@jbrowse/core 4.3.0 → 5.0.0-beta.10

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 (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  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 -5
  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 +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  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 +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
  1057. package/esm/util/springAnimate.js +80 -0
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  1064. package/esm/util/stringUtils.d.ts +5 -0
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  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
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  1070. package/esm/util/systemColorScheme.d.ts +12 -0
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  1074. package/esm/util/tags.d.ts +2 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1082. package/esm/util/timeGate.d.ts +25 -0
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  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
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  1086. package/esm/util/tracks.d.ts +431 -30
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  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
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  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
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  1116. package/esm/util/types/services.d.ts +55 -0
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  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
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  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
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  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1151. package/esm/util/virtualRange.d.ts +36 -0
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  1153. package/esm/util/webStorage.d.ts +26 -0
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  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
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  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
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  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
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  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,45 @@
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { observer } from 'mobx-react';
3
+ import { groupByPlace } from '../../TextSearch/places.js';
4
+ import { getTrackName } from '../../util/tracks.js';
5
+ import { makeStyles } from '../../util/tss-react/index.js';
6
+ import { optionDetail } from './util.js';
7
+ const useStyles = makeStyles()(theme => ({
8
+ row: {
9
+ display: 'flex',
10
+ alignItems: 'baseline',
11
+ gap: theme.spacing(2),
12
+ },
13
+ label: {
14
+ flexShrink: 0,
15
+ whiteSpace: 'nowrap',
16
+ },
17
+ detail: {
18
+ marginLeft: 'auto',
19
+ minWidth: 0,
20
+ overflow: 'hidden',
21
+ textOverflow: 'ellipsis',
22
+ whiteSpace: 'nowrap',
23
+ fontSize: '0.8em',
24
+ color: theme.palette.text.secondary,
25
+ },
26
+ }));
27
+ const SearchOption = observer(function SearchOption({ props, option, session, assembly, }) {
28
+ const { classes, cx } = useStyles();
29
+ const { key, className, ...rest } = props;
30
+ const { result } = option;
31
+ const detail = optionDetail(result, {
32
+ trackNameOf: trackId => {
33
+ const conf = session.getTrackById(trackId);
34
+ return conf ? getTrackName(conf, session) : undefined;
35
+ },
36
+ lengthOf: refName => {
37
+ const index = assembly?.refNameToIndex?.get(refName);
38
+ const region = index === undefined ? undefined : assembly?.regions?.[index];
39
+ return region ? region.end - region.start : undefined;
40
+ },
41
+ placesOf: results => groupByPlace(results, assembly),
42
+ });
43
+ return (_jsxs("li", { className: cx(className, classes.row), ...rest, children: [_jsx("span", { className: classes.label, children: result.getDisplayString() }), detail ? _jsx("span", { className: classes.detail, children: detail }) : null] }, key));
44
+ });
45
+ export default SearchOption;
@@ -0,0 +1,21 @@
1
+ import type BaseResult from '../../TextSearch/BaseResults.ts';
2
+ import type { AbstractSessionModel } from '../../util/index.ts';
3
+ import type { CSSProperties, ReactNode } from 'react';
4
+ declare const RefNameAutocomplete: ({ session, assemblyName, value, fetchResults, onSelect, onChange, minWidth, maxWidth, adornmentWidth, style, endAdornment, helperText, inputStyle, }: {
5
+ session: AbstractSessionModel;
6
+ assemblyName?: string;
7
+ value?: string;
8
+ fetchResults: (query: string, signal?: AbortSignal) => Promise<BaseResult[]>;
9
+ onSelect?: (region: BaseResult) => void;
10
+ onChange?: (val: string) => void;
11
+ minWidth?: number;
12
+ maxWidth?: number;
13
+ adornmentWidth?: number;
14
+ style?: CSSProperties;
15
+ endAdornment?: ReactNode;
16
+ helperText?: string;
17
+ inputStyle?: CSSProperties;
18
+ }) => import("react").JSX.Element;
19
+ export default RefNameAutocomplete;
20
+ export { default as RefNameAutocompleteEndAdornment } from './EndAdornment.tsx';
21
+ export { adornmentReservePx, getInputWidth } from './util.ts';
@@ -0,0 +1,84 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { useState } from 'react';
3
+ import { Autocomplete, TextField } from '@mui/material';
4
+ import { observer } from 'mobx-react';
5
+ import { useDebounce } from '../../util/hooks.js';
6
+ import { useFetch } from '../../util/useFetch.js';
7
+ import SearchOption from './SearchOption.js';
8
+ import { cap, coerceToResult, getDeduplicatedResult, getInputWidth, getOptionLabel, getRefNameOptions, } from './util.js';
9
+ const RefNameAutocomplete = observer(function RefNameAutocomplete({ session, assemblyName, value, fetchResults, onSelect, onChange, minWidth = 200, maxWidth = 550, adornmentWidth, style, endAdornment, helperText, inputStyle, }) {
10
+ const { assemblyManager } = session;
11
+ const externalValue = value ?? '';
12
+ // MUI Autocomplete tracks `inputValue` (displayed text) separately from
13
+ // `value` (selected item). We echo every MUI event into `inputValue` so
14
+ // external value changes, blur snap-back, and keystrokes all stay in sync.
15
+ const [inputValue, setInputValue] = useState(externalValue);
16
+ // `searchQuery` drives the fetch and filter — only updated on real typing
17
+ // so blur/reset events don't trigger phantom searches.
18
+ const [searchQuery, setSearchQuery] = useState('');
19
+ const debouncedSearch = useDebounce(searchQuery, 50);
20
+ const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
21
+ const shouldSearch = !!assemblyName && debouncedSearch !== '';
22
+ const { data: searchOptions, isLoading } = useFetch(
23
+ // `as const` so the key is a fixed-arity tuple: useFetch derives the
24
+ // fetcher's parameter list from it, and a plain array widens to a variadic
25
+ // the named parameters below cannot be destructured out of
26
+ shouldSearch
27
+ ? ['refNameSearch', assemblyName, debouncedSearch]
28
+ : null, async (_tag, _assembly, query, signal) => getDeduplicatedResult(await fetchResults(query, signal)), {
29
+ onError: e => {
30
+ session.notifyError(`${e}`, e);
31
+ },
32
+ });
33
+ const width = getInputWidth(externalValue, minWidth, maxWidth, adornmentWidth);
34
+ const hasSearchResults = !!searchOptions?.length;
35
+ return (_jsx(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, clearOnBlur: true, style: { ...style, width }, value: externalValue, loading: isLoading, inputValue: inputValue, onInputChange: (_event, newInputValue, reason) => {
36
+ setInputValue(newInputValue);
37
+ if (reason === 'input') {
38
+ setSearchQuery(newInputValue);
39
+ onChange?.(newInputValue);
40
+ }
41
+ else if (reason === 'blur' || reason === 'selectOption') {
42
+ // clear so stale results don't linger; skip 'reset' because MUI
43
+ // fires that during its own re-render loop and clearing it kills
44
+ // an in-flight search
45
+ setSearchQuery('');
46
+ }
47
+ }, loadingText: "loading results", onChange: (_event, selectedOption) => {
48
+ if (selectedOption) {
49
+ onSelect?.(coerceToResult(selectedOption));
50
+ // snap back to the current loc; if navigation succeeds the parent
51
+ // updates `value` and MUI's 'reset' event will reflect the new loc
52
+ setInputValue(externalValue);
53
+ }
54
+ },
55
+ // built inside the branch rather than every render: it scans the
56
+ // assembly's regions and materializes up to the cap in option objects,
57
+ // which is wasted work on the keystrokes that do have search results
58
+ options: hasSearchResults
59
+ ? searchOptions
60
+ : getRefNameOptions(assembly, searchQuery), getOptionDisabled: option => !!option.isLimit,
61
+ // both sources arrive already matched against a query — searchOptions
62
+ // server-side for `debouncedSearch`, regionOptions live for `searchQuery`
63
+ // — so MUI must not re-filter them (its default filter would drop hits
64
+ // matching on a description rather than the display string). Only cap.
65
+ filterOptions: cap, renderInput: ({ slotProps: paramSlotProps, ...restParams }) => (_jsx(TextField, { ...restParams, variant: "outlined", size: "small",
66
+ // override global theme default (margin="dense") whose asymmetric
67
+ // 8/4 top/bottom margins offset the input 2px downward
68
+ margin: "none", helperText: helperText, slotProps: {
69
+ ...paramSlotProps,
70
+ input: {
71
+ ...paramSlotProps.input,
72
+ style: inputStyle,
73
+ ...(endAdornment !== undefined && { endAdornment }),
74
+ },
75
+ }, placeholder: "Search for location" })), getOptionLabel: getOptionLabel, slotProps: {
76
+ popper: {
77
+ placement: 'bottom-start',
78
+ style: { width: 'max-content', minWidth: width, maxWidth: 480 },
79
+ },
80
+ }, renderOption: (props, option) => (_jsx(SearchOption, { props: props, option: option, session: session, assembly: assembly }, props.key)) }));
81
+ });
82
+ export default RefNameAutocomplete;
83
+ export { default as RefNameAutocompleteEndAdornment } from './EndAdornment.js';
84
+ export { adornmentReservePx, getInputWidth } from './util.js';
@@ -0,0 +1,62 @@
1
+ import BaseResult from '../../TextSearch/BaseResults.ts';
2
+ import type { RefNameMatchSource } from '../../util/selectNamedRegions.ts';
3
+ export interface Option {
4
+ isLimit?: boolean;
5
+ result: BaseResult;
6
+ }
7
+ export declare function cap(options: Option[]): Option[];
8
+ /**
9
+ * The browse/pre-fetch fallback list, shown while a typed query is in flight and
10
+ * when it comes back empty (typed queries otherwise resolve through
11
+ * fetchResults).
12
+ *
13
+ * The matching itself is `matchRefNames`, in core beside the glob semantics,
14
+ * because Enter answers for the same typed text and the two must not each grow
15
+ * their own reading of it. What is left here is presentation: how many rows to
16
+ * materialize, and the bulk row.
17
+ *
18
+ * **AN EXACT REFNAME BEATS THE GLOB READING here too**, the rule
19
+ * `selectNamedRegions` states and `searchUtils` orders its glob branch after.
20
+ * `*` is a legal refName character and GRCh38's ALT decoys are HLA allele names,
21
+ * so `HLA-A*01:01:01:01` is a contig somebody typed in full — offering "Show all
22
+ * 4 regions matching HLA-A*01:01:01:01" above it is the box promising a set that
23
+ * Enter, on the same text, does not open. The individual matches still list: the
24
+ * pattern reading is not wrong, it is just not what leads.
25
+ *
26
+ * A glob may gather up to MAX_GLOB_REGIONS for that bulk row; a plain query
27
+ * never needs more than the visible list, so it keeps the tighter bound and the
28
+ * cost it always had. Collecting one past MAX_OPTIONS is what lets `cap` render
29
+ * its "keep typing" hint.
30
+ */
31
+ export declare function getRefNameOptions(assembly: RefNameMatchSource | undefined, inputValue: string): Option[];
32
+ export declare function getDeduplicatedResult(results: BaseResult[]): Option[];
33
+ /**
34
+ * The muted line under a row: a sequence's length, where a hit goes and the
35
+ * track it came from, or how many places share the row. A row sharing its name
36
+ * with a sequence is about the sequence, since an annotation's region feature
37
+ * names it too. A row whose hits all go to one place says where, without a
38
+ * track, since the pick lands through whichever of them the view has open. A
39
+ * row standing for many regions needs none.
40
+ */
41
+ export declare function optionDetail(result: BaseResult, lookups: {
42
+ trackNameOf: (trackId: string) => string | undefined;
43
+ lengthOf: (refName: string) => number | undefined;
44
+ placesOf: (results: BaseResult[]) => BaseResult[][];
45
+ }): string | undefined;
46
+ export declare function coerceToResult(option: string | Option): BaseResult;
47
+ export declare function getOptionLabel(option: string | Option): string;
48
+ /**
49
+ * What the end adornment occupies, and the number a caller passes as
50
+ * `adornmentWidth`.
51
+ *
52
+ * The ⋮ button is drawn for consumer-supplied rows as well as for the help one,
53
+ * so the reservation follows `menuItemCount || showHelp` — the same expression
54
+ * `EndAdornment` renders on. Both read it here rather than adding the constants
55
+ * up at the call site, which yields a box that has the button and is sized as
56
+ * if it did not.
57
+ */
58
+ export declare function adornmentReservePx({ showHelp, menuItemCount, }: {
59
+ showHelp?: boolean;
60
+ menuItemCount?: number;
61
+ }): number;
62
+ export declare function getInputWidth(value: string, minWidth: number, maxWidth: number, adornmentWidth?: number): number;
@@ -0,0 +1,209 @@
1
+ import BaseResult, { RefSequenceResult } from '../../TextSearch/BaseResults.js';
2
+ import { getBpDisplayStr, measureText, toLocale } from '../../util/index.js';
3
+ import { MAX_GLOB_REGIONS, matchRefNames, } from '../../util/selectNamedRegions.js';
4
+ // Above the 13.71px the TextField renders at, and left there deliberately. The
5
+ // table is Helvetica's and the box draws in Roboto, so measuring the value at 14
6
+ // comes out about 3% over what the browser paints — `ctgA:1..20,000` measures
7
+ // 90.04 against a drawn 87.74 — and that margin is what lets the reserves below
8
+ // be the chrome's exact width rather than a padded guess.
9
+ const INPUT_FONT_SIZE = 14;
10
+ // What the box spends on everything that is not the locstring, less the ⋮
11
+ // button: the search icon (17), the adornment's right margin (7), and the input
12
+ // padding and border (20). Measured in a built jbrowse-web, where
13
+ // `products/jbrowse-web/browser-tests/probe-lgv-header-fit.ts` prints the box
14
+ // decomposed — adding MUI's documented defaults up instead is what had this
15
+ // reserving 100 for a 71px chrome, so every box stood 29px wider than its
16
+ // contents.
17
+ const ADORNMENT_RESERVE_PX = 44;
18
+ // The ⋮ IconButton, only reserved when it is actually drawn
19
+ const OVERFLOW_BUTTON_RESERVE_PX = 27;
20
+ // quantize the computed width to this step so short locstring length changes (a
21
+ // digit/comma appearing while panning/zooming) don't reflow the box and jitter
22
+ // the surrounding header; also gives short values a little pleasant slack
23
+ const WIDTH_STEP_PX = 30;
24
+ // MUI Autocomplete is not virtualized, so a broad query that returns thousands
25
+ // of hits would render thousands of DOM nodes; cap the visible list instead
26
+ const MAX_OPTIONS = 100;
27
+ export function cap(options) {
28
+ return options.length > MAX_OPTIONS
29
+ ? [
30
+ ...options.slice(0, MAX_OPTIONS),
31
+ {
32
+ isLimit: true,
33
+ result: new BaseResult({ label: 'keep typing for more results' }),
34
+ },
35
+ ]
36
+ : options;
37
+ }
38
+ /**
39
+ * One option carrying every match as a whitespace-separated locstring — the
40
+ * multi-region form the box already accepts, and the form it already displays
41
+ * once a view holds more than one region. So picking it takes exactly the path
42
+ * typing those names by hand takes (`parseLocStrings` → `navToLocations` →
43
+ * `setDisplayedRegions` + `showAllRegions`), and there is no bulk-navigation
44
+ * code anywhere to keep in step with the single-region kind.
45
+ *
46
+ * It goes first in the list, and it is the reason a glob belongs in the picker
47
+ * rather than in the locstring parser: the set is on screen, and counted, before
48
+ * it is committed to. A pattern typed straight at the parser would resolve to
49
+ * however many regions it happened to match, sight unseen.
50
+ */
51
+ function selectAllOption(matches, pattern) {
52
+ return {
53
+ result: new BaseResult({
54
+ label: `Show all ${matches.length} regions matching ${pattern}`,
55
+ locString: matches.join(' '),
56
+ }),
57
+ };
58
+ }
59
+ /**
60
+ * The refName the typed text names outright, canonicalized — or undefined.
61
+ *
62
+ * Reading the name out of `allRefNames` before canonicalizing is what keeps
63
+ * `getCanonicalRefName`, which throws before aliases load, off a name the
64
+ * assembly never listed.
65
+ */
66
+ function literalRefName(assembly, inputValue) {
67
+ const query = inputValue.toLowerCase();
68
+ const named = assembly?.allRefNames?.find(n => n.toLowerCase() === query);
69
+ return named === undefined
70
+ ? undefined
71
+ : (assembly?.getCanonicalRefName(named) ?? named);
72
+ }
73
+ /**
74
+ * The browse/pre-fetch fallback list, shown while a typed query is in flight and
75
+ * when it comes back empty (typed queries otherwise resolve through
76
+ * fetchResults).
77
+ *
78
+ * The matching itself is `matchRefNames`, in core beside the glob semantics,
79
+ * because Enter answers for the same typed text and the two must not each grow
80
+ * their own reading of it. What is left here is presentation: how many rows to
81
+ * materialize, and the bulk row.
82
+ *
83
+ * **AN EXACT REFNAME BEATS THE GLOB READING here too**, the rule
84
+ * `selectNamedRegions` states and `searchUtils` orders its glob branch after.
85
+ * `*` is a legal refName character and GRCh38's ALT decoys are HLA allele names,
86
+ * so `HLA-A*01:01:01:01` is a contig somebody typed in full — offering "Show all
87
+ * 4 regions matching HLA-A*01:01:01:01" above it is the box promising a set that
88
+ * Enter, on the same text, does not open. The individual matches still list: the
89
+ * pattern reading is not wrong, it is just not what leads.
90
+ *
91
+ * A glob may gather up to MAX_GLOB_REGIONS for that bulk row; a plain query
92
+ * never needs more than the visible list, so it keeps the tighter bound and the
93
+ * cost it always had. Collecting one past MAX_OPTIONS is what lets `cap` render
94
+ * its "keep typing" hint.
95
+ */
96
+ export function getRefNameOptions(assembly, inputValue) {
97
+ const literal = literalRefName(assembly, inputValue);
98
+ const isGlob = literal === undefined && inputValue.includes('*');
99
+ const matches = matchRefNames(assembly, inputValue, isGlob ? MAX_GLOB_REGIONS : MAX_OPTIONS);
100
+ // hoisted only when the scan actually reached it — past the ceiling
101
+ // `matchRefNames` stops early, and a name with no region behind it is not an
102
+ // option anyone can pick
103
+ const ordered = literal !== undefined && matches.includes(literal)
104
+ ? [literal, ...matches.filter(refName => refName !== literal)]
105
+ : matches;
106
+ const options = ordered.slice(0, MAX_OPTIONS + 1).map(refName => ({
107
+ result: new RefSequenceResult({ refName, label: refName }),
108
+ }));
109
+ return isGlob && matches.length > 1 && matches.length <= MAX_GLOB_REGIONS
110
+ ? [selectAllOption(matches, inputValue), ...options]
111
+ : options;
112
+ }
113
+ // group hits sharing a display string into a single multi-result option (the
114
+ // picker pops a dialog), leaving unique hits as plain options
115
+ export function getDeduplicatedResult(results) {
116
+ const m = new Map();
117
+ for (const result of results) {
118
+ const key = result.getDisplayString();
119
+ const dupes = m.get(key);
120
+ if (dupes) {
121
+ dupes.push(result);
122
+ }
123
+ else {
124
+ m.set(key, [result]);
125
+ }
126
+ }
127
+ return [...m].map(([displayString, dupes]) => dupes.length === 1
128
+ ? { result: dupes[0] }
129
+ : {
130
+ result: new BaseResult({
131
+ displayString,
132
+ results: dupes,
133
+ label: displayString,
134
+ }),
135
+ });
136
+ }
137
+ function formatLocString(locString) {
138
+ const match = /^(.+):(\d+)\.\.(\d+)$/.exec(locString);
139
+ return match
140
+ ? `${match[1]}:${toLocale(Number(match[2]))}-${toLocale(Number(match[3]))}`
141
+ : locString;
142
+ }
143
+ /**
144
+ * The muted line under a row: a sequence's length, where a hit goes and the
145
+ * track it came from, or how many places share the row. A row sharing its name
146
+ * with a sequence is about the sequence, since an annotation's region feature
147
+ * names it too. A row whose hits all go to one place says where, without a
148
+ * track, since the pick lands through whichever of them the view has open. A
149
+ * row standing for many regions needs none.
150
+ */
151
+ export function optionDetail(result, lookups) {
152
+ const { trackNameOf, lengthOf, placesOf } = lookups;
153
+ const locString = result.getLocation();
154
+ const trackId = result.getTrackId();
155
+ const sequence = result.results?.find(r => r instanceof RefSequenceResult);
156
+ if (sequence) {
157
+ return optionDetail(sequence, lookups);
158
+ }
159
+ else if (result.results?.length) {
160
+ const places = placesOf(result.results);
161
+ const only = places.length === 1 ? places[0][0].getLocation() : undefined;
162
+ return only === undefined
163
+ ? `${places.length} matches`
164
+ : formatLocString(only);
165
+ }
166
+ else if (!locString || /\s/.test(locString)) {
167
+ return undefined;
168
+ }
169
+ else if (result instanceof RefSequenceResult) {
170
+ const length = lengthOf(locString);
171
+ return length === undefined ? undefined : getBpDisplayStr(length);
172
+ }
173
+ else {
174
+ const trackName = trackId === undefined ? undefined : trackNameOf(trackId);
175
+ return [formatLocString(locString), trackName].filter(Boolean).join(' · ');
176
+ }
177
+ }
178
+ // MUI freeSolo hands back the raw typed string when nothing in the list is
179
+ // selected; wrap it so callers always get a BaseResult
180
+ export function coerceToResult(option) {
181
+ return typeof option === 'string'
182
+ ? new BaseResult({ label: option })
183
+ : option.result;
184
+ }
185
+ export function getOptionLabel(option) {
186
+ return typeof option === 'string' ? option : option.result.getDisplayString();
187
+ }
188
+ /**
189
+ * What the end adornment occupies, and the number a caller passes as
190
+ * `adornmentWidth`.
191
+ *
192
+ * The ⋮ button is drawn for consumer-supplied rows as well as for the help one,
193
+ * so the reservation follows `menuItemCount || showHelp` — the same expression
194
+ * `EndAdornment` renders on. Both read it here rather than adding the constants
195
+ * up at the call site, which yields a box that has the button and is sized as
196
+ * if it did not.
197
+ */
198
+ export function adornmentReservePx({ showHelp, menuItemCount = 0, }) {
199
+ return (ADORNMENT_RESERVE_PX +
200
+ (menuItemCount || showHelp ? OVERFLOW_BUTTON_RESERVE_PX : 0));
201
+ }
202
+ // sized to the committed locstring, not the in-progress typed text, so the box
203
+ // doesn't jitter while typing a long query. Quantized to WIDTH_STEP_PX so small
204
+ // length changes during navigation don't continuously reflow the box.
205
+ export function getInputWidth(value, minWidth, maxWidth, adornmentWidth = ADORNMENT_RESERVE_PX + OVERFLOW_BUTTON_RESERVE_PX) {
206
+ const raw = measureText(value, INPUT_FONT_SIZE) + adornmentWidth;
207
+ const stepped = Math.ceil(raw / WIDTH_STEP_PX) * WIDTH_STEP_PX;
208
+ return Math.min(Math.max(stepped, minWidth), maxWidth);
209
+ }
@@ -0,0 +1,19 @@
1
+ /**
2
+ * The second way out of a launch dialog: put the view it builds in the slot the
3
+ * launching view occupies instead of appending it below. Offered by every launch
4
+ * that is anchored on what the current view is already showing — the synteny
5
+ * launches, "read vs ref" — where keeping both leaves two views of one place
6
+ * stacked and the taller of the two below the fold.
7
+ *
8
+ * Lives here rather than in one of those plugins because the gotcha it exists to
9
+ * carry belongs to `SubmitForm`, which is also here: an extra action is rendered
10
+ * inside that form, where an unset `type` means submit and one click would run
11
+ * BOTH actions.
12
+ *
13
+ * Pair it with `isSessionWithViewReplacement` — a session that cannot replace a
14
+ * view should not be offered the choice.
15
+ */
16
+ export default function ReplaceCurrentViewButton({ disabled, onClick, }: {
17
+ disabled?: boolean;
18
+ onClick: () => void;
19
+ }): import("react").JSX.Element;
@@ -0,0 +1,22 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { Button } from '@mui/material';
3
+ /**
4
+ * The second way out of a launch dialog: put the view it builds in the slot the
5
+ * launching view occupies instead of appending it below. Offered by every launch
6
+ * that is anchored on what the current view is already showing — the synteny
7
+ * launches, "read vs ref" — where keeping both leaves two views of one place
8
+ * stacked and the taller of the two below the fold.
9
+ *
10
+ * Lives here rather than in one of those plugins because the gotcha it exists to
11
+ * carry belongs to `SubmitForm`, which is also here: an extra action is rendered
12
+ * inside that form, where an unset `type` means submit and one click would run
13
+ * BOTH actions.
14
+ *
15
+ * Pair it with `isSessionWithViewReplacement` — a session that cannot replace a
16
+ * view should not be offered the choice.
17
+ */
18
+ export default function ReplaceCurrentViewButton({ disabled, onClick, }) {
19
+ return (_jsx(Button, { type: "button", variant: "contained", color: "primary", disabled: disabled, onClick: () => {
20
+ onClick();
21
+ }, children: "Replace current view" }));
22
+ }
@@ -1,9 +1,17 @@
1
- declare function ResizeHandle({ onDrag, vertical, flexbox, className: originalClassName, onMouseDown, ...props }: {
2
- onDrag: (lastFrameDistance: number, totalDistance: number) => number | undefined;
3
- onMouseDown?: (event: React.MouseEvent) => void;
1
+ import type React from 'react';
2
+ declare function ResizeHandle({ onDrag, onDragStart, onDragEnd, vertical, bar, grip, gain, className: originalClassName, onPointerDown, ...props }: {
3
+ onDrag: (distance: number) => void;
4
+ onDragStart?: () => void;
5
+ onDragEnd?: () => void;
4
6
  vertical?: boolean;
5
- flexbox?: boolean;
6
- className?: string;
7
- [props: string]: unknown;
8
- }): import("react/jsx-runtime").JSX.Element;
7
+ bar?: boolean;
8
+ /** An opaque `bar` with a grip pill, for the bottom edge of a view */
9
+ grip?: boolean | 'hover';
10
+ /**
11
+ * How many px this handle moves per px of the value it drags — see
12
+ * `useResizeDrag`. Pass it when the value is shared by several stacked bands
13
+ * and this handle sits below more than one of them.
14
+ */
15
+ gain?: number;
16
+ } & Omit<React.ComponentPropsWithoutRef<'div'>, 'onDrag' | 'onDragStart' | 'onDragEnd'>): React.JSX.Element;
9
17
  export default ResizeHandle;
@@ -1,67 +1,87 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
- import { useCallback, useEffect, useRef, useState } from 'react';
3
- import { cx, makeStyles } from "../util/tss-react/index.js";
4
- const useStyles = makeStyles()({
2
+ import { cx, makeStyles } from '../util/tss-react/index.js';
3
+ import { useResizeDrag } from '../util/useResizeDrag.js';
4
+ const layer = (color) => `linear-gradient(${color}, ${color})`;
5
+ // Three kinds of handle, one ladder of weight between them. A handle that draws
6
+ // nothing at rest reveals itself under the pointer at exactly the weight a
7
+ // visible one rests at (`action.disabled`); a visible one then goes past that,
8
+ // to `action.active` — the same resting/hover pair `VerticalScrollbar`'s thumb
9
+ // uses. A `grip` bar sits on an opaque paper fill so a view's gridlines stop at
10
+ // it, and a centred pill marks it as something to grab. `grip="hover"` draws
11
+ // that grip only under the pointer or mid-drag.
12
+ const useStyles = makeStyles()(theme => ({
5
13
  horizontalHandle: {
6
14
  cursor: 'row-resize',
7
15
  width: '100%',
16
+ // stop the browser turning a touch-drag into a scroll/pan gesture so the
17
+ // pointer stream reaches us
18
+ touchAction: 'none',
19
+ '&:hover': { backgroundColor: theme.palette.action.disabled },
8
20
  },
9
21
  verticalHandle: {
10
22
  cursor: 'col-resize',
11
23
  height: '100%',
24
+ touchAction: 'none',
25
+ '&:hover': { backgroundColor: theme.palette.action.disabled },
12
26
  },
13
- flexbox_verticalHandle: {
14
- cursor: 'col-resize',
15
- alignSelf: 'stretch',
27
+ // `bar` opt-in: the standard always-visible resize divider used at the bottom
28
+ // (or side) of views and tracks. Other call sites stay invisible until hover.
29
+ bar: { '&:hover': { background: theme.palette.action.active } },
30
+ horizontalBar: { height: 4, background: theme.palette.action.disabled },
31
+ verticalBar: { width: 4, background: theme.palette.action.disabled },
32
+ grip: {
33
+ backgroundColor: theme.palette.background.paper,
34
+ backgroundImage: `${layer(theme.palette.text.disabled)}, ${layer(theme.palette.action.disabled)}`,
35
+ backgroundPosition: 'center',
36
+ backgroundRepeat: 'no-repeat',
37
+ '&:hover': {
38
+ backgroundColor: theme.palette.background.paper,
39
+ backgroundImage: `${layer(theme.palette.text.secondary)}, ${layer(theme.palette.text.disabled)}`,
40
+ },
16
41
  },
17
- flexbox_horizontalHandle: {
18
- cursor: 'row-resize',
19
- alignSelf: 'stretch',
42
+ gripOnHover: {
43
+ '&:not(:hover):not(:active)': {
44
+ backgroundColor: 'transparent',
45
+ backgroundImage: 'none',
46
+ borderColor: 'transparent',
47
+ },
48
+ },
49
+ horizontalGrip: {
50
+ height: 6,
51
+ backgroundSize: '24px 3px, auto',
52
+ borderTop: `1px solid ${theme.palette.text.disabled}`,
53
+ },
54
+ verticalGrip: {
55
+ width: 6,
56
+ backgroundSize: '3px 24px, auto',
57
+ borderLeft: `1px solid ${theme.palette.text.disabled}`,
20
58
  },
21
- });
22
- function ResizeHandle({ onDrag, vertical = false, flexbox = false, className: originalClassName, onMouseDown, ...props }) {
23
- const [mouseDragging, setMouseDragging] = useState(false);
24
- const initialPosition = useRef(0);
25
- const prevPos = useRef(0);
59
+ }));
60
+ function ResizeHandle({ onDrag, onDragStart, onDragEnd, vertical = false, bar = false, grip = false, gain, className: originalClassName, onPointerDown, ...props }) {
26
61
  const { classes } = useStyles();
27
- const getPosition = useCallback((event) => vertical ? event.clientX : event.clientY, [vertical]);
28
- useEffect(() => {
29
- if (!mouseDragging) {
30
- return;
31
- }
32
- function mouseMove(event) {
33
- event.preventDefault();
34
- const pos = getPosition(event);
35
- const totalDistance = initialPosition.current - pos;
36
- const lastFrameDistance = pos - prevPos.current;
37
- prevPos.current = pos;
38
- onDrag(lastFrameDistance, totalDistance);
39
- }
40
- function mouseUp() {
41
- setMouseDragging(false);
42
- }
43
- window.addEventListener('mousemove', mouseMove, true);
44
- window.addEventListener('mouseup', mouseUp, true);
45
- return () => {
46
- window.removeEventListener('mousemove', mouseMove, true);
47
- window.removeEventListener('mouseup', mouseUp, true);
48
- };
49
- }, [mouseDragging, onDrag, getPosition]);
50
- const handleMouseDown = useCallback((event) => {
51
- event.preventDefault();
52
- const pos = getPosition(event);
53
- initialPosition.current = pos;
54
- prevPos.current = pos;
55
- setMouseDragging(true);
56
- onMouseDown?.(event);
57
- }, [getPosition, onMouseDown]);
58
- const className = flexbox
59
- ? vertical
60
- ? classes.flexbox_verticalHandle
61
- : classes.flexbox_horizontalHandle
62
- : vertical
63
- ? classes.verticalHandle
64
- : classes.horizontalHandle;
65
- return (_jsx("div", { "data-resizer": "true", onMouseDown: handleMouseDown, className: cx(originalClassName, className), ...props }));
62
+ // The gesture, including the per-frame coalescing, the delta measurement and
63
+ // the `data-gesture-owner` marker that keeps ancestor drags (the LGV
64
+ // click-drag pan, MAF's drag-selection) off this press. All of it is published
65
+ // as a hook rather than living here, because an embedder drawing their own
66
+ // track divider needs exactly this and none of the styling below.
67
+ const handleProps = useResizeDrag({
68
+ onDrag,
69
+ onDragStart,
70
+ onDragEnd,
71
+ vertical,
72
+ gain,
73
+ });
74
+ return (_jsx("div", { ...props, className: cx(originalClassName, vertical ? classes.verticalHandle : classes.horizontalHandle, grip && [
75
+ classes.grip,
76
+ vertical ? classes.verticalGrip : classes.horizontalGrip,
77
+ grip === 'hover' && classes.gripOnHover,
78
+ ], bar &&
79
+ !grip && [
80
+ classes.bar,
81
+ vertical ? classes.verticalBar : classes.horizontalBar,
82
+ ]), ...handleProps, onPointerDown: event => {
83
+ handleProps.onPointerDown(event);
84
+ onPointerDown?.(event);
85
+ } }));
66
86
  }
67
87
  export default ResizeHandle;
@@ -3,5 +3,5 @@ declare const ReturnToImportFormDialog: ({ model, handleClose, }: {
3
3
  clearView: () => void;
4
4
  };
5
5
  handleClose: () => void;
6
- }) => import("react/jsx-runtime").JSX.Element;
6
+ }) => import("react").JSX.Element;
7
7
  export default ReturnToImportFormDialog;