@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 +1,299 @@
1
+ import type { SpreadsheetModel } from './SpreadsheetModel';
2
+ import type { MenuItem } from '@jbrowse/core/ui';
3
+ import type { Instance } from 'mobx-state-tree';
4
+ export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
5
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
6
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
7
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ } & {
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+ type: import("mobx-state-tree").ISimpleType<"SpreadsheetView">;
10
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
11
+ height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
12
+ hideVerticalResizeHandle: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ hideFilterControls: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
14
+ importWizard: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
15
+ fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
16
+ hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
17
+ columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
18
+ selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
19
+ cachedFileLocation: import("mobx-state-tree").IType<import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined>;
20
+ }, {
21
+ fileTypes: string[];
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+ fileSource: any;
23
+ error: unknown;
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+ loading: boolean;
25
+ } & {
26
+ readonly isReadyToOpen: any;
27
+ readonly fileName: any;
28
+ readonly requiresUnzip: any;
29
+ isValidRefName(refName: string, assemblyName?: string): boolean;
30
+ tracksForAssembly(selectedAssembly: string): {
31
+ track: {
32
+ [x: string]: any;
33
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
34
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
35
+ [x: string]: any;
36
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
37
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
38
+ [x: string]: any;
39
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
40
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
41
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
42
+ label: string;
43
+ assemblyNames: any;
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+ type: string;
45
+ loc: import("@jbrowse/core/util").FileLocation;
46
+ }[];
47
+ } & {
48
+ setSelectedAssemblyName(s: string): void;
49
+ setFileSource(newSource: unknown): void;
50
+ setColumnNameLineNumber(newnumber: number): void;
51
+ setFileType(typeName: string): void;
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+ setError(error: unknown): void;
53
+ setLoading(arg: boolean): void;
54
+ cancelButton(): void;
55
+ setCachedFileHandle(arg: import("@jbrowse/core/util").FileLocation): void;
56
+ } & {
57
+ import(assemblyName: string): Promise<void>;
58
+ } & {
59
+ afterAttach(): void;
60
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
61
+ spreadsheet: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
62
+ rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
63
+ columns: import("mobx-state-tree").IType<{
64
+ name: string;
65
+ }[], {
66
+ name: string;
67
+ }[], {
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+ name: string;
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+ }[]>;
70
+ assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
71
+ visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
72
+ }, {
73
+ visibleRowFlags: Record<number, boolean> | undefined;
74
+ } & {
75
+ readonly rows: {
76
+ id: number;
77
+ feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
78
+ }[] | undefined;
79
+ readonly initialized: boolean | undefined;
80
+ } & {
81
+ readonly dataGridColumns: ({
82
+ field: string;
83
+ width: number;
84
+ type: "number" | undefined;
85
+ } | {
86
+ field: string;
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+ width: number;
88
+ renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
89
+ id: number;
90
+ feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
91
+ }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
92
+ type?: undefined;
93
+ valueGetter?: undefined;
94
+ valueFormatter?: undefined;
95
+ } | {
96
+ field: string;
97
+ type: "number";
98
+ width: number;
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+ valueGetter: (_val: unknown, row: {
100
+ feature?: import("@jbrowse/core/util").SimpleFeatureSerialized;
101
+ }) => number | undefined;
102
+ valueFormatter: (arg: never) => string;
103
+ renderCell?: undefined;
104
+ })[] | undefined;
105
+ } & {
106
+ readonly visibleRows: {
107
+ id: number;
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+ feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
109
+ }[] | undefined;
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+ } & {
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+ setVisibleRows(arg?: Record<number, boolean>): void;
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+ setVisibleColumns(arg: Record<string, boolean>): void;
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+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
114
+ rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
115
+ columns: import("mobx-state-tree").IType<{
116
+ name: string;
117
+ }[], {
118
+ name: string;
119
+ }[], {
120
+ name: string;
121
+ }[]>;
122
+ assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
123
+ visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
124
+ }>>, import("mobx-state-tree")._NotCustomized>>;
125
+ }, {
126
+ width: number;
127
+ } & {
128
+ menuItems(): MenuItem[];
129
+ } & {
130
+ setDisplayName(name: string): void;
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+ setWidth(newWidth: number): void;
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+ setMinimized(flag: boolean): void;
133
+ } & {
134
+ width: number;
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+ rowMenuItems: MenuItem[];
136
+ } & {
137
+ readonly assembly: any;
138
+ } & {
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+ setRowMenuItems(newItems: MenuItem[]): void;
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+ setWidth(newWidth: number): number;
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+ setHeight(newHeight: number): number;
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+ resizeHeight(distance: number): number;
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+ resizeWidth(distance: number): number;
144
+ displaySpreadsheet(spreadsheet?: SpreadsheetModel): void;
145
+ } & {
146
+ menuItems(): {
147
+ label: string;
148
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
149
+ muiName: string;
150
+ };
151
+ onClick: () => void;
152
+ }[];
153
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree").ModelSnapshotType<{
154
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
155
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
156
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
157
+ } & {
158
+ type: import("mobx-state-tree").ISimpleType<"SpreadsheetView">;
159
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
160
+ height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
161
+ hideVerticalResizeHandle: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
162
+ hideFilterControls: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
163
+ importWizard: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
164
+ fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
165
+ hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
166
+ columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
167
+ selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
168
+ cachedFileLocation: import("mobx-state-tree").IType<import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined>;
169
+ }, {
170
+ fileTypes: string[];
171
+ fileSource: any;
172
+ error: unknown;
173
+ loading: boolean;
174
+ } & {
175
+ readonly isReadyToOpen: any;
176
+ readonly fileName: any;
177
+ readonly requiresUnzip: any;
178
+ isValidRefName(refName: string, assemblyName?: string): boolean;
179
+ tracksForAssembly(selectedAssembly: string): {
180
+ track: {
181
+ [x: string]: any;
182
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
183
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
184
+ [x: string]: any;
185
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
186
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
187
+ [x: string]: any;
188
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
189
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
190
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
191
+ label: string;
192
+ assemblyNames: any;
193
+ type: string;
194
+ loc: import("@jbrowse/core/util").FileLocation;
195
+ }[];
196
+ } & {
197
+ setSelectedAssemblyName(s: string): void;
198
+ setFileSource(newSource: unknown): void;
199
+ setColumnNameLineNumber(newnumber: number): void;
200
+ setFileType(typeName: string): void;
201
+ setError(error: unknown): void;
202
+ setLoading(arg: boolean): void;
203
+ cancelButton(): void;
204
+ setCachedFileHandle(arg: import("@jbrowse/core/util").FileLocation): void;
205
+ } & {
206
+ import(assemblyName: string): Promise<void>;
207
+ } & {
208
+ afterAttach(): void;
209
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
210
+ spreadsheet: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
211
+ rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
212
+ columns: import("mobx-state-tree").IType<{
213
+ name: string;
214
+ }[], {
215
+ name: string;
216
+ }[], {
217
+ name: string;
218
+ }[]>;
219
+ assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
220
+ visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
221
+ }, {
222
+ visibleRowFlags: Record<number, boolean> | undefined;
223
+ } & {
224
+ readonly rows: {
225
+ id: number;
226
+ feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
227
+ }[] | undefined;
228
+ readonly initialized: boolean | undefined;
229
+ } & {
230
+ readonly dataGridColumns: ({
231
+ field: string;
232
+ width: number;
233
+ type: "number" | undefined;
234
+ } | {
235
+ field: string;
236
+ width: number;
237
+ renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
238
+ id: number;
239
+ feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
240
+ }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
241
+ type?: undefined;
242
+ valueGetter?: undefined;
243
+ valueFormatter?: undefined;
244
+ } | {
245
+ field: string;
246
+ type: "number";
247
+ width: number;
248
+ valueGetter: (_val: unknown, row: {
249
+ feature?: import("@jbrowse/core/util").SimpleFeatureSerialized;
250
+ }) => number | undefined;
251
+ valueFormatter: (arg: never) => string;
252
+ renderCell?: undefined;
253
+ })[] | undefined;
254
+ } & {
255
+ readonly visibleRows: {
256
+ id: number;
257
+ feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
258
+ }[] | undefined;
259
+ } & {
260
+ setVisibleRows(arg?: Record<number, boolean>): void;
261
+ setVisibleColumns(arg: Record<string, boolean>): void;
262
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
263
+ rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
264
+ columns: import("mobx-state-tree").IType<{
265
+ name: string;
266
+ }[], {
267
+ name: string;
268
+ }[], {
269
+ name: string;
270
+ }[]>;
271
+ assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
272
+ visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
273
+ }>>, import("mobx-state-tree")._NotCustomized>>;
274
+ }> | {
275
+ spreadsheet: {
276
+ columns: {
277
+ name: string;
278
+ }[];
279
+ assemblyName: string | undefined;
280
+ visibleColumns: Record<string, boolean>;
281
+ };
282
+ id: string;
283
+ type: "SpreadsheetView";
284
+ height: number;
285
+ displayName: string | undefined;
286
+ minimized: boolean;
287
+ hideVerticalResizeHandle: boolean;
288
+ offsetPx: number;
289
+ hideFilterControls: boolean;
290
+ importWizard: import("mobx-state-tree").ModelSnapshotType<{
291
+ fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
292
+ hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
293
+ columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
294
+ selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
295
+ cachedFileLocation: import("mobx-state-tree").IType<import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined>;
296
+ }>;
297
+ }>;
298
+ export type SpreadsheetViewStateModel = ReturnType<typeof stateModelFactory>;
299
+ export type SpreadsheetViewModel = Instance<SpreadsheetViewStateModel>;
@@ -0,0 +1,101 @@
1
+ "use strict";
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ exports.default = stateModelFactory;
7
+ const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
8
+ const util_1 = require("@jbrowse/core/util");
9
+ const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
10
+ const mobx_state_tree_1 = require("mobx-state-tree");
11
+ const ImportWizard_1 = __importDefault(require("./ImportWizard"));
12
+ const SpreadsheetModel_1 = __importDefault(require("./SpreadsheetModel"));
13
+ const minHeight = 40;
14
+ const defaultHeight = 440;
15
+ function x() { }
16
+ function stateModelFactory() {
17
+ const ImportWizardModel = (0, ImportWizard_1.default)();
18
+ return mobx_state_tree_1.types
19
+ .compose(models_1.BaseViewModel, mobx_state_tree_1.types
20
+ .model('SpreadsheetView', {
21
+ type: mobx_state_tree_1.types.literal('SpreadsheetView'),
22
+ offsetPx: 0,
23
+ height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, defaultHeight),
24
+ hideVerticalResizeHandle: false,
25
+ hideFilterControls: false,
26
+ importWizard: mobx_state_tree_1.types.optional(ImportWizardModel, () => ImportWizardModel.create()),
27
+ spreadsheet: mobx_state_tree_1.types.maybe((0, SpreadsheetModel_1.default)()),
28
+ })
29
+ .volatile(() => ({
30
+ width: 400,
31
+ rowMenuItems: [],
32
+ }))
33
+ .views(self => ({
34
+ get assembly() {
35
+ var _a, _b;
36
+ const name = (_a = self.spreadsheet) === null || _a === void 0 ? void 0 : _a.assemblyName;
37
+ return name
38
+ ? (_b = (0, util_1.getSession)(self).assemblyManager.get(name)) === null || _b === void 0 ? void 0 : _b.configuration
39
+ : undefined;
40
+ },
41
+ }))
42
+ .actions(self => ({
43
+ setRowMenuItems(newItems) {
44
+ self.rowMenuItems = newItems;
45
+ },
46
+ setWidth(newWidth) {
47
+ self.width = newWidth;
48
+ return self.width;
49
+ },
50
+ setHeight(newHeight) {
51
+ self.height = Math.max(newHeight, minHeight);
52
+ return self.height;
53
+ },
54
+ resizeHeight(distance) {
55
+ const oldHeight = self.height;
56
+ const newHeight = this.setHeight(self.height + distance);
57
+ return newHeight - oldHeight;
58
+ },
59
+ resizeWidth(distance) {
60
+ const oldWidth = self.width;
61
+ const newWidth = this.setWidth(self.width + distance);
62
+ return newWidth - oldWidth;
63
+ },
64
+ displaySpreadsheet(spreadsheet) {
65
+ self.spreadsheet = (0, mobx_state_tree_1.cast)(spreadsheet);
66
+ },
67
+ }))
68
+ .views(self => ({
69
+ menuItems() {
70
+ return [
71
+ {
72
+ label: 'Return to import form',
73
+ icon: FolderOpen_1.default,
74
+ onClick: () => {
75
+ self.displaySpreadsheet(undefined);
76
+ },
77
+ },
78
+ ];
79
+ },
80
+ })))
81
+ .postProcessSnapshot(snap => {
82
+ const { importWizard, spreadsheet } = snap;
83
+ if (importWizard.cachedFileLocation && spreadsheet) {
84
+ const { rowSet, ...rest } = spreadsheet;
85
+ return {
86
+ ...snap,
87
+ spreadsheet: rest,
88
+ };
89
+ }
90
+ else if (spreadsheet) {
91
+ const { rowSet, ...rest } = spreadsheet;
92
+ return rowSet && JSON.stringify(rowSet).length > 1000000
93
+ ? {
94
+ ...snap,
95
+ spreadsheet: rest,
96
+ }
97
+ : snap;
98
+ }
99
+ return snap;
100
+ });
101
+ }
@@ -0,0 +1 @@
1
+ export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';
@@ -0,0 +1,5 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.default = void 0;
4
+ var sv_core_1 = require("@jbrowse/sv-core");
5
+ Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });
@@ -0,0 +1 @@
1
+ export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';
@@ -0,0 +1,5 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.default = void 0;
4
+ var sv_core_1 = require("@jbrowse/sv-core");
5
+ Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });
@@ -0,0 +1,7 @@
1
+ import type { AbstractSessionModel, SimpleFeatureSerialized } from '@jbrowse/core/util';
2
+ export default function FeatureMenu({ assemblyName, session, spreadsheetViewId, feature, }: {
3
+ spreadsheetViewId: string;
4
+ assemblyName: string;
5
+ session: AbstractSessionModel;
6
+ feature: SimpleFeatureSerialized;
7
+ }): import("react/jsx-runtime").JSX.Element;
@@ -0,0 +1,105 @@
1
+ "use strict";
2
+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
+ if (k2 === undefined) k2 = k;
4
+ var desc = Object.getOwnPropertyDescriptor(m, k);
5
+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
+ desc = { enumerable: true, get: function() { return m[k]; } };
7
+ }
8
+ Object.defineProperty(o, k2, desc);
9
+ }) : (function(o, m, k, k2) {
10
+ if (k2 === undefined) k2 = k;
11
+ o[k2] = m[k];
12
+ }));
13
+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
+ Object.defineProperty(o, "default", { enumerable: true, value: v });
15
+ }) : function(o, v) {
16
+ o["default"] = v;
17
+ });
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
+ })();
35
+ var __importDefault = (this && this.__importDefault) || function (mod) {
36
+ return (mod && mod.__esModule) ? mod : { "default": mod };
37
+ };
38
+ Object.defineProperty(exports, "__esModule", { value: true });
39
+ exports.default = FeatureMenu;
40
+ const jsx_runtime_1 = require("react/jsx-runtime");
41
+ const react_1 = require("react");
42
+ const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
43
+ const util_1 = require("@jbrowse/core/util");
44
+ const ArrowDropDown_1 = __importDefault(require("@mui/icons-material/ArrowDropDown"));
45
+ const mobx_state_tree_1 = require("mobx-state-tree");
46
+ const util_2 = require("../util");
47
+ const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
48
+ const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
49
+ function FeatureMenu({ assemblyName, session, spreadsheetViewId, feature, }) {
50
+ return ((0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
51
+ {
52
+ label: 'Open in linear genome view',
53
+ onClick: async () => {
54
+ try {
55
+ await (0, util_2.locationLinkClick)({
56
+ spreadsheetViewId,
57
+ assemblyName,
58
+ session,
59
+ locString: (0, util_1.assembleLocStringFast)(feature),
60
+ });
61
+ }
62
+ catch (e) {
63
+ console.error(e);
64
+ session.notifyError(`${e}`, e);
65
+ }
66
+ },
67
+ },
68
+ {
69
+ label: 'Open in single-level split view',
70
+ onClick: async () => {
71
+ const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
72
+ const viewType = pluginManager.getViewType('BreakpointSplitView');
73
+ session.queueDialog(handleClose => [
74
+ BreakendSingleLevelOptionDialog,
75
+ {
76
+ handleClose,
77
+ session,
78
+ stableViewId: `${spreadsheetViewId}_${assemblyName}_breakpointsplitview_singlelevel`,
79
+ feature: new util_1.SimpleFeature(feature),
80
+ viewType,
81
+ assemblyName,
82
+ },
83
+ ]);
84
+ },
85
+ },
86
+ {
87
+ label: 'Open in multi-level split view',
88
+ onClick: async () => {
89
+ const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
90
+ const viewType = pluginManager.getViewType('BreakpointSplitView');
91
+ session.queueDialog(handleClose => [
92
+ BreakendMultiLevelOptionDialog,
93
+ {
94
+ handleClose,
95
+ session,
96
+ stableViewId: `${spreadsheetViewId}_${assemblyName}_breakpointsplitview_multilevel`,
97
+ feature: new util_1.SimpleFeature(feature),
98
+ viewType,
99
+ assemblyName,
100
+ },
101
+ ]);
102
+ },
103
+ },
104
+ ], children: (0, jsx_runtime_1.jsx)(ArrowDropDown_1.default, {}) }));
105
+ }
@@ -1,6 +1,5 @@
1
- import React from 'react';
2
- import { ImportWizardModel } from '../models/ImportWizard';
3
- declare const ImportWizard: ({ model }: {
1
+ import type { ImportWizardModel } from '../ImportWizard';
2
+ declare const ImportWizard: ({ model, }: {
4
3
  model: ImportWizardModel;
5
- }) => React.JSX.Element;
4
+ }) => import("react/jsx-runtime").JSX.Element;
6
5
  export default ImportWizard;