@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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package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js DELETED
@@ -1,1116 +0,0 @@
1
- export default {
2
- source: 'BestRefSeq',
3
- type: 'gene',
4
- start: 36023399,
5
- end: 36032380,
6
- strand: 1,
7
- phase: 0,
8
- refName: 'NC_000001.10',
9
- id: 'gene634',
10
- dbxref: ['GeneID:23154', 'HGNC:HGNC:17597', 'MIM:608458'],
11
- name: 'NCDN',
12
- description: 'neurochondrin',
13
- gbkey: 'Gene',
14
- gene: 'NCDN',
15
- gene_biotype: 'protein_coding',
16
- subfeatures: [
17
- {
18
- source: 'BestRefSeq',
19
- type: 'mRNA',
20
- start: 36023399,
21
- end: 36032380,
22
- strand: 1,
23
- phase: 0,
24
- refName: 'NC_000001.10',
25
- id: 'mRNA1331',
26
- parent: 'gene634',
27
- dbxref: [
28
- 'GeneID:23154',
29
- 'Genbank:NM_014284.3',
30
- 'HGNC:HGNC:17597',
31
- 'MIM:608458',
32
- ],
33
- name: 'NM_014284.3',
34
- gbkey: 'mRNA',
35
- gene: 'NCDN',
36
- product: 'neurochondrin, transcript variant 3',
37
- tag: 'RefSeq Select',
38
- transcript_id: 'NM_014284.3',
39
- subfeatures: [
40
- {
41
- source: 'BestRefSeq',
42
- type: 'exon',
43
- start: 36023399,
44
- end: 36023824,
45
- strand: 1,
46
- phase: 0,
47
- refName: 'NC_000001.10',
48
- parent: 'mRNA1331',
49
- dbxref: [
50
- 'GeneID:23154',
51
- 'Genbank:NM_014284.3',
52
- 'HGNC:HGNC:17597',
53
- 'MIM:608458',
54
- ],
55
- gbkey: 'mRNA',
56
- gene: 'NCDN',
57
- product: 'neurochondrin, transcript variant 3',
58
- tag: 'RefSeq Select',
59
- transcript_id: 'NM_014284.3',
60
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-0',
61
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
62
- },
63
- {
64
- source: 'BestRefSeq',
65
- type: 'CDS',
66
- start: 36023791,
67
- end: 36023824,
68
- strand: 1,
69
- phase: 0,
70
- refName: 'NC_000001.10',
71
- id: 'CDS1286',
72
- parent: 'mRNA1331',
73
- dbxref: [
74
- 'CCDS:CCDS392.1',
75
- 'GeneID:23154',
76
- 'Genbank:NP_055099.1',
77
- 'HGNC:HGNC:17597',
78
- 'MIM:608458',
79
- ],
80
- name: 'NP_055099.1',
81
- note: 'isoform 1 is encoded by transcript variant 3',
82
- gbkey: 'CDS',
83
- gene: 'NCDN',
84
- product: 'neurochondrin isoform 1',
85
- protein_id: 'NP_055099.1',
86
- tag: 'RefSeq Select',
87
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-1',
88
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
89
- },
90
- {
91
- source: 'BestRefSeq',
92
- type: 'CDS',
93
- start: 36024707,
94
- end: 36024848,
95
- strand: 1,
96
- phase: 0,
97
- refName: 'NC_000001.10',
98
- id: 'CDS1286',
99
- parent: 'mRNA1331',
100
- dbxref: [
101
- 'CCDS:CCDS392.1',
102
- 'GeneID:23154',
103
- 'Genbank:NP_055099.1',
104
- 'HGNC:HGNC:17597',
105
- 'MIM:608458',
106
- ],
107
- name: 'NP_055099.1',
108
- note: 'isoform 1 is encoded by transcript variant 3',
109
- gbkey: 'CDS',
110
- gene: 'NCDN',
111
- product: 'neurochondrin isoform 1',
112
- protein_id: 'NP_055099.1',
113
- tag: 'RefSeq Select',
114
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-2',
115
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
116
- },
117
- {
118
- source: 'BestRefSeq',
119
- type: 'CDS',
120
- start: 36025926,
121
- end: 36026895,
122
- strand: 1,
123
- phase: 0,
124
- refName: 'NC_000001.10',
125
- id: 'CDS1286',
126
- parent: 'mRNA1331',
127
- dbxref: [
128
- 'CCDS:CCDS392.1',
129
- 'GeneID:23154',
130
- 'Genbank:NP_055099.1',
131
- 'HGNC:HGNC:17597',
132
- 'MIM:608458',
133
- ],
134
- name: 'NP_055099.1',
135
- note: 'isoform 1 is encoded by transcript variant 3',
136
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137
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- source: 'BestRefSeq',
1068
- type: 'exon',
1069
- start: 36029367,
1070
- end: 36029510,
1071
- strand: 1,
1072
- phase: 0,
1073
- refName: 'NC_000001.10',
1074
- parent: 'mRNA1332',
1075
- dbxref: [
1076
- 'GeneID:23154',
1077
- 'Genbank:NM_001014839.2',
1078
- 'HGNC:HGNC:17597',
1079
- 'MIM:608458',
1080
- ],
1081
- gbkey: 'mRNA',
1082
- gene: 'NCDN',
1083
- product: 'neurochondrin, transcript variant 1',
1084
- transcript_id: 'NM_001014839.2',
1085
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-2-13',
1086
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-2',
1087
- },
1088
- {
1089
- source: 'BestRefSeq',
1090
- type: 'exon',
1091
- start: 36030827,
1092
- end: 36032380,
1093
- strand: 1,
1094
- phase: 0,
1095
- refName: 'NC_000001.10',
1096
- parent: 'mRNA1332',
1097
- dbxref: [
1098
- 'GeneID:23154',
1099
- 'Genbank:NM_001014839.2',
1100
- 'HGNC:HGNC:17597',
1101
- 'MIM:608458',
1102
- ],
1103
- gbkey: 'mRNA',
1104
- gene: 'NCDN',
1105
- product: 'neurochondrin, transcript variant 1',
1106
- transcript_id: 'NM_001014839.2',
1107
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-2-14',
1108
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-2',
1109
- },
1110
- ],
1111
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-2',
1112
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638',
1113
- },
1114
- ],
1115
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638',
1116
- };