStatus = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4(statusMsg, statusCallback, fn) {
|
|
1251
1240
|
var result;
|
|
1252
|
-
return
|
|
1241
|
+
return _index["default"].wrap(function _callee4$(_context4) {
|
|
1253
1242
|
while (1) {
|
|
1254
1243
|
switch (_context4.prev = _context4.next) {
|
|
1255
1244
|
case 0:
|
|
@@ -1274,15 +1263,13 @@ function _updateStatus() {
|
|
|
1274
1263
|
|
|
1275
1264
|
function hashCode(str) {
|
|
1276
1265
|
var hash = 0;
|
|
1277
|
-
var i;
|
|
1278
|
-
var chr;
|
|
1279
1266
|
|
|
1280
1267
|
if (str.length === 0) {
|
|
1281
1268
|
return hash;
|
|
1282
1269
|
}
|
|
1283
1270
|
|
|
1284
|
-
for (i = 0; i < str.length; i++) {
|
|
1285
|
-
chr = str.charCodeAt(i);
|
|
1271
|
+
for (var i = 0; i < str.length; i++) {
|
|
1272
|
+
var chr = str.charCodeAt(i);
|
|
1286
1273
|
hash = (hash << 5) - hash + chr;
|
|
1287
1274
|
hash |= 0; // Convert to 32bit integer
|
|
1288
1275
|
}
|
package/util/index.test.js
CHANGED
|
@@ -1,17 +1,13 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
|
|
3
|
-
var _interopRequireDefault = require("
|
|
3
|
+
var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
|
|
4
4
|
|
|
5
|
-
var
|
|
5
|
+
var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
|
|
6
6
|
|
|
7
|
-
var _slicedToArray2 = _interopRequireDefault(require("
|
|
7
|
+
var _slicedToArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
|
|
8
8
|
|
|
9
9
|
var _index = require("./index");
|
|
10
10
|
|
|
11
|
-
function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
|
|
12
|
-
|
|
13
|
-
function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
|
|
14
|
-
|
|
15
11
|
describe('parseLocString', function () {
|
|
16
12
|
var cases = [['chr1:1..200', {
|
|
17
13
|
start: 0,
|
|
@@ -70,7 +66,7 @@ describe('parseLocString', function () {
|
|
|
70
66
|
refName: 'chr1'
|
|
71
67
|
}]];
|
|
72
68
|
cases.forEach(function (_ref) {
|
|
73
|
-
var _ref2 = (0, _slicedToArray2
|
|
69
|
+
var _ref2 = (0, _slicedToArray2["default"])(_ref, 2),
|
|
74
70
|
input = _ref2[0],
|
|
75
71
|
output = _ref2[1];
|
|
76
72
|
|
|
@@ -118,7 +114,7 @@ describe('assembleLocString', function () {
|
|
|
118
114
|
refName: 'chr1'
|
|
119
115
|
}, 'chr1:-99..-1']];
|
|
120
116
|
cases.forEach(function (_ref3) {
|
|
121
|
-
var _ref4 = (0, _slicedToArray2
|
|
117
|
+
var _ref4 = (0, _slicedToArray2["default"])(_ref3, 2),
|
|
122
118
|
input = _ref4[0],
|
|
123
119
|
output = _ref4[1];
|
|
124
120
|
|
|
@@ -151,7 +147,7 @@ describe('assembleLocString', function () {
|
|
|
151
147
|
test("assemble and parse 'chr1:1..100'", function () {
|
|
152
148
|
expect((0, _index.parseLocString)((0, _index.assembleLocString)(location), function (refName) {
|
|
153
149
|
return refName === 'chr1' || refName === 'chr2';
|
|
154
|
-
})).toEqual(
|
|
150
|
+
})).toEqual((0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, location), {}, {
|
|
155
151
|
start: 0
|
|
156
152
|
}));
|
|
157
153
|
});
|
|
@@ -159,7 +155,7 @@ describe('assembleLocString', function () {
|
|
|
159
155
|
describe('compareLocStrings', function () {
|
|
160
156
|
var cases = [['chr1:1..200', 'chr1:1-200', 0], ['chr1:1-200', '{hg19}chr1:1-200', -1], ['{hg19}chr1:1-200', 'chr1:1-200', 1], ['{hg19}chr1:1-200', '{hg19}chr1:2-200', -1]];
|
|
161
157
|
cases.forEach(function (_ref5) {
|
|
162
|
-
var _ref6 = (0, _slicedToArray2
|
|
158
|
+
var _ref6 = (0, _slicedToArray2["default"])(_ref5, 3),
|
|
163
159
|
input1 = _ref6[0],
|
|
164
160
|
input2 = _ref6[1],
|
|
165
161
|
output = _ref6[2];
|