@jbrowse/plugin-spreadsheet-view 2.17.0 → 3.0.0

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 (201) hide show
  1. package/dist/LaunchSpreadsheetView/index.d.ts +1 -1
  2. package/dist/LaunchSpreadsheetView/index.js +1 -3
  3. package/dist/SpreadsheetView/ImportWizard.d.ts +51 -0
  4. package/dist/SpreadsheetView/ImportWizard.js +250 -0
  5. package/dist/SpreadsheetView/SpreadsheetModel.d.ts +78 -0
  6. package/dist/SpreadsheetView/SpreadsheetModel.js +119 -0
  7. package/dist/SpreadsheetView/SpreadsheetViewModel.d.ts +299 -0
  8. package/dist/SpreadsheetView/SpreadsheetViewModel.js +101 -0
  9. package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +1 -0
  10. package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +5 -0
  11. package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +1 -0
  12. package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +5 -0
  13. package/dist/SpreadsheetView/components/FeatureMenu.d.ts +7 -0
  14. package/dist/SpreadsheetView/components/FeatureMenu.js +105 -0
  15. package/dist/SpreadsheetView/components/ImportWizard.d.ts +3 -4
  16. package/dist/SpreadsheetView/components/ImportWizard.js +25 -68
  17. package/dist/SpreadsheetView/components/LocationCell.d.ts +7 -0
  18. package/dist/SpreadsheetView/components/LocationCell.js +29 -0
  19. package/dist/SpreadsheetView/components/NumberEditor.d.ts +2 -3
  20. package/dist/SpreadsheetView/components/NumberEditor.js +4 -28
  21. package/dist/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +5 -0
  22. package/dist/SpreadsheetView/components/SpreadsheetDataGrid.js +23 -0
  23. package/dist/SpreadsheetView/components/SpreadsheetView.d.ts +4 -5
  24. package/dist/SpreadsheetView/components/SpreadsheetView.js +25 -63
  25. package/dist/SpreadsheetView/components/SpreadsheetViewActual.d.ts +5 -0
  26. package/dist/SpreadsheetView/components/SpreadsheetViewActual.js +34 -0
  27. package/dist/SpreadsheetView/components/TrackSelector.d.ts +6 -0
  28. package/dist/SpreadsheetView/components/TrackSelector.js +27 -0
  29. package/dist/SpreadsheetView/importAdapters/BedImport.d.ts +26 -17
  30. package/dist/SpreadsheetView/importAdapters/BedImport.js +53 -139
  31. package/dist/SpreadsheetView/importAdapters/BedpeImport.d.ts +36 -0
  32. package/dist/SpreadsheetView/importAdapters/BedpeImport.js +79 -0
  33. package/dist/SpreadsheetView/importAdapters/STARFusionImport.d.ts +25 -9
  34. package/dist/SpreadsheetView/importAdapters/STARFusionImport.js +27 -62
  35. package/dist/SpreadsheetView/importAdapters/VcfImport.d.ts +19 -12
  36. package/dist/SpreadsheetView/importAdapters/VcfImport.js +53 -98
  37. package/dist/SpreadsheetView/importAdapters/isNumber.d.ts +1 -0
  38. package/dist/SpreadsheetView/importAdapters/isNumber.js +14 -0
  39. package/dist/SpreadsheetView/importAdapters/util.d.ts +2 -0
  40. package/dist/SpreadsheetView/importAdapters/util.js +22 -0
  41. package/dist/SpreadsheetView/index.d.ts +2 -2
  42. package/dist/SpreadsheetView/index.js +19 -9
  43. package/dist/SpreadsheetView/util.d.ts +7 -0
  44. package/dist/SpreadsheetView/util.js +13 -0
  45. package/dist/index.d.ts +1 -1
  46. package/dist/index.js +1 -3
  47. package/esm/LaunchSpreadsheetView/index.d.ts +1 -1
  48. package/esm/LaunchSpreadsheetView/index.js +1 -3
  49. package/esm/SpreadsheetView/ImportWizard.d.ts +51 -0
  50. package/esm/SpreadsheetView/ImportWizard.js +214 -0
  51. package/esm/SpreadsheetView/SpreadsheetModel.d.ts +78 -0
  52. package/esm/SpreadsheetView/SpreadsheetModel.js +113 -0
  53. package/esm/SpreadsheetView/SpreadsheetViewModel.d.ts +299 -0
  54. package/esm/SpreadsheetView/SpreadsheetViewModel.js +95 -0
  55. package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +1 -0
  56. package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +1 -0
  57. package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +1 -0
  58. package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +1 -0
  59. package/esm/SpreadsheetView/components/FeatureMenu.d.ts +7 -0
  60. package/esm/SpreadsheetView/components/FeatureMenu.js +66 -0
  61. package/esm/SpreadsheetView/components/ImportWizard.d.ts +3 -4
  62. package/esm/SpreadsheetView/components/ImportWizard.js +26 -46
  63. package/esm/SpreadsheetView/components/LocationCell.d.ts +7 -0
  64. package/esm/SpreadsheetView/components/LocationCell.js +23 -0
  65. package/esm/SpreadsheetView/components/NumberEditor.d.ts +2 -3
  66. package/esm/SpreadsheetView/components/NumberEditor.js +4 -5
  67. package/esm/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +5 -0
  68. package/esm/SpreadsheetView/components/SpreadsheetDataGrid.js +21 -0
  69. package/esm/SpreadsheetView/components/SpreadsheetView.d.ts +4 -5
  70. package/esm/SpreadsheetView/components/SpreadsheetView.js +8 -56
  71. package/esm/SpreadsheetView/components/SpreadsheetViewActual.d.ts +5 -0
  72. package/esm/SpreadsheetView/components/SpreadsheetViewActual.js +29 -0
  73. package/esm/SpreadsheetView/components/TrackSelector.d.ts +6 -0
  74. package/esm/SpreadsheetView/components/TrackSelector.js +25 -0
  75. package/esm/SpreadsheetView/importAdapters/BedImport.d.ts +26 -17
  76. package/esm/SpreadsheetView/importAdapters/BedImport.js +53 -137
  77. package/esm/SpreadsheetView/importAdapters/BedpeImport.d.ts +36 -0
  78. package/esm/SpreadsheetView/importAdapters/BedpeImport.js +76 -0
  79. package/esm/SpreadsheetView/importAdapters/STARFusionImport.d.ts +25 -9
  80. package/esm/SpreadsheetView/importAdapters/STARFusionImport.js +27 -62
  81. package/esm/SpreadsheetView/importAdapters/VcfImport.d.ts +19 -12
  82. package/esm/SpreadsheetView/importAdapters/VcfImport.js +53 -97
  83. package/esm/SpreadsheetView/importAdapters/isNumber.d.ts +1 -0
  84. package/esm/SpreadsheetView/importAdapters/isNumber.js +11 -0
  85. package/esm/SpreadsheetView/importAdapters/util.d.ts +2 -0
  86. package/esm/SpreadsheetView/importAdapters/util.js +18 -0
  87. package/esm/SpreadsheetView/index.d.ts +2 -2
  88. package/esm/SpreadsheetView/index.js +2 -2
  89. package/esm/SpreadsheetView/util.d.ts +7 -0
  90. package/esm/SpreadsheetView/util.js +10 -0
  91. package/esm/index.d.ts +1 -1
  92. package/esm/index.js +1 -3
  93. package/package.json +7 -7
  94. package/dist/SpreadsheetView/components/CellData.d.ts +0 -9
  95. package/dist/SpreadsheetView/components/CellData.js +0 -14
  96. package/dist/SpreadsheetView/components/ColumnFilterControls.d.ts +0 -3
  97. package/dist/SpreadsheetView/components/ColumnFilterControls.js +0 -58
  98. package/dist/SpreadsheetView/components/ColumnMenu.d.ts +0 -16
  99. package/dist/SpreadsheetView/components/ColumnMenu.js +0 -140
  100. package/dist/SpreadsheetView/components/DataRow.d.ts +0 -12
  101. package/dist/SpreadsheetView/components/DataRow.js +0 -81
  102. package/dist/SpreadsheetView/components/DataTable.d.ts +0 -10
  103. package/dist/SpreadsheetView/components/DataTable.js +0 -42
  104. package/dist/SpreadsheetView/components/DataTableHeader.d.ts +0 -6
  105. package/dist/SpreadsheetView/components/DataTableHeader.js +0 -104
  106. package/dist/SpreadsheetView/components/GlobalFilterControls.d.ts +0 -5
  107. package/dist/SpreadsheetView/components/GlobalFilterControls.js +0 -68
  108. package/dist/SpreadsheetView/components/RowCountMessage.d.ts +0 -6
  109. package/dist/SpreadsheetView/components/RowCountMessage.js +0 -33
  110. package/dist/SpreadsheetView/components/RowMenu.d.ts +0 -9
  111. package/dist/SpreadsheetView/components/RowMenu.js +0 -39
  112. package/dist/SpreadsheetView/components/SortIndicator.d.ts +0 -6
  113. package/dist/SpreadsheetView/components/SortIndicator.js +0 -27
  114. package/dist/SpreadsheetView/components/Spreadsheet.d.ts +0 -11
  115. package/dist/SpreadsheetView/components/Spreadsheet.js +0 -25
  116. package/dist/SpreadsheetView/components/StatusBar.d.ts +0 -11
  117. package/dist/SpreadsheetView/components/StatusBar.js +0 -44
  118. package/dist/SpreadsheetView/importAdapters/ImportUtils.d.ts +0 -42
  119. package/dist/SpreadsheetView/importAdapters/ImportUtils.js +0 -123
  120. package/dist/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts +0 -12
  121. package/dist/SpreadsheetView/models/ColumnDataTypes/LocEnd.js +0 -20
  122. package/dist/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts +0 -12
  123. package/dist/SpreadsheetView/models/ColumnDataTypes/LocRef.js +0 -20
  124. package/dist/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts +0 -12
  125. package/dist/SpreadsheetView/models/ColumnDataTypes/LocStart.js +0 -20
  126. package/dist/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts +0 -13
  127. package/dist/SpreadsheetView/models/ColumnDataTypes/LocString.js +0 -183
  128. package/dist/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts +0 -19
  129. package/dist/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js +0 -23
  130. package/dist/SpreadsheetView/models/ColumnDataTypes/Number.d.ts +0 -30
  131. package/dist/SpreadsheetView/models/ColumnDataTypes/Number.js +0 -126
  132. package/dist/SpreadsheetView/models/ColumnDataTypes/Text.d.ts +0 -28
  133. package/dist/SpreadsheetView/models/ColumnDataTypes/Text.js +0 -129
  134. package/dist/SpreadsheetView/models/ColumnDataTypes/index.d.ts +0 -71
  135. package/dist/SpreadsheetView/models/ColumnDataTypes/index.js +0 -37
  136. package/dist/SpreadsheetView/models/FilterControls.d.ts +0 -26
  137. package/dist/SpreadsheetView/models/FilterControls.js +0 -85
  138. package/dist/SpreadsheetView/models/ImportWizard.d.ts +0 -31
  139. package/dist/SpreadsheetView/models/ImportWizard.js +0 -186
  140. package/dist/SpreadsheetView/models/Row.d.ts +0 -17
  141. package/dist/SpreadsheetView/models/Row.js +0 -43
  142. package/dist/SpreadsheetView/models/Spreadsheet.d.ts +0 -260
  143. package/dist/SpreadsheetView/models/Spreadsheet.js +0 -174
  144. package/dist/SpreadsheetView/models/SpreadsheetView.d.ts +0 -482
  145. package/dist/SpreadsheetView/models/SpreadsheetView.js +0 -199
  146. package/dist/SpreadsheetView/models/StaticRowSet.d.ts +0 -163
  147. package/dist/SpreadsheetView/models/StaticRowSet.js +0 -56
  148. package/esm/SpreadsheetView/components/CellData.d.ts +0 -9
  149. package/esm/SpreadsheetView/components/CellData.js +0 -9
  150. package/esm/SpreadsheetView/components/ColumnFilterControls.d.ts +0 -3
  151. package/esm/SpreadsheetView/components/ColumnFilterControls.js +0 -53
  152. package/esm/SpreadsheetView/components/ColumnMenu.d.ts +0 -16
  153. package/esm/SpreadsheetView/components/ColumnMenu.js +0 -135
  154. package/esm/SpreadsheetView/components/DataRow.d.ts +0 -12
  155. package/esm/SpreadsheetView/components/DataRow.js +0 -76
  156. package/esm/SpreadsheetView/components/DataTable.d.ts +0 -10
  157. package/esm/SpreadsheetView/components/DataTable.js +0 -37
  158. package/esm/SpreadsheetView/components/DataTableHeader.d.ts +0 -6
  159. package/esm/SpreadsheetView/components/DataTableHeader.js +0 -76
  160. package/esm/SpreadsheetView/components/GlobalFilterControls.d.ts +0 -5
  161. package/esm/SpreadsheetView/components/GlobalFilterControls.js +0 -40
  162. package/esm/SpreadsheetView/components/RowCountMessage.d.ts +0 -6
  163. package/esm/SpreadsheetView/components/RowCountMessage.js +0 -28
  164. package/esm/SpreadsheetView/components/RowMenu.d.ts +0 -9
  165. package/esm/SpreadsheetView/components/RowMenu.js +0 -34
  166. package/esm/SpreadsheetView/components/SortIndicator.d.ts +0 -6
  167. package/esm/SpreadsheetView/components/SortIndicator.js +0 -21
  168. package/esm/SpreadsheetView/components/Spreadsheet.d.ts +0 -11
  169. package/esm/SpreadsheetView/components/Spreadsheet.js +0 -20
  170. package/esm/SpreadsheetView/components/StatusBar.d.ts +0 -11
  171. package/esm/SpreadsheetView/components/StatusBar.js +0 -39
  172. package/esm/SpreadsheetView/importAdapters/ImportUtils.d.ts +0 -42
  173. package/esm/SpreadsheetView/importAdapters/ImportUtils.js +0 -95
  174. package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts +0 -12
  175. package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.js +0 -15
  176. package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts +0 -12
  177. package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.js +0 -15
  178. package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts +0 -12
  179. package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.js +0 -15
  180. package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts +0 -13
  181. package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.js +0 -178
  182. package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts +0 -19
  183. package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js +0 -20
  184. package/esm/SpreadsheetView/models/ColumnDataTypes/Number.d.ts +0 -30
  185. package/esm/SpreadsheetView/models/ColumnDataTypes/Number.js +0 -119
  186. package/esm/SpreadsheetView/models/ColumnDataTypes/Text.d.ts +0 -28
  187. package/esm/SpreadsheetView/models/ColumnDataTypes/Text.js +0 -122
  188. package/esm/SpreadsheetView/models/ColumnDataTypes/index.d.ts +0 -71
  189. package/esm/SpreadsheetView/models/ColumnDataTypes/index.js +0 -29
  190. package/esm/SpreadsheetView/models/FilterControls.d.ts +0 -26
  191. package/esm/SpreadsheetView/models/FilterControls.js +0 -83
  192. package/esm/SpreadsheetView/models/ImportWizard.d.ts +0 -31
  193. package/esm/SpreadsheetView/models/ImportWizard.js +0 -161
  194. package/esm/SpreadsheetView/models/Row.d.ts +0 -17
  195. package/esm/SpreadsheetView/models/Row.js +0 -41
  196. package/esm/SpreadsheetView/models/Spreadsheet.d.ts +0 -260
  197. package/esm/SpreadsheetView/models/Spreadsheet.js +0 -169
  198. package/esm/SpreadsheetView/models/SpreadsheetView.d.ts +0 -482
  199. package/esm/SpreadsheetView/models/SpreadsheetView.js +0 -194
  200. package/esm/SpreadsheetView/models/StaticRowSet.d.ts +0 -163
  201. package/esm/SpreadsheetView/models/StaticRowSet.js +0 -51
@@ -0,0 +1,14 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.isNumber = isNumber;
4
+ function isNumber(num) {
5
+ if (typeof num === 'number') {
6
+ return num - num === 0;
7
+ }
8
+ else if (typeof num === 'string' && num.trim() !== '') {
9
+ return Number.isFinite(+num);
10
+ }
11
+ else {
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+ return false;
13
+ }
14
+ }
@@ -0,0 +1,2 @@
1
+ export declare function parseStrand(strand?: string): 1 | -1 | undefined;
2
+ export declare function bufferToLines(buffer: Uint8Array): string[];
@@ -0,0 +1,22 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.parseStrand = parseStrand;
4
+ exports.bufferToLines = bufferToLines;
5
+ function parseStrand(strand) {
6
+ if (strand === '+') {
7
+ return 1;
8
+ }
9
+ else if (strand === '-') {
10
+ return -1;
11
+ }
12
+ else {
13
+ return undefined;
14
+ }
15
+ }
16
+ function bufferToLines(buffer) {
17
+ return new TextDecoder('utf8')
18
+ .decode(buffer)
19
+ .split(/\n|\r\n|\r/)
20
+ .map(f => f.trim())
21
+ .filter(f => !!f);
22
+ }
@@ -1,3 +1,3 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
1
+ import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  export default function SpreadsheetViewF(pluginManager: PluginManager): void;
3
- export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './models/SpreadsheetView';
3
+ export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel';
@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
15
15
  }) : function(o, v) {
16
16
  o["default"] = v;
17
17
  });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
18
+ var __importStar = (this && this.__importStar) || (function () {
19
+ var ownKeys = function(o) {
20
+ ownKeys = Object.getOwnPropertyNames || function (o) {
21
+ var ar = [];
22
+ for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
23
+ return ar;
24
+ };
25
+ return ownKeys(o);
26
+ };
27
+ return function (mod) {
28
+ if (mod && mod.__esModule) return mod;
29
+ var result = {};
30
+ if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
31
+ __setModuleDefault(result, mod);
32
+ return result;
33
+ };
34
+ })();
25
35
  var __importDefault = (this && this.__importDefault) || function (mod) {
26
36
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
37
  };
@@ -29,13 +39,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
29
39
  exports.default = SpreadsheetViewF;
30
40
  const react_1 = require("react");
31
41
  const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
32
- const SpreadsheetView_1 = __importDefault(require("./models/SpreadsheetView"));
42
+ const SpreadsheetViewModel_1 = __importDefault(require("./SpreadsheetViewModel"));
33
43
  function SpreadsheetViewF(pluginManager) {
34
44
  pluginManager.addViewType(() => {
35
45
  return new pluggableElementTypes_1.ViewType({
36
46
  name: 'SpreadsheetView',
37
47
  displayName: 'Spreadsheet view',
38
- stateModel: SpreadsheetView_1.default,
48
+ stateModel: (0, SpreadsheetViewModel_1.default)(),
39
49
  ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SpreadsheetView')))),
40
50
  });
41
51
  });
@@ -0,0 +1,7 @@
1
+ import type { AbstractSessionModel } from '@jbrowse/core/util';
2
+ export declare function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }: {
3
+ assemblyName: string;
4
+ session: AbstractSessionModel;
5
+ locString: string;
6
+ spreadsheetViewId: string;
7
+ }): Promise<void>;
@@ -0,0 +1,13 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.locationLinkClick = locationLinkClick;
4
+ function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }) {
5
+ const newViewId = `${spreadsheetViewId}_${assemblyName}`;
6
+ let view = session.views.find(v => v.id === newViewId);
7
+ if (!view) {
8
+ view = session.addView('LinearGenomeView', {
9
+ id: newViewId,
10
+ });
11
+ }
12
+ return view.navToLocString(locString, assemblyName);
13
+ }
package/dist/index.d.ts CHANGED
@@ -1,5 +1,5 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
1
  import Plugin from '@jbrowse/core/Plugin';
2
+ import type PluginManager from '@jbrowse/core/PluginManager';
3
3
  export default class SpreadsheetViewPlugin extends Plugin {
4
4
  name: string;
5
5
  install(pluginManager: PluginManager): void;
package/dist/index.js CHANGED
@@ -5,11 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
7
7
  const util_1 = require("@jbrowse/core/util");
8
- // icons
9
8
  const ViewComfy_1 = __importDefault(require("@mui/icons-material/ViewComfy"));
10
- // locals
11
- const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
12
9
  const LaunchSpreadsheetView_1 = __importDefault(require("./LaunchSpreadsheetView"));
10
+ const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
13
11
  class SpreadsheetViewPlugin extends Plugin_1.default {
14
12
  constructor() {
15
13
  super(...arguments);
@@ -1,2 +1,2 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
1
+ import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  export default function LaunchSpreadsheetViewF(pluginManager: PluginManager): void;
@@ -1,7 +1,5 @@
1
1
  export default function LaunchSpreadsheetViewF(pluginManager) {
2
- pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView',
3
- // @ts-expect-error
4
- async ({ session, assembly, uri, fileType, }) => {
2
+ pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView', async ({ session, assembly, uri, fileType, }) => {
5
3
  var _a, _b;
6
4
  const view = session.addView('SpreadsheetView');
7
5
  const exts = uri.split('.');
@@ -0,0 +1,51 @@
1
+ import type { FileLocation } from '@jbrowse/core/util';
2
+ import type { Instance } from 'mobx-state-tree';
3
+ export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
4
+ fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
+ hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
6
+ columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
7
+ selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
8
+ cachedFileLocation: import("mobx-state-tree").IType<FileLocation | undefined, FileLocation | undefined, FileLocation | undefined>;
9
+ }, {
10
+ fileTypes: string[];
11
+ fileSource: any;
12
+ error: unknown;
13
+ loading: boolean;
14
+ } & {
15
+ readonly isReadyToOpen: any;
16
+ readonly fileName: any;
17
+ readonly requiresUnzip: any;
18
+ isValidRefName(refName: string, assemblyName?: string): boolean;
19
+ tracksForAssembly(selectedAssembly: string): {
20
+ track: {
21
+ [x: string]: any;
22
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
23
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
24
+ [x: string]: any;
25
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
26
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
27
+ [x: string]: any;
28
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
29
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
30
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
31
+ label: string;
32
+ assemblyNames: any;
33
+ type: string;
34
+ loc: FileLocation;
35
+ }[];
36
+ } & {
37
+ setSelectedAssemblyName(s: string): void;
38
+ setFileSource(newSource: unknown): void;
39
+ setColumnNameLineNumber(newnumber: number): void;
40
+ setFileType(typeName: string): void;
41
+ setError(error: unknown): void;
42
+ setLoading(arg: boolean): void;
43
+ cancelButton(): void;
44
+ setCachedFileHandle(arg: FileLocation): void;
45
+ } & {
46
+ import(assemblyName: string): Promise<void>;
47
+ } & {
48
+ afterAttach(): void;
49
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
50
+ export type ImportWizardStateModel = ReturnType<typeof stateModelFactory>;
51
+ export type ImportWizardModel = Instance<ImportWizardStateModel>;
@@ -0,0 +1,214 @@
1
+ import { readConfObject } from '@jbrowse/core/configuration';
2
+ import { getEnv, getSession } from '@jbrowse/core/util';
3
+ import { openLocation } from '@jbrowse/core/util/io';
4
+ import { getTrackName } from '@jbrowse/core/util/tracks';
5
+ import { getParent, types } from 'mobx-state-tree';
6
+ const IMPORT_SIZE_LIMIT = 100000000;
7
+ const fileTypes = ['VCF', 'BED', 'BEDPE', 'STAR-Fusion'];
8
+ const fileTypeParsers = {
9
+ VCF: () => import('./importAdapters/VcfImport').then(r => r.parseVcfBuffer),
10
+ BED: () => import('./importAdapters/BedImport').then(r => r.parseBedBuffer),
11
+ BEDPE: () => import('./importAdapters/BedpeImport').then(r => r.parseBedPEBuffer),
12
+ 'STAR-Fusion': () => import('./importAdapters/STARFusionImport').then(r => r.parseSTARFusionBuffer),
13
+ };
14
+ function getType(adapter) {
15
+ if (adapter.vcfLocation || adapter.vcfGzLocation) {
16
+ return 'VCF';
17
+ }
18
+ else if (adapter.bedLocation || adapter.bedGzLocation) {
19
+ return 'BED';
20
+ }
21
+ else if (adapter.bedpeLocation) {
22
+ return 'BEDPE';
23
+ }
24
+ else {
25
+ return undefined;
26
+ }
27
+ }
28
+ function getAdapterLoc(adapter) {
29
+ return (adapter.vcfLocation ||
30
+ adapter.vcfGzLocation ||
31
+ adapter.bedLocation ||
32
+ adapter.bedGzLocation ||
33
+ adapter.bedpeLocation);
34
+ }
35
+ const fileTypesRegexp = new RegExp(`\\.(${fileTypes.join('|')})(\\.gz)?$`, 'i');
36
+ function x() { }
37
+ export default function stateModelFactory() {
38
+ return types
39
+ .model('SpreadsheetImportWizard', {
40
+ fileType: types.optional(types.enumeration(fileTypes), 'VCF'),
41
+ hasColumnNameLine: true,
42
+ columnNameLineNumber: 1,
43
+ selectedAssemblyName: types.maybe(types.string),
44
+ cachedFileLocation: types.frozen(),
45
+ })
46
+ .volatile(() => ({
47
+ fileTypes,
48
+ fileSource: undefined,
49
+ error: undefined,
50
+ loading: false,
51
+ }))
52
+ .views(self => ({
53
+ get isReadyToOpen() {
54
+ return (self.fileSource &&
55
+ (self.fileSource.blobId ||
56
+ self.fileSource.localPath ||
57
+ self.fileSource.uri));
58
+ },
59
+ get fileName() {
60
+ return (self.fileSource.uri ||
61
+ self.fileSource.localPath ||
62
+ (self.fileSource.blobId && self.fileSource.name));
63
+ },
64
+ get requiresUnzip() {
65
+ return this.fileName.endsWith('gz');
66
+ },
67
+ isValidRefName(refName, assemblyName) {
68
+ const { assemblyManager } = getSession(self);
69
+ return !assemblyName
70
+ ? false
71
+ : assemblyManager.isValidRefName(refName, assemblyName);
72
+ },
73
+ tracksForAssembly(selectedAssembly) {
74
+ const session = getSession(self);
75
+ const { tracks = [], sessionTracks = [] } = session;
76
+ const allTracks = [
77
+ ...tracks,
78
+ ...sessionTracks,
79
+ ];
80
+ return allTracks
81
+ .map(track => {
82
+ const assemblyNames = readConfObject(track, 'assemblyNames');
83
+ const adapter = readConfObject(track, 'adapter');
84
+ const category = readConfObject(track, 'category').join(',');
85
+ const loc = getAdapterLoc(adapter);
86
+ return assemblyNames.includes(selectedAssembly) && loc
87
+ ? {
88
+ track,
89
+ label: [
90
+ category ? `[${category}]` : '',
91
+ getTrackName(track, session),
92
+ ]
93
+ .filter(f => !!f)
94
+ .join(' '),
95
+ assemblyNames,
96
+ type: getType(adapter) || 'UNKNOWN',
97
+ loc,
98
+ }
99
+ : undefined;
100
+ })
101
+ .filter(f => !!f)
102
+ .sort((a, b) => a.label.localeCompare(b.label));
103
+ },
104
+ }))
105
+ .actions(self => ({
106
+ setSelectedAssemblyName(s) {
107
+ self.selectedAssemblyName = s;
108
+ },
109
+ setFileSource(newSource) {
110
+ var _a;
111
+ self.fileSource = newSource;
112
+ self.error = undefined;
113
+ if (self.fileSource) {
114
+ const name = self.fileName;
115
+ if (name) {
116
+ const firstMatch = (_a = fileTypesRegexp.exec(name)) === null || _a === void 0 ? void 0 : _a[1];
117
+ if (firstMatch) {
118
+ self.fileType =
119
+ firstMatch === 'tsv' && name.includes('star-fusion')
120
+ ? 'STAR-Fusion'
121
+ : firstMatch.toUpperCase();
122
+ }
123
+ }
124
+ }
125
+ },
126
+ setColumnNameLineNumber(newnumber) {
127
+ if (newnumber > 0) {
128
+ self.columnNameLineNumber = newnumber;
129
+ }
130
+ },
131
+ setFileType(typeName) {
132
+ self.fileType = typeName;
133
+ },
134
+ setError(error) {
135
+ self.error = error;
136
+ },
137
+ setLoading(arg) {
138
+ self.loading = arg;
139
+ },
140
+ cancelButton() {
141
+ self.error = undefined;
142
+ getParent(self).setDisplayMode();
143
+ },
144
+ setCachedFileHandle(arg) {
145
+ self.cachedFileLocation = arg;
146
+ },
147
+ }))
148
+ .actions(self => ({
149
+ async import(assemblyName) {
150
+ if (!self.fileSource) {
151
+ return;
152
+ }
153
+ self.selectedAssemblyName = assemblyName;
154
+ const type = self.fileType;
155
+ const typeParser = await fileTypeParsers[type]();
156
+ const { fetchAndMaybeUnzip } = await import('@jbrowse/core/util');
157
+ const { pluginManager } = getEnv(self);
158
+ const filehandle = openLocation(self.fileSource, pluginManager);
159
+ self.setLoading(true);
160
+ try {
161
+ const stat = await filehandle.stat();
162
+ if (stat.size > IMPORT_SIZE_LIMIT) {
163
+ self.setError(`File is too big. Tabular files are limited to at most ${(IMPORT_SIZE_LIMIT / 1000).toLocaleString()}kb.`);
164
+ return;
165
+ }
166
+ }
167
+ catch (e) {
168
+ console.warn(e);
169
+ }
170
+ finally {
171
+ self.setLoading(false);
172
+ }
173
+ self.setLoading(true);
174
+ try {
175
+ if (self.fileSource.uri) {
176
+ self.setCachedFileHandle({
177
+ uri: self.fileSource.uri,
178
+ baseUri: self.fileSource.baseUri,
179
+ locationType: 'UriLocation',
180
+ });
181
+ }
182
+ const data = await fetchAndMaybeUnzip(filehandle);
183
+ getParent(self).displaySpreadsheet({
184
+ ...typeParser(data),
185
+ assemblyName,
186
+ });
187
+ }
188
+ catch (e) {
189
+ console.error(e);
190
+ self.setError(e);
191
+ }
192
+ finally {
193
+ self.setLoading(false);
194
+ }
195
+ },
196
+ }))
197
+ .actions(self => ({
198
+ afterAttach() {
199
+ ;
200
+ (async () => {
201
+ try {
202
+ if (self.cachedFileLocation && self.selectedAssemblyName) {
203
+ self.setFileSource(self.cachedFileLocation);
204
+ await self.import(self.selectedAssemblyName);
205
+ }
206
+ }
207
+ catch (e) {
208
+ console.error(e);
209
+ getSession(self).notifyError(`${e}`, e);
210
+ }
211
+ })();
212
+ },
213
+ }));
214
+ }
@@ -0,0 +1,78 @@
1
+ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
2
+ import type { Instance } from 'mobx-state-tree';
3
+ export interface Row {
4
+ feature?: SimpleFeatureSerialized;
5
+ cellData?: Record<string, unknown>;
6
+ cells?: {
7
+ text: unknown;
8
+ }[];
9
+ }
10
+ export interface RowSet {
11
+ rows: Row[];
12
+ }
13
+ export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
14
+ rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
15
+ columns: import("mobx-state-tree").IType<{
16
+ name: string;
17
+ }[], {
18
+ name: string;
19
+ }[], {
20
+ name: string;
21
+ }[]>;
22
+ assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
23
+ visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
24
+ }, {
25
+ visibleRowFlags: Record<number, boolean> | undefined;
26
+ } & {
27
+ readonly rows: {
28
+ id: number;
29
+ feature: SimpleFeatureSerialized | undefined;
30
+ }[] | undefined;
31
+ readonly initialized: boolean | undefined;
32
+ } & {
33
+ readonly dataGridColumns: ({
34
+ field: string;
35
+ width: number;
36
+ type: "number" | undefined;
37
+ } | {
38
+ field: string;
39
+ width: number;
40
+ renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
41
+ id: number;
42
+ feature: SimpleFeatureSerialized | undefined;
43
+ }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
44
+ type?: undefined;
45
+ valueGetter?: undefined;
46
+ valueFormatter?: undefined;
47
+ } | {
48
+ field: string;
49
+ type: "number";
50
+ width: number;
51
+ valueGetter: (_val: unknown, row: {
52
+ feature?: SimpleFeatureSerialized;
53
+ }) => number | undefined;
54
+ valueFormatter: (arg: never) => string;
55
+ renderCell?: undefined;
56
+ })[] | undefined;
57
+ } & {
58
+ readonly visibleRows: {
59
+ id: number;
60
+ feature: SimpleFeatureSerialized | undefined;
61
+ }[] | undefined;
62
+ } & {
63
+ setVisibleRows(arg?: Record<number, boolean>): void;
64
+ setVisibleColumns(arg: Record<string, boolean>): void;
65
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
66
+ rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
67
+ columns: import("mobx-state-tree").IType<{
68
+ name: string;
69
+ }[], {
70
+ name: string;
71
+ }[], {
72
+ name: string;
73
+ }[]>;
74
+ assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
75
+ visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
76
+ }>>, import("mobx-state-tree")._NotCustomized>;
77
+ export type SpreadsheetStateModel = ReturnType<typeof stateModelFactory>;
78
+ export type SpreadsheetModel = Instance<SpreadsheetStateModel>;
@@ -0,0 +1,113 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { assembleLocStringFast, getSession, measureGridWidth, toLocale, } from '@jbrowse/core/util';
3
+ import { types } from 'mobx-state-tree';
4
+ import LocationCell from './components/LocationCell';
5
+ export default function stateModelFactory() {
6
+ return types
7
+ .model('Spreadsheet', {
8
+ rowSet: types.frozen(),
9
+ columns: types.frozen(),
10
+ assemblyName: types.maybe(types.string),
11
+ visibleColumns: types.frozen(),
12
+ })
13
+ .volatile(() => ({
14
+ visibleRowFlags: undefined,
15
+ }))
16
+ .views(self => ({
17
+ get rows() {
18
+ var _a;
19
+ return (_a = self.rowSet) === null || _a === void 0 ? void 0 : _a.rows.map((row, i) => ({
20
+ id: i,
21
+ feature: row.feature,
22
+ ...Object.fromEntries(self.columns.map((c, idx) => {
23
+ var _a, _b, _c, _d;
24
+ return [
25
+ c.name,
26
+ (_b = (_a = row.cellData) === null || _a === void 0 ? void 0 : _a[c.name]) !== null && _b !== void 0 ? _b : (_d = (_c = row.cells) === null || _c === void 0 ? void 0 : _c[idx]) === null || _d === void 0 ? void 0 : _d.text,
27
+ ];
28
+ })),
29
+ }));
30
+ },
31
+ get initialized() {
32
+ var _a;
33
+ const session = getSession(self);
34
+ const name = self.assemblyName;
35
+ return (self.rowSet &&
36
+ (name ? (_a = session.assemblyManager.get(name)) === null || _a === void 0 ? void 0 : _a.initialized : false));
37
+ },
38
+ }))
39
+ .views(self => ({
40
+ get dataGridColumns() {
41
+ const { rows } = self;
42
+ return rows
43
+ ? [
44
+ {
45
+ field: 'Location',
46
+ width: measureGridWidth(rows.map(row => row.feature ? assembleLocStringFast(row.feature) : 0)) + 40,
47
+ renderCell: ({ row }) => {
48
+ const { feature } = row;
49
+ return feature ? (_jsx(LocationCell, { model: self, feature: feature })) : ('N/A');
50
+ },
51
+ },
52
+ {
53
+ field: 'Length',
54
+ type: 'number',
55
+ width: measureGridWidth(rows.map(row => {
56
+ const { feature } = row;
57
+ return feature ? feature.end - feature.start : 0;
58
+ })),
59
+ valueGetter: (_val, row) => {
60
+ const { feature } = row;
61
+ return feature ? feature.end - feature.start : undefined;
62
+ },
63
+ valueFormatter: arg => toLocale(arg),
64
+ },
65
+ ...self.columns.map(f => ({
66
+ field: f.name,
67
+ width: measureGridWidth([...rows.map(r => r[f.name]), f.name], { minWidth: 20 }),
68
+ type: typeof rows[0][f.name] === 'number'
69
+ ? 'number'
70
+ : undefined,
71
+ })),
72
+ ]
73
+ : undefined;
74
+ },
75
+ }))
76
+ .views(self => ({
77
+ get visibleRows() {
78
+ var _a;
79
+ const { visibleRowFlags } = self;
80
+ return visibleRowFlags
81
+ ? (_a = self.rows) === null || _a === void 0 ? void 0 : _a.filter((_f, idx) => !!visibleRowFlags[idx])
82
+ : self.rows;
83
+ },
84
+ }))
85
+ .actions(self => ({
86
+ setVisibleRows(arg) {
87
+ self.visibleRowFlags = arg;
88
+ },
89
+ setVisibleColumns(arg) {
90
+ self.visibleColumns = arg;
91
+ },
92
+ }))
93
+ .preProcessSnapshot(snap => {
94
+ return snap
95
+ ? {
96
+ ...snap,
97
+ columns: snap.columns.filter(f => !f.isDerived),
98
+ rowSet: snap.rowSet
99
+ ? {
100
+ ...snap.rowSet,
101
+ rows: snap.rowSet.rows.map(r => {
102
+ var _a, _b;
103
+ return ({
104
+ ...r,
105
+ feature: (_a = r.feature) !== null && _a !== void 0 ? _a : (_b = r.extendedData) === null || _b === void 0 ? void 0 : _b.vcfFeature,
106
+ });
107
+ }),
108
+ }
109
+ : undefined,
110
+ }
111
+ : snap;
112
+ });
113
+ }