@jbrowse/core 4.3.0 → 5.0.0-beta.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1124) hide show
  1. package/README.md +783 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +40 -40
  113. package/esm/PluginLoader.js +166 -82
  114. package/esm/PluginManager.d.ts +368 -55
  115. package/esm/PluginManager.js +326 -85
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +84 -65
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/TextSearch/BaseResults.d.ts +20 -21
  135. package/esm/TextSearch/BaseResults.js +8 -33
  136. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  137. package/esm/TextSearch/TextSearchManager.js +87 -34
  138. package/esm/assemblyManager/assembly.d.ts +307 -34
  139. package/esm/assemblyManager/assembly.js +551 -262
  140. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  141. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  142. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  143. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  144. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  145. package/esm/assemblyManager/assemblyManager.js +351 -46
  146. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  147. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  148. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  149. package/esm/assemblyManager/geneticCodes.js +47 -0
  150. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  151. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  152. package/esm/assemblyManager/index.d.ts +1 -1
  153. package/esm/assemblyManager/index.js +2 -2
  154. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  155. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  156. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  157. package/esm/assemblyManager/refNameColors.js +32 -0
  158. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  159. package/esm/assemblyManager/refNameMaps.js +87 -0
  160. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  161. package/esm/assemblyManager/refNameMismatch.js +66 -0
  162. package/esm/checkPlugins.d.ts +11 -0
  163. package/esm/checkPlugins.js +77 -0
  164. package/esm/configuration/configurationSchema.d.ts +154 -19
  165. package/esm/configuration/configurationSchema.js +359 -138
  166. package/esm/configuration/configurationSlot.d.ts +283 -30
  167. package/esm/configuration/configurationSlot.js +205 -226
  168. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  169. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  170. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  171. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  172. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  173. package/esm/configuration/fullConfSnapshot.js +66 -0
  174. package/esm/configuration/getConf.d.ts +88 -0
  175. package/esm/configuration/getConf.js +74 -0
  176. package/esm/configuration/index.d.ts +19 -3
  177. package/esm/configuration/index.js +19 -2
  178. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  179. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  180. package/esm/configuration/promotableDefaults.d.ts +199 -0
  181. package/esm/configuration/promotableDefaults.js +326 -0
  182. package/esm/configuration/promotablePin.d.ts +55 -0
  183. package/esm/configuration/promotableResolve.d.ts +108 -0
  184. package/esm/configuration/promotableResolve.js +117 -0
  185. package/esm/configuration/promotableSlots.d.ts +12 -0
  186. package/esm/configuration/promotableSlots.js +45 -0
  187. package/esm/configuration/readConfObject.d.ts +56 -0
  188. package/esm/configuration/readConfObject.js +161 -0
  189. package/esm/configuration/schemaRegistry.d.ts +35 -0
  190. package/esm/configuration/schemaRegistry.js +50 -0
  191. package/esm/configuration/schemaTypes.d.ts +23 -0
  192. package/esm/configuration/schemaTypes.js +94 -0
  193. package/esm/configuration/slotFacade.d.ts +82 -0
  194. package/esm/configuration/slotFacade.js +89 -0
  195. package/esm/configuration/slotShape.d.ts +12 -0
  196. package/esm/configuration/slotShape.js +84 -0
  197. package/esm/configuration/slotValueUtils.d.ts +17 -0
  198. package/esm/configuration/slotValueUtils.js +25 -0
  199. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  200. package/esm/configuration/tabixIndexFields.js +45 -0
  201. package/esm/configuration/tabixShorthand.d.ts +34 -0
  202. package/esm/configuration/tabixShorthand.js +45 -0
  203. package/esm/configuration/types.d.ts +170 -7
  204. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  205. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  206. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
  207. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
  208. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  209. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  210. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  211. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  212. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  213. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  214. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  215. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  216. package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
  217. package/esm/data_adapters/BaseAdapter/index.js +5 -5
  218. package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
  219. package/esm/data_adapters/BaseAdapter/stats.js +48 -22
  220. package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
  221. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  222. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  223. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  224. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  225. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  226. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  227. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  228. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  229. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  230. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  231. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  232. package/esm/data_adapters/dataAdapterCache.js +62 -22
  233. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  234. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  235. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  236. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  237. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  238. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  239. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  240. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  241. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  242. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  243. package/esm/pluggableElementTypes/DisplayType.d.ts +10 -0
  244. package/esm/pluggableElementTypes/DisplayType.js +14 -1
  245. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  246. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  247. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  248. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  249. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  250. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  251. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  252. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  253. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  254. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  255. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  256. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  257. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  258. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  259. package/esm/pluggableElementTypes/TrackType.js +1 -1
  260. package/esm/pluggableElementTypes/ViewType.d.ts +2 -1
  261. package/esm/pluggableElementTypes/ViewType.js +9 -2
  262. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  263. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  264. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  265. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  266. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  267. package/esm/pluggableElementTypes/extendElementType.js +68 -0
  268. package/esm/pluggableElementTypes/index.d.ts +7 -7
  269. package/esm/pluggableElementTypes/index.js +24 -14
  270. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  271. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  272. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
  273. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
  274. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +195 -35
  275. package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
  276. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
  277. package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
  278. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  279. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  280. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  281. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  282. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
  283. package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
  284. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  285. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  286. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  287. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  288. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  289. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  290. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  291. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  292. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  293. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  294. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  295. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  296. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  297. package/esm/pluggableElementTypes/models/index.js +10 -8
  298. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  299. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  300. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  301. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  302. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  303. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  304. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  305. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  306. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  307. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  308. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
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  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -1,3 +1,18 @@
1
+ import { MUI_COMPONENT_NAMES } from './muiComponentNames.js';
2
+ /**
3
+ * Used by plugin build systems to determine if a module is provided by JBrowse
4
+ * globally and thus doesn't need to be bundled. A check in ./modules.tsx makes
5
+ * sure this is in sync with the re-exported modules.
6
+ *
7
+ * Using this instead of just Object.keys(modules) allows this file to be
8
+ * easily used by downstream tooling like simple esbuild scripts, rollup
9
+ * configs, etc. without actually importing all the modules in modules.tsx,
10
+ * which a Object.keys(modules) would do
11
+ */
12
+ // Per-component MUI subpaths, and the legacy `@material-ui/core/*` aliases
13
+ // below, both derived from the one name list — see muiComponentNames.ts for why
14
+ // that list is its own MUI-free module.
15
+ const muiComponentSubpaths = MUI_COMPONENT_NAMES.map(n => `@mui/material/${n}`);
1
16
  export default [
2
17
  'mobx',
3
18
  '@jbrowse/mobx-state-tree',
@@ -16,260 +31,70 @@ export default [
16
31
  '@mui/material',
17
32
  '@mui/material/styles',
18
33
  '@material-ui/core/styles',
19
- '@material-ui/core/Accordion',
20
- '@material-ui/core/AccordionActions',
21
- '@material-ui/core/AccordionDetails',
22
- '@material-ui/core/AccordionSummary',
23
- '@material-ui/core/Alert',
24
- '@material-ui/core/AlertTitle',
25
- '@material-ui/core/Autocomplete',
26
- '@material-ui/core/Avatar',
27
- '@material-ui/core/AvatarGroup',
28
- '@material-ui/core/Backdrop',
29
- '@material-ui/core/Badge',
30
- '@material-ui/core/Box',
31
- '@material-ui/core/Breadcrumbs',
32
- '@material-ui/core/Button',
33
- '@material-ui/core/ButtonGroup',
34
- '@material-ui/core/Card',
35
- '@material-ui/core/CardActions',
36
- '@material-ui/core/CardActionArea',
37
- '@material-ui/core/CardContent',
38
- '@material-ui/core/CardHeader',
39
- '@material-ui/core/CardMedia',
40
- '@material-ui/core/CircularProgress',
41
- '@material-ui/core/Collapse',
42
- '@material-ui/core/ClickAwayListener',
43
- '@material-ui/core/Chip',
44
- '@material-ui/core/Checkbox',
45
- '@material-ui/core/Container',
46
- '@material-ui/core/Dialog',
47
- '@material-ui/core/DialogActions',
48
- '@material-ui/core/DialogTitle',
49
- '@material-ui/core/DialogContent',
50
- '@material-ui/core/DialogContentText',
51
- '@material-ui/core/Divider',
52
- '@material-ui/core/Drawer',
53
- '@material-ui/core/Fab',
54
- '@material-ui/core/Fade',
55
- '@material-ui/core/FilledInput',
56
- '@material-ui/core/FormLabel',
57
- '@material-ui/core/FormControl',
58
- '@material-ui/core/FormControlLabel',
59
- '@material-ui/core/FormHelperText',
60
- '@material-ui/core/FormGroup',
61
- '@material-ui/core/Grid',
62
- '@material-ui/core/Grid2',
63
- '@material-ui/core/Grow',
64
- '@material-ui/core/Icon',
65
- '@material-ui/core/IconButton',
66
- '@material-ui/core/Input',
67
- '@material-ui/core/InputBase',
68
- '@material-ui/core/InputLabel',
69
- '@material-ui/core/InputAdornment',
70
- '@material-ui/core/Link',
71
- '@material-ui/core/LinearProgress',
72
- '@material-ui/core/List',
73
- '@material-ui/core/ListItem',
74
- '@material-ui/core/ListItemAvatar',
75
- '@material-ui/core/ListItemButton',
76
- '@material-ui/core/ListItemSecondaryAction',
77
- '@material-ui/core/ListItemIcon',
78
- '@material-ui/core/ListSubheader',
79
- '@material-ui/core/ListItemText',
80
- '@material-ui/core/Menu',
81
- '@material-ui/core/MenuItem',
82
- '@material-ui/core/MenuList',
83
- '@material-ui/core/Modal',
84
- '@material-ui/core/NativeSelect',
85
- '@material-ui/core/OutlinedInput',
86
- '@material-ui/core/Pagination',
87
- '@material-ui/core/PaginationItem',
88
- '@material-ui/core/Paper',
89
- '@material-ui/core/Popover',
90
- '@material-ui/core/Popper',
91
- '@material-ui/core/Portal',
92
- '@material-ui/core/Radio',
93
- '@material-ui/core/RadioGroup',
94
- '@material-ui/core/Rating',
95
- '@material-ui/core/ScopedCssBaseline',
96
- '@material-ui/core/Select',
97
- '@material-ui/core/Skeleton',
98
- '@material-ui/core/Slider',
99
- '@material-ui/core/Snackbar',
100
- '@material-ui/core/SnackbarContent',
101
- '@material-ui/core/SpeedDial',
102
- '@material-ui/core/SpeedDialAction',
103
- '@material-ui/core/SpeedDialIcon',
104
- '@material-ui/core/Stack',
105
- '@material-ui/core/Step',
106
- '@material-ui/core/StepButton',
107
- '@material-ui/core/StepConnector',
108
- '@material-ui/core/StepLabel',
109
- '@material-ui/core/StepIcon',
110
- '@material-ui/core/Stepper',
111
- '@material-ui/core/SvgIcon',
112
- '@material-ui/core/Switch',
113
- '@material-ui/core/Tab',
114
- '@material-ui/core/Table',
115
- '@material-ui/core/TableBody',
116
- '@material-ui/core/TableCell',
117
- '@material-ui/core/TableContainer',
118
- '@material-ui/core/TableFooter',
119
- '@material-ui/core/TableHead',
120
- '@material-ui/core/TablePagination',
121
- '@material-ui/core/TableRow',
122
- '@material-ui/core/TableSortLabel',
123
- '@material-ui/core/Tabs',
124
- '@material-ui/core/TextField',
125
- '@material-ui/core/TextareaAutosize',
126
- '@material-ui/core/ToggleButton',
127
- '@material-ui/core/ToggleButtonGroup',
128
- '@material-ui/core/Toolbar',
129
- '@material-ui/core/Tooltip',
130
- '@material-ui/core/Typography',
131
- '@mui/material/Accordion',
132
- '@mui/material/AccordionActions',
133
- '@mui/material/AccordionDetails',
134
- '@mui/material/AccordionSummary',
135
- '@mui/material/Alert',
136
- '@mui/material/AlertTitle',
137
- '@mui/material/Autocomplete',
138
- '@mui/material/Avatar',
139
- '@mui/material/AvatarGroup',
140
- '@mui/material/Backdrop',
141
- '@mui/material/Badge',
142
- '@mui/material/Box',
143
- '@mui/material/Breadcrumbs',
144
- '@mui/material/Button',
145
- '@mui/material/ButtonGroup',
146
- '@mui/material/Card',
147
- '@mui/material/CardActions',
148
- '@mui/material/CardActionArea',
149
- '@mui/material/CardContent',
150
- '@mui/material/CardHeader',
151
- '@mui/material/CardMedia',
152
- '@mui/material/CircularProgress',
153
- '@mui/material/Collapse',
154
- '@mui/material/ClickAwayListener',
155
- '@mui/material/Chip',
156
- '@mui/material/Checkbox',
157
- '@mui/material/Container',
158
- '@mui/material/Dialog',
159
- '@mui/material/DialogActions',
160
- '@mui/material/DialogTitle',
161
- '@mui/material/DialogContent',
162
- '@mui/material/DialogContentText',
163
- '@mui/material/Divider',
164
- '@mui/material/Drawer',
165
- '@mui/material/Fab',
166
- '@mui/material/Fade',
167
- '@mui/material/FilledInput',
168
- '@mui/material/FormLabel',
169
- '@mui/material/FormControl',
170
- '@mui/material/FormControlLabel',
171
- '@mui/material/FormHelperText',
172
- '@mui/material/FormGroup',
173
- '@mui/material/Grid',
174
- '@mui/material/Grid2',
175
- '@mui/material/Grow',
176
- '@mui/material/Icon',
177
- '@mui/material/IconButton',
178
- '@mui/material/Input',
179
- '@mui/material/InputBase',
180
- '@mui/material/InputLabel',
181
- '@mui/material/InputAdornment',
182
- '@mui/material/Link',
183
- '@mui/material/LinearProgress',
184
- '@mui/material/List',
185
- '@mui/material/ListItem',
186
- '@mui/material/ListItemAvatar',
187
- '@mui/material/ListItemButton',
188
- '@mui/material/ListItemSecondaryAction',
189
- '@mui/material/ListItemIcon',
190
- '@mui/material/ListSubheader',
191
- '@mui/material/ListItemText',
192
- '@mui/material/Menu',
193
- '@mui/material/MenuItem',
194
- '@mui/material/MenuList',
195
- '@mui/material/Modal',
196
- '@mui/material/NativeSelect',
197
- '@mui/material/OutlinedInput',
198
- '@mui/material/Pagination',
199
- '@mui/material/PaginationItem',
200
- '@mui/material/Paper',
201
- '@mui/material/Popover',
202
- '@mui/material/Popper',
203
- '@mui/material/Portal',
204
- '@mui/material/Radio',
205
- '@mui/material/RadioGroup',
206
- '@mui/material/Rating',
207
- '@mui/material/ScopedCssBaseline',
208
- '@mui/material/Select',
209
- '@mui/material/Skeleton',
210
- '@mui/material/Slider',
211
- '@mui/material/Snackbar',
212
- '@mui/material/SnackbarContent',
213
- '@mui/material/SpeedDial',
214
- '@mui/material/SpeedDialAction',
215
- '@mui/material/SpeedDialIcon',
216
- '@mui/material/Stack',
217
- '@mui/material/Step',
218
- '@mui/material/StepButton',
219
- '@mui/material/StepConnector',
220
- '@mui/material/StepLabel',
221
- '@mui/material/StepIcon',
222
- '@mui/material/Stepper',
223
- '@mui/material/SvgIcon',
224
- '@mui/material/Switch',
225
- '@mui/material/Tab',
226
- '@mui/material/Table',
227
- '@mui/material/TableBody',
228
- '@mui/material/TableCell',
229
- '@mui/material/TableContainer',
230
- '@mui/material/TableFooter',
231
- '@mui/material/TableHead',
232
- '@mui/material/TablePagination',
233
- '@mui/material/TableRow',
234
- '@mui/material/TableSortLabel',
235
- '@mui/material/Tabs',
236
- '@mui/material/TextField',
237
- '@mui/material/TextareaAutosize',
238
- '@mui/material/ToggleButton',
239
- '@mui/material/ToggleButtonGroup',
240
- '@mui/material/Toolbar',
241
- '@mui/material/Tooltip',
242
- '@mui/material/Typography',
34
+ ...muiComponentSubpaths.map(p => p.replace('@mui/material/', '@material-ui/core/')),
35
+ ...muiComponentSubpaths,
243
36
  '@material-ui/lab/ToggleButton',
244
37
  '@material-ui/lab/ToggleButtonGroup',
245
38
  '@material-ui/lab/Autocomplete',
246
39
  '@material-ui/lab/Alert',
247
40
  '@material-ui/lab',
41
+ // The `@jbrowse/core` subpaths below are the ones a plugin may import and get
42
+ // the host's copy of. Each carries a `#reexport <what it provides>` line,
43
+ // which renders the table in the dependencies-and-re-exports guide
44
+ // (website/scripts/api-docs/generateReExportDocs.ts) — so the guide stops
45
+ // restating this list, which is what left it five paths short. A new subpath
46
+ // needs the tag or the generator fails.
47
+ //
48
+ // Only the `@jbrowse/core` entries are tagged: the framework and MUI ones
49
+ // above are described by category in the guide's prose, not one row each.
50
+ // #reexport The base `Plugin` class your plugin extends
248
51
  '@jbrowse/core/Plugin',
52
+ // #reexport `ViewType`, `AdapterType`, `DisplayType`, `TrackType`, `WidgetType` in one import, for the `install` method that registers several
249
53
  '@jbrowse/core/pluggableElementTypes',
54
+ // #reexport Just the `ViewType` class, registered with `addViewType`
250
55
  '@jbrowse/core/pluggableElementTypes/ViewType',
56
+ // #reexport Just the `AdapterType` class, registered with `addAdapterType`
251
57
  '@jbrowse/core/pluggableElementTypes/AdapterType',
58
+ // #reexport Just the `DisplayType` class, registered with `addDisplayType`
252
59
  '@jbrowse/core/pluggableElementTypes/DisplayType',
60
+ // #reexport Just the `TrackType` class, registered with `addTrackType`
253
61
  '@jbrowse/core/pluggableElementTypes/TrackType',
62
+ // #reexport Just the `WidgetType` class, registered with `addWidgetType`
254
63
  '@jbrowse/core/pluggableElementTypes/WidgetType',
64
+ // #reexport Base MST models for tracks and displays to compose with
255
65
  '@jbrowse/core/pluggableElementTypes/models',
256
- '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType',
257
- '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType',
258
- '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType',
259
- '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType',
260
- '@jbrowse/core/pluggableElementTypes/renderers/RendererType',
66
+ // #reexport `ConfigurationSchema`, `ConfigurationReference`, `readConfObject`, `getConf`
261
67
  '@jbrowse/core/configuration',
68
+ // #reexport Reusable MST types like `ElementId` and `Region`
262
69
  '@jbrowse/core/util/types/mst',
70
+ // #reexport Shared UI components — dialogs, menus, error and loading states
263
71
  '@jbrowse/core/ui',
72
+ // #reexport The JBrowse MUI theme
264
73
  '@jbrowse/core/ui/theme',
74
+ // #reexport The same colors and `resolvePalette` without Material UI in the module graph, for worker and renderer code
75
+ '@jbrowse/core/ui/palette',
76
+ // #reexport The hover tooltip, kept out of the `ui` barrel so @floating-ui stays off the startup path
77
+ '@jbrowse/core/ui/BaseTooltip',
78
+ // #reexport Core helpers: `getSession`, `getContainingView`, `Feature`, region and coordinate utilities
265
79
  '@jbrowse/core/util',
80
+ // #reexport Color parsing and manipulation helpers
266
81
  '@jbrowse/core/util/color',
82
+ // #reexport Feature layout (packing) helpers
267
83
  '@jbrowse/core/util/layouts',
84
+ // #reexport Track and adapter config helpers
268
85
  '@jbrowse/core/util/tracks',
86
+ // #reexport The 1D (bp↔px) view model the linear views are built on
269
87
  '@jbrowse/core/util/Base1DViewModel',
88
+ // #reexport `openLocation` and the file-handle helpers
270
89
  '@jbrowse/core/util/io',
90
+ // #reexport Helpers for inspecting MST types
271
91
  '@jbrowse/core/util/mst-reflection',
92
+ // #reexport The RxJS re-exports an adapter's `getFeatures` stream is built from
272
93
  '@jbrowse/core/util/rxjs',
94
+ // #reexport `FeatureDetails`, `BaseCard` and the other feature-detail building blocks
273
95
  '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail',
96
+ // #reexport `BaseFeatureDataAdapter` and the adapter base classes
274
97
  '@jbrowse/core/data_adapters/BaseAdapter',
98
+ // #reexport `getAdapter`, the worker-side adapter cache an RPC method resolves its adapter through
99
+ '@jbrowse/core/data_adapters/dataAdapterCache',
275
100
  ];
@@ -1,46 +1,52 @@
1
+ // eslint-disable-next-line no-restricted-imports
1
2
  import * as React from 'react';
2
3
  import * as mst from '@jbrowse/mobx-state-tree';
3
4
  import { alpha, createTheme, useTheme } from '@mui/material';
4
- import * as MUIStyles from '@mui/material/styles';
5
+ import SvgIcon, { createSvgIcon } from '@mui/material/SvgIcon';
5
6
  import * as MUIUtils from '@mui/material/utils';
6
- import { useGridApiContext, useGridApiRef, useGridRootProps, } from '@mui/x-data-grid';
7
7
  import * as mobx from 'mobx';
8
8
  import * as mxreact from 'mobx-react';
9
- import * as ReactJSXRuntime from 'react/jsx-runtime';
10
9
  import * as ReactDom from 'react-dom';
11
10
  import * as ReactDomClient from 'react-dom/client';
12
- import Plugin from "../Plugin.js";
13
- import { BaseFeatureDetail } from "./BaseFeatureDetails.js";
14
- import { DataGridEntries } from "./MuiDataGridReExports.js";
15
- import { Entries } from "./MuiReExports.js";
16
- import { lazyMap } from "./lazify.js";
17
- import reExportsList from "./list.js";
18
- import * as Configuration from "../configuration/index.js";
19
- import * as BaseAdapterExports from "../data_adapters/BaseAdapter/index.js";
20
- import AdapterType from "../pluggableElementTypes/AdapterType.js";
21
- import DisplayType from "../pluggableElementTypes/DisplayType.js";
22
- import TrackType from "../pluggableElementTypes/TrackType.js";
23
- import ViewType from "../pluggableElementTypes/ViewType.js";
24
- import WidgetType from "../pluggableElementTypes/WidgetType.js";
25
- import * as pluggableElementTypes from "../pluggableElementTypes/index.js";
26
- import * as pluggableElementTypeModels from "../pluggableElementTypes/models/index.js";
27
- import * as BoxRendererType from "../pluggableElementTypes/renderers/BoxRendererType.js";
28
- import CircularChordRendererType from "../pluggableElementTypes/renderers/CircularChordRendererType.js";
29
- import * as FeatureRendererType from "../pluggableElementTypes/renderers/FeatureRendererType.js";
30
- import * as RendererType from "../pluggableElementTypes/renderers/RendererType.js";
31
- import * as ServerSideRendererType from "../pluggableElementTypes/renderers/ServerSideRendererType.js";
32
- import * as coreUi from "../ui/index.js";
33
- import * as coreTheme from "../ui/theme.js";
34
- import Base1DView from "../util/Base1DViewModel.js";
35
- import * as coreColor from "../util/color/index.js";
36
- import * as coreUtil from "../util/index.js";
37
- import * as coreIo from "../util/io/index.js";
38
- import * as coreLayouts from "../util/layouts/index.js";
39
- import * as coreMstReflection from "../util/mst-reflection.js";
40
- import * as rxjs from "../util/rxjs.js";
41
- import * as trackUtils from "../util/tracks.js";
42
- import { cx, keyframes, makeStyles } from "../util/tss-react/index.js";
43
- import * as mstTypes from "../util/types/mst.js";
11
+ import * as ReactJSXRuntime from 'react/jsx-runtime';
12
+ import Plugin from '../Plugin.js';
13
+ import * as Configuration from '../configuration/index.js';
14
+ import * as BaseAdapterExports from '../data_adapters/BaseAdapter/index.js';
15
+ import * as dataAdapterCache from '../data_adapters/dataAdapterCache.js';
16
+ import AdapterType from '../pluggableElementTypes/AdapterType.js';
17
+ import DisplayType from '../pluggableElementTypes/DisplayType.js';
18
+ import TrackType from '../pluggableElementTypes/TrackType.js';
19
+ import ViewType from '../pluggableElementTypes/ViewType.js';
20
+ import WidgetType from '../pluggableElementTypes/WidgetType.js';
21
+ import * as pluggableElementTypes from '../pluggableElementTypes/index.js';
22
+ import * as pluggableElementTypeModels from '../pluggableElementTypes/models/index.js';
23
+ import * as coreUi from '../ui/index.js';
24
+ import * as corePalette from '../ui/palette.js';
25
+ import * as coreTheme from '../ui/theme.js';
26
+ import Base1DView from '../util/Base1DViewModel.js';
27
+ import * as coreColor from '../util/color/index.js';
28
+ import * as coreIo from '../util/io/index.js';
29
+ import * as coreLayouts from '../util/layouts/index.js';
30
+ import * as coreMstReflection from '../util/mst-reflection.js';
31
+ import * as rxjs from '../util/rxjs.js';
32
+ import * as trackUtils from '../util/tracks.js';
33
+ import { cx, keyframes, makeStyles } from '../util/tss-react/index.js';
34
+ import * as mstTypes from '../util/types/mst.js';
35
+ import { BaseFeatureDetail } from './BaseFeatureDetails.js';
36
+ import { DataGridEntries } from './MuiDataGridReExports.js';
37
+ import { Entries } from './MuiReExports.js';
38
+ import { MUIStyles } from './MuiStylesReExports.js';
39
+ import { lazyMap } from './lazify.js';
40
+ import reExportsList from './list.js';
41
+ import * as coreUtil from './publicUtil.js';
42
+ function makeLegacyMakeStyles() {
43
+ return (args) => {
44
+ const useStyles = makeStyles()(args);
45
+ return () => useStyles().classes;
46
+ };
47
+ }
48
+ const tssReact = { cx, keyframes, makeStyles };
49
+ const legacyMakeStyles = makeLegacyMakeStyles();
44
50
  const libs = {
45
51
  mobx,
46
52
  '@jbrowse/mobx-state-tree': mst,
@@ -50,32 +56,24 @@ const libs = {
50
56
  'react-dom': ReactDom,
51
57
  'react-dom/client': ReactDomClient,
52
58
  'mobx-react': mxreact,
59
+ // Only lazy component entries are re-exported. The grid *hooks*
60
+ // (useGridApiContext/useGridApiRef/useGridRootProps) are intentionally left
61
+ // out: statically importing them here pulled the entire ~1.2 MB
62
+ // @mui/x-data-grid package into the eager first-paint graph, defeating the
63
+ // lazy import('@mui/x-data-grid') in MuiDataGridReExports. First-party code
64
+ // that needs the hooks imports them directly from '@mui/x-data-grid'.
53
65
  '@mui/x-data-grid': {
54
- useGridApiContext,
55
- useGridApiRef,
56
- useGridRootProps,
57
66
  ...lazyMap(DataGridEntries),
58
67
  },
59
68
  '@mui/material/utils': MUIUtils,
60
69
  '@material-ui/core/utils': MUIUtils,
61
- 'tss-react': {
62
- cx,
63
- keyframes,
64
- makeStyles,
65
- },
66
- 'tss-react/mui': {
67
- cx,
68
- keyframes,
69
- makeStyles,
70
- },
70
+ 'tss-react': tssReact,
71
+ 'tss-react/mui': tssReact,
71
72
  '@material-ui/core': {
72
73
  ...lazyMap(Entries),
73
74
  useTheme,
74
75
  alpha,
75
- makeStyles: (args) => {
76
- const useStyles = makeStyles()(args);
77
- return () => useStyles().classes;
78
- },
76
+ makeStyles: legacyMakeStyles,
79
77
  },
80
78
  '@mui/material': {
81
79
  ...lazyMap(Entries),
@@ -85,20 +83,27 @@ const libs = {
85
83
  },
86
84
  ...lazyMap(Entries, '@mui/material/'),
87
85
  ...lazyMap(Entries, '@material-ui/core/'),
86
+ // @mui/icons-material — bundled into external plugins — reads the
87
+ // `createSvgIcon` *named* export from @mui/material/SvgIcon, but lazyMap
88
+ // exposes only the component (its default). SvgIcon is a primitive that's
89
+ // eagerly loaded in practice, so expose it directly with createSvgIcon
90
+ // attached: a default import still lands on a usable component (rollup-plugin-
91
+ // external-globals substitutes the value itself, esbuild's globalExternals
92
+ // reads `.default`), while the named import and icons-material's CJS
93
+ // `require(...).createSvgIcon` both find the util. A shallow copy carries the
94
+ // forwardRef's $$typeof/render so the shared SvgIcon export isn't mutated.
95
+ // Overrides the lazy entry above; verified against both bundlers.
96
+ // GMOD/jbrowse-components#5606.
97
+ '@mui/material/SvgIcon': Object.assign({}, SvgIcon, { createSvgIcon }),
88
98
  '@mui/material/styles': {
89
99
  ...MUIStyles,
90
- makeStyles: (args) => {
91
- const useStyles = makeStyles()(args);
92
- return () => useStyles().classes;
93
- },
100
+ makeStyles: legacyMakeStyles,
94
101
  },
95
102
  '@material-ui/core/styles': {
96
103
  ...MUIStyles,
97
- makeStyles: (args) => {
98
- const useStyles = makeStyles()(args);
99
- return () => useStyles().classes;
100
- },
104
+ makeStyles: legacyMakeStyles,
101
105
  },
106
+ // these are core in @mui/material, but used to be in @material-ui/lab
102
107
  '@material-ui/lab/ToggleButton': Entries.ToggleButton,
103
108
  '@material-ui/lab/ToggleButtonGroup': Entries.ToggleButtonGroup,
104
109
  '@material-ui/lab/Autocomplete': Entries.Autocomplete,
@@ -110,11 +115,19 @@ const libs = {
110
115
  ToggleButtonGroup: Entries.ToggleButtonGroup,
111
116
  },
112
117
  '@jbrowse/core/Plugin': Plugin,
113
- '@jbrowse/core/pluggableElementTypes/renderers/RendererType': RendererType,
114
118
  '@jbrowse/core/configuration': Configuration,
115
119
  '@jbrowse/core/util/types/mst': mstTypes,
116
120
  '@jbrowse/core/ui': coreUi,
117
121
  '@jbrowse/core/ui/theme': coreTheme,
122
+ '@jbrowse/core/ui/palette': corePalette,
123
+ // BaseTooltip is deliberately absent from the '@jbrowse/core/ui' barrel: the
124
+ // re-export alone held @floating-ui (~266KB) on the startup path, since eager
125
+ // plugin entries import that barrel. Serving it as its own module behind
126
+ // React.lazy keeps it off that path while leaving external plugins a way to
127
+ // reach it -- published apollo deep-imports this exact path, and react-msaview
128
+ // (bundled by tview and msaview) reads it too, so dropping it from the barrel
129
+ // with no ABI home is what broke them.
130
+ ...lazyMap({ BaseTooltip: React.lazy(() => import('../ui/BaseTooltip.js')) }, '@jbrowse/core/ui/'),
118
131
  '@jbrowse/core/util': coreUtil,
119
132
  '@jbrowse/core/util/color': coreColor,
120
133
  '@jbrowse/core/util/layouts': coreLayouts,
@@ -130,14 +143,20 @@ const libs = {
130
143
  '@jbrowse/core/pluggableElementTypes/TrackType': TrackType,
131
144
  '@jbrowse/core/pluggableElementTypes/WidgetType': WidgetType,
132
145
  '@jbrowse/core/pluggableElementTypes/models': pluggableElementTypeModels,
133
- '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType': ServerSideRendererType,
134
- '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType': CircularChordRendererType,
135
- '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType': BoxRendererType,
136
- '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType': FeatureRendererType,
137
146
  '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': BaseFeatureDetail,
138
147
  '@jbrowse/core/data_adapters/BaseAdapter': BaseAdapterExports,
148
+ // `adapterCache` is module-level state, so a plugin that bundles its own copy
149
+ // of this file gets a second cache in the RPC worker — and `freeAdapterResources`,
150
+ // which CoreFreeResources calls on the host's copy when the last track using
151
+ // an adapter config closes, never sees it. The cache is the only strong
152
+ // reference to an adapter (see the comment on that function), so those
153
+ // adapters and everything they hold live as long as the worker. Serving the
154
+ // module is what makes an external RPC method share the host's cache.
155
+ '@jbrowse/core/data_adapters/dataAdapterCache': dataAdapterCache,
139
156
  };
140
157
  const libsList = Object.keys(libs);
158
+ // make sure that all the items in the ReExports/list array (used by build
159
+ // systems and such) are included here, and vice versa
141
160
  const inLibsOnly = libsList.filter(mod => !reExportsList.includes(mod));
142
161
  if (inLibsOnly.length > 0) {
143
162
  throw new Error(`The following modules are in the modules libs, but not the re-exports list: ${inLibsOnly.join(', ')}`);
@@ -0,0 +1,18 @@
1
+ /**
2
+ * Every MUI component name the host re-exports to plugins.
3
+ *
4
+ * Its own module, with **no MUI imports**, because the two things that need it
5
+ * cannot both reach the other: `MuiReExports.ts` holds the components
6
+ * themselves, and `list.ts` must stay importable by bundler configs and
7
+ * esbuild scripts without pulling MUI in behind it (see that file's header).
8
+ * The names were therefore written out twice — 112 of them — and kept in
9
+ * agreement by a load-time throw in `modules.ts`.
10
+ *
11
+ * Declaring them here instead makes `Entries` a `Record` over this union, so a
12
+ * name with no component and a component with no name are both compile errors,
13
+ * and `list.ts` derives its subpaths by mapping. The runtime check in
14
+ * `modules.ts` stays: it still covers the framework and `@jbrowse/core` entries,
15
+ * which are not this list.
16
+ */
17
+ export declare const MUI_COMPONENT_NAMES: readonly ['Accordion', 'AccordionActions', 'AccordionDetails', 'AccordionSummary', 'Alert', 'AlertTitle', 'Autocomplete', 'Avatar', 'AvatarGroup', 'Backdrop', 'Badge', 'Box', 'Breadcrumbs', 'Button', 'ButtonGroup', 'Card', 'CardActions', 'CardActionArea', 'CardContent', 'CardHeader', 'CardMedia', 'Chip', 'CircularProgress', 'Collapse', 'ClickAwayListener', 'Checkbox', 'Container', 'Dialog', 'DialogActions', 'DialogTitle', 'DialogContent', 'DialogContentText', 'Divider', 'Drawer', 'Fab', 'Fade', 'FilledInput', 'FormLabel', 'FormControl', 'FormControlLabel', 'FormHelperText', 'FormGroup', 'Grid', 'Grid2', 'Grow', 'Icon', 'IconButton', 'Input', 'InputBase', 'InputLabel', 'InputAdornment', 'Link', 'LinearProgress', 'List', 'ListItem', 'ListItemAvatar', 'ListItemButton', 'ListItemSecondaryAction', 'ListItemIcon', 'ListSubheader', 'ListItemText', 'Menu', 'MenuItem', 'MenuList', 'Modal', 'NativeSelect', 'OutlinedInput', 'Pagination', 'PaginationItem', 'Paper', 'Popover', 'Popper', 'Portal', 'Radio', 'RadioGroup', 'Rating', 'ScopedCssBaseline', 'Select', 'Skeleton', 'Slider', 'Snackbar', 'SnackbarContent', 'SpeedDial', 'SpeedDialAction', 'SpeedDialIcon', 'Stack', 'Step', 'StepButton', 'StepConnector', 'StepLabel', 'StepIcon', 'Stepper', 'SvgIcon', 'Switch', 'Tab', 'Table', 'TableBody', 'TableCell', 'TableContainer', 'TableFooter', 'TableHead', 'TablePagination', 'TableRow', 'TableSortLabel', 'Tabs', 'TextField', 'TextareaAutosize', 'ToggleButton', 'ToggleButtonGroup', 'Toolbar', 'Tooltip', 'Typography'];
18
+ export type MuiComponentName = (typeof MUI_COMPONENT_NAMES)[number];