@jbrowse/plugin-linear-genome-view 3.6.5 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (392) hide show
  1. package/esm/BaseLinearDisplay/SVGLegend.d.ts +6 -0
  2. package/esm/BaseLinearDisplay/SVGLegend.js +17 -0
  3. package/esm/BaseLinearDisplay/calculateSvgLegendWidth.d.ts +2 -0
  4. package/esm/BaseLinearDisplay/calculateSvgLegendWidth.js +11 -0
  5. package/esm/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +3 -3
  6. package/esm/BaseLinearDisplay/components/BaseLinearDisplay.js +13 -24
  7. package/esm/BaseLinearDisplay/components/Block.js +2 -2
  8. package/esm/BaseLinearDisplay/components/BlockErrorMessage.js +2 -2
  9. package/esm/BaseLinearDisplay/components/BlockMsg.js +11 -2
  10. package/esm/BaseLinearDisplay/components/CollapseIntronsDialog/CollapseIntronsDialog.d.ts +9 -0
  11. package/esm/BaseLinearDisplay/components/CollapseIntronsDialog/CollapseIntronsDialog.js +42 -0
  12. package/esm/BaseLinearDisplay/components/CollapseIntronsDialog/TranscriptTable.d.ts +11 -0
  13. package/esm/BaseLinearDisplay/components/CollapseIntronsDialog/TranscriptTable.js +40 -0
  14. package/esm/BaseLinearDisplay/components/CollapseIntronsDialog/util.d.ts +19 -0
  15. package/esm/BaseLinearDisplay/components/CollapseIntronsDialog/util.js +45 -0
  16. package/esm/BaseLinearDisplay/components/FloatingLabels.d.ts +5 -0
  17. package/esm/BaseLinearDisplay/components/FloatingLabels.js +89 -0
  18. package/esm/BaseLinearDisplay/components/FloatingLegend.d.ts +8 -0
  19. package/esm/BaseLinearDisplay/components/FloatingLegend.js +43 -0
  20. package/esm/BaseLinearDisplay/components/LinearBlocks.d.ts +1 -5
  21. package/esm/BaseLinearDisplay/components/LinearBlocks.js +5 -42
  22. package/esm/BaseLinearDisplay/components/LoadingOverlay.d.ts +4 -0
  23. package/esm/BaseLinearDisplay/components/LoadingOverlay.js +49 -0
  24. package/esm/BaseLinearDisplay/components/MaxHeightReachedIndicator.d.ts +4 -0
  25. package/esm/BaseLinearDisplay/components/MaxHeightReachedIndicator.js +26 -0
  26. package/esm/BaseLinearDisplay/components/MenuPage.d.ts +8 -0
  27. package/esm/BaseLinearDisplay/components/MenuPage.js +24 -0
  28. package/esm/BaseLinearDisplay/components/NonBlockCanvasDisplayComponent.d.ts +19 -0
  29. package/esm/BaseLinearDisplay/components/NonBlockCanvasDisplayComponent.js +48 -0
  30. package/esm/BaseLinearDisplay/components/RenderedBlocks.d.ts +12 -0
  31. package/esm/BaseLinearDisplay/components/RenderedBlocks.js +22 -0
  32. package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.d.ts +4 -4
  33. package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +5 -8
  34. package/esm/BaseLinearDisplay/components/TooLargeMessage.js +3 -3
  35. package/esm/BaseLinearDisplay/components/Tooltip.d.ts +2 -0
  36. package/esm/BaseLinearDisplay/components/Tooltip.js +10 -7
  37. package/esm/BaseLinearDisplay/components/types.d.ts +1 -0
  38. package/esm/BaseLinearDisplay/components/types.js +1 -0
  39. package/esm/BaseLinearDisplay/components/util.d.ts +21 -0
  40. package/esm/BaseLinearDisplay/components/util.js +116 -0
  41. package/esm/BaseLinearDisplay/index.d.ts +17 -8
  42. package/esm/BaseLinearDisplay/index.js +13 -6
  43. package/esm/BaseLinearDisplay/model.d.ts +1177 -0
  44. package/esm/BaseLinearDisplay/model.js +424 -0
  45. package/esm/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +5 -5
  46. package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js +11 -14
  47. package/esm/BaseLinearDisplay/models/NonBlockCanvasDisplayMixin.d.ts +21 -0
  48. package/esm/BaseLinearDisplay/models/NonBlockCanvasDisplayMixin.js +46 -0
  49. package/esm/BaseLinearDisplay/models/TrackHeightMixin.d.ts +3 -3
  50. package/esm/BaseLinearDisplay/models/TrackHeightMixin.js +2 -3
  51. package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts +1 -1
  52. package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js +2 -3
  53. package/esm/BaseLinearDisplay/models/calculateLabelPositions.d.ts +24 -0
  54. package/esm/BaseLinearDisplay/models/calculateLabelPositions.js +60 -0
  55. package/esm/BaseLinearDisplay/models/configSchema.d.ts +2 -2
  56. package/esm/BaseLinearDisplay/models/configSchema.js +3 -3
  57. package/esm/BaseLinearDisplay/models/renderSvg.d.ts +3 -7
  58. package/esm/BaseLinearDisplay/models/renderSvg.js +22 -11
  59. package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +37 -19
  60. package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js +151 -135
  61. package/esm/BaseLinearDisplay/models/util.d.ts +4 -4
  62. package/esm/BaseLinearDisplay/models/util.js +16 -13
  63. package/esm/BaseLinearDisplay/renderSvg.d.ts +3 -0
  64. package/esm/BaseLinearDisplay/renderSvg.js +59 -0
  65. package/esm/BaseLinearDisplay/types.d.ts +47 -0
  66. package/esm/BaseLinearDisplay/types.js +3 -0
  67. package/esm/BaseLinearDisplay/util.d.ts +15 -0
  68. package/esm/BaseLinearDisplay/util.js +61 -0
  69. package/esm/BasicTrack/configSchema.d.ts +16 -11
  70. package/esm/BasicTrack/index.js +1 -1
  71. package/esm/FeatureTrack/configSchema.d.ts +16 -11
  72. package/esm/FeatureTrack/index.js +1 -1
  73. package/esm/LaunchLinearGenomeView/index.js +12 -62
  74. package/esm/LinearBareDisplay/configSchema.d.ts +4 -4
  75. package/esm/LinearBareDisplay/configSchema.js +1 -1
  76. package/esm/LinearBareDisplay/index.d.ts +2 -2
  77. package/esm/LinearBareDisplay/index.js +5 -5
  78. package/esm/LinearBareDisplay/model.d.ts +959 -92
  79. package/esm/LinearBareDisplay/model.js +3 -6
  80. package/esm/LinearBasicDisplay/components/LinearBasicDisplayComponent.d.ts +5 -0
  81. package/esm/LinearBasicDisplay/components/LinearBasicDisplayComponent.js +9 -0
  82. package/esm/LinearBasicDisplay/configSchema.d.ts +4 -4
  83. package/esm/LinearBasicDisplay/configSchema.js +1 -1
  84. package/esm/LinearBasicDisplay/index.d.ts +2 -2
  85. package/esm/LinearBasicDisplay/index.js +6 -6
  86. package/esm/LinearBasicDisplay/model.d.ts +1134 -122
  87. package/esm/LinearBasicDisplay/model.js +116 -116
  88. package/esm/{LinearBasicDisplay → LinearFeatureDisplay}/components/AddFiltersDialog.js +2 -2
  89. package/esm/{LinearBasicDisplay → LinearFeatureDisplay}/components/SetMaxHeightDialog.js +3 -3
  90. package/{dist/LinearBasicDisplay → esm/LinearFeatureDisplay}/configSchema.d.ts +4 -4
  91. package/esm/LinearFeatureDisplay/configSchema.js +11 -0
  92. package/esm/LinearFeatureDisplay/index.d.ts +3 -0
  93. package/esm/LinearFeatureDisplay/index.js +2 -0
  94. package/esm/LinearFeatureDisplay/model.d.ts +1415 -0
  95. package/esm/LinearFeatureDisplay/model.js +265 -0
  96. package/esm/LinearGenomeView/SVGErrorBox.d.ts +5 -0
  97. package/esm/LinearGenomeView/SVGErrorBox.js +4 -0
  98. package/esm/LinearGenomeView/afterAttach.d.ts +5 -0
  99. package/esm/LinearGenomeView/afterAttach.js +95 -0
  100. package/esm/LinearGenomeView/components/CenterLine.js +6 -4
  101. package/esm/LinearGenomeView/components/Cytobands.js +4 -4
  102. package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts +1 -1
  103. package/esm/LinearGenomeView/components/ExportSvgDialog.js +5 -1
  104. package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts +8 -2
  105. package/esm/LinearGenomeView/components/GetSequenceDialog.js +13 -16
  106. package/esm/LinearGenomeView/components/Gridlines.js +18 -15
  107. package/esm/LinearGenomeView/components/Header.js +9 -9
  108. package/esm/LinearGenomeView/components/HeaderPanControls.js +2 -2
  109. package/esm/LinearGenomeView/components/HeaderRegionWidth.js +4 -5
  110. package/esm/LinearGenomeView/components/HeaderTrackSelectorButton.js +2 -2
  111. package/esm/LinearGenomeView/components/HeaderZoomControls.js +3 -3
  112. package/esm/LinearGenomeView/components/Highlight.d.ts +1 -1
  113. package/esm/LinearGenomeView/components/Highlight.js +6 -6
  114. package/esm/LinearGenomeView/components/ImportForm.d.ts +1 -1
  115. package/esm/LinearGenomeView/components/ImportForm.js +14 -12
  116. package/esm/LinearGenomeView/components/ImportFormRefNameAutocomplete.js +3 -3
  117. package/esm/LinearGenomeView/components/LinearGenomeView.js +7 -7
  118. package/esm/LinearGenomeView/components/LinearGenomeViewContainer.js +7 -8
  119. package/esm/LinearGenomeView/components/MiniControls.js +6 -6
  120. package/esm/LinearGenomeView/components/NoTracksActiveButton.js +2 -2
  121. package/esm/LinearGenomeView/components/OverviewHighlight.d.ts +1 -1
  122. package/esm/LinearGenomeView/components/OverviewHighlight.js +5 -5
  123. package/esm/LinearGenomeView/components/OverviewRubberband.js +4 -4
  124. package/esm/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js +9 -5
  125. package/esm/LinearGenomeView/components/OverviewScalebar.js +36 -28
  126. package/esm/LinearGenomeView/components/OverviewScalebarPolygon.js +5 -5
  127. package/esm/LinearGenomeView/components/OverviewScalebarTickLabels.js +7 -7
  128. package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +1 -1
  129. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +1 -1
  130. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js +10 -10
  131. package/esm/LinearGenomeView/components/RegionWidthEditorDialog.d.ts +1 -1
  132. package/esm/LinearGenomeView/components/RegionWidthEditorDialog.js +6 -4
  133. package/esm/LinearGenomeView/components/Rubberband.js +9 -7
  134. package/esm/LinearGenomeView/components/RubberbandSpan.js +4 -5
  135. package/esm/LinearGenomeView/components/Scalebar.js +8 -10
  136. package/esm/LinearGenomeView/components/ScalebarCoordinateLabels.d.ts +1 -1
  137. package/esm/LinearGenomeView/components/ScalebarCoordinateLabels.js +50 -17
  138. package/esm/LinearGenomeView/components/ScalebarRefNameLabels.d.ts +1 -1
  139. package/esm/LinearGenomeView/components/ScalebarRefNameLabels.js +13 -11
  140. package/esm/LinearGenomeView/components/SearchBox.d.ts +1 -1
  141. package/esm/LinearGenomeView/components/SearchBox.js +8 -9
  142. package/esm/LinearGenomeView/components/SearchResultsDialog.d.ts +1 -1
  143. package/esm/LinearGenomeView/components/SearchResultsDialog.js +2 -2
  144. package/esm/LinearGenomeView/components/SearchResultsTable.d.ts +1 -1
  145. package/esm/LinearGenomeView/components/SearchResultsTable.js +4 -6
  146. package/esm/LinearGenomeView/components/SequenceSearchDialog.js +6 -6
  147. package/esm/LinearGenomeView/components/TrackContainer.js +32 -20
  148. package/esm/LinearGenomeView/components/TrackLabel.js +10 -11
  149. package/esm/LinearGenomeView/components/TrackLabelContainer.js +7 -8
  150. package/esm/LinearGenomeView/components/TrackLabelDragHandle.js +1 -1
  151. package/esm/LinearGenomeView/components/TrackLabelMenu.js +80 -68
  152. package/esm/LinearGenomeView/components/TrackRenderingContainer.d.ts +1 -2
  153. package/esm/LinearGenomeView/components/TrackRenderingContainer.js +5 -5
  154. package/esm/LinearGenomeView/components/TracksContainer.js +18 -15
  155. package/esm/LinearGenomeView/components/VerticalGuide.js +5 -3
  156. package/esm/LinearGenomeView/components/fetchSequence.d.ts +7 -2
  157. package/esm/LinearGenomeView/components/useRangeSelect.d.ts +27 -2
  158. package/esm/LinearGenomeView/components/useRangeSelect.js +26 -20
  159. package/esm/LinearGenomeView/components/useWheelScroll.js +22 -12
  160. package/esm/LinearGenomeView/components/util.d.ts +2 -13
  161. package/esm/LinearGenomeView/components/util.js +12 -31
  162. package/esm/LinearGenomeView/index.d.ts +1 -1
  163. package/esm/LinearGenomeView/index.js +3 -3
  164. package/esm/LinearGenomeView/keyboardHandler.d.ts +2 -0
  165. package/esm/LinearGenomeView/keyboardHandler.js +29 -0
  166. package/esm/LinearGenomeView/menuItems.d.ts +7 -0
  167. package/esm/LinearGenomeView/menuItems.js +299 -0
  168. package/esm/LinearGenomeView/model.d.ts +92 -89
  169. package/esm/LinearGenomeView/model.js +166 -414
  170. package/esm/LinearGenomeView/svgExportUtil.d.ts +9 -0
  171. package/esm/LinearGenomeView/svgExportUtil.js +6 -0
  172. package/{dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts → esm/LinearGenomeView/svgcomponents/SVGGridlines.d.ts} +2 -2
  173. package/esm/LinearGenomeView/svgcomponents/SVGGridlines.js +20 -0
  174. package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +5 -5
  175. package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.d.ts +4 -3
  176. package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +24 -12
  177. package/esm/LinearGenomeView/svgcomponents/SVGRuler.js +13 -5
  178. package/esm/LinearGenomeView/svgcomponents/SVGTracks.js +2 -2
  179. package/esm/LinearGenomeView/types.d.ts +5 -1
  180. package/esm/LinearGenomeView/util.d.ts +2 -2
  181. package/esm/LinearGenomeView/util.js +8 -6
  182. package/esm/index.d.ts +975 -94
  183. package/esm/index.js +37 -38
  184. package/esm/searchUtils.d.ts +1 -1
  185. package/esm/searchUtils.js +6 -4
  186. package/package.json +28 -33
  187. package/dist/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +0 -8
  188. package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js +0 -72
  189. package/dist/BaseLinearDisplay/components/Block.d.ts +0 -14
  190. package/dist/BaseLinearDisplay/components/Block.js +0 -50
  191. package/dist/BaseLinearDisplay/components/BlockErrorMessage.d.ts +0 -7
  192. package/dist/BaseLinearDisplay/components/BlockErrorMessage.js +0 -27
  193. package/dist/BaseLinearDisplay/components/BlockLoadingMessage.d.ts +0 -6
  194. package/dist/BaseLinearDisplay/components/BlockLoadingMessage.js +0 -26
  195. package/dist/BaseLinearDisplay/components/BlockMsg.d.ts +0 -6
  196. package/dist/BaseLinearDisplay/components/BlockMsg.js +0 -20
  197. package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts +0 -9
  198. package/dist/BaseLinearDisplay/components/LinearBlocks.js +0 -61
  199. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.d.ts +0 -11
  200. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +0 -59
  201. package/dist/BaseLinearDisplay/components/TooLargeMessage.d.ts +0 -10
  202. package/dist/BaseLinearDisplay/components/TooLargeMessage.js +0 -25
  203. package/dist/BaseLinearDisplay/components/Tooltip.d.ts +0 -11
  204. package/dist/BaseLinearDisplay/components/Tooltip.js +0 -24
  205. package/dist/BaseLinearDisplay/index.d.ts +0 -8
  206. package/dist/BaseLinearDisplay/index.js +0 -20
  207. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +0 -311
  208. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +0 -325
  209. package/dist/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +0 -32
  210. package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js +0 -122
  211. package/dist/BaseLinearDisplay/models/TrackHeightMixin.d.ts +0 -11
  212. package/dist/BaseLinearDisplay/models/TrackHeightMixin.js +0 -35
  213. package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts +0 -2
  214. package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.js +0 -33
  215. package/dist/BaseLinearDisplay/models/configSchema.d.ts +0 -29
  216. package/dist/BaseLinearDisplay/models/configSchema.js +0 -35
  217. package/dist/BaseLinearDisplay/models/renderSvg.d.ts +0 -7
  218. package/dist/BaseLinearDisplay/models/renderSvg.js +0 -80
  219. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +0 -78
  220. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +0 -229
  221. package/dist/BaseLinearDisplay/models/util.d.ts +0 -22
  222. package/dist/BaseLinearDisplay/models/util.js +0 -45
  223. package/dist/BasicTrack/configSchema.d.ts +0 -80
  224. package/dist/BasicTrack/configSchema.js +0 -10
  225. package/dist/BasicTrack/index.d.ts +0 -2
  226. package/dist/BasicTrack/index.js +0 -18
  227. package/dist/FeatureTrack/configSchema.d.ts +0 -80
  228. package/dist/FeatureTrack/configSchema.js +0 -10
  229. package/dist/FeatureTrack/index.d.ts +0 -2
  230. package/dist/FeatureTrack/index.js +0 -19
  231. package/dist/LaunchLinearGenomeView/index.d.ts +0 -2
  232. package/dist/LaunchLinearGenomeView/index.js +0 -70
  233. package/dist/LinearBareDisplay/configSchema.d.ts +0 -32
  234. package/dist/LinearBareDisplay/configSchema.js +0 -13
  235. package/dist/LinearBareDisplay/index.d.ts +0 -4
  236. package/dist/LinearBareDisplay/index.js +0 -26
  237. package/dist/LinearBareDisplay/model.d.ts +0 -309
  238. package/dist/LinearBareDisplay/model.js +0 -38
  239. package/dist/LinearBasicDisplay/components/AddFiltersDialog.js +0 -61
  240. package/dist/LinearBasicDisplay/components/SetMaxHeightDialog.js +0 -28
  241. package/dist/LinearBasicDisplay/configSchema.js +0 -13
  242. package/dist/LinearBasicDisplay/index.d.ts +0 -4
  243. package/dist/LinearBasicDisplay/index.js +0 -29
  244. package/dist/LinearBasicDisplay/model.d.ts +0 -346
  245. package/dist/LinearBasicDisplay/model.js +0 -192
  246. package/dist/LinearGenomeView/components/CenterLine.d.ts +0 -6
  247. package/dist/LinearGenomeView/components/CenterLine.js +0 -38
  248. package/dist/LinearGenomeView/components/Cytobands.d.ts +0 -9
  249. package/dist/LinearGenomeView/components/Cytobands.js +0 -89
  250. package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts +0 -7
  251. package/dist/LinearGenomeView/components/ExportSvgDialog.js +0 -57
  252. package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts +0 -6
  253. package/dist/LinearGenomeView/components/GetSequenceDialog.js +0 -109
  254. package/dist/LinearGenomeView/components/Gridlines.d.ts +0 -7
  255. package/dist/LinearGenomeView/components/Gridlines.js +0 -70
  256. package/dist/LinearGenomeView/components/Header.d.ts +0 -5
  257. package/dist/LinearGenomeView/components/Header.js +0 -38
  258. package/dist/LinearGenomeView/components/HeaderPanControls.d.ts +0 -6
  259. package/dist/LinearGenomeView/components/HeaderPanControls.js +0 -27
  260. package/dist/LinearGenomeView/components/HeaderRegionWidth.d.ts +0 -5
  261. package/dist/LinearGenomeView/components/HeaderRegionWidth.js +0 -21
  262. package/dist/LinearGenomeView/components/HeaderTrackSelectorButton.d.ts +0 -5
  263. package/dist/LinearGenomeView/components/HeaderTrackSelectorButton.js +0 -19
  264. package/dist/LinearGenomeView/components/HeaderZoomControls.d.ts +0 -5
  265. package/dist/LinearGenomeView/components/HeaderZoomControls.js +0 -109
  266. package/dist/LinearGenomeView/components/Highlight.d.ts +0 -12
  267. package/dist/LinearGenomeView/components/Highlight.js +0 -95
  268. package/dist/LinearGenomeView/components/ImportForm.d.ts +0 -6
  269. package/dist/LinearGenomeView/components/ImportForm.js +0 -80
  270. package/dist/LinearGenomeView/components/ImportFormRefNameAutocomplete.d.ts +0 -11
  271. package/dist/LinearGenomeView/components/ImportFormRefNameAutocomplete.js +0 -32
  272. package/dist/LinearGenomeView/components/LinearGenomeView.d.ts +0 -5
  273. package/dist/LinearGenomeView/components/LinearGenomeView.js +0 -57
  274. package/dist/LinearGenomeView/components/LinearGenomeViewContainer.d.ts +0 -5
  275. package/dist/LinearGenomeView/components/LinearGenomeViewContainer.js +0 -98
  276. package/dist/LinearGenomeView/components/MiniControls.d.ts +0 -5
  277. package/dist/LinearGenomeView/components/MiniControls.js +0 -36
  278. package/dist/LinearGenomeView/components/NoTracksActiveButton.d.ts +0 -5
  279. package/dist/LinearGenomeView/components/NoTracksActiveButton.js +0 -23
  280. package/dist/LinearGenomeView/components/OverviewHighlight.d.ts +0 -8
  281. package/dist/LinearGenomeView/components/OverviewHighlight.js +0 -50
  282. package/dist/LinearGenomeView/components/OverviewRubberband.d.ts +0 -9
  283. package/dist/LinearGenomeView/components/OverviewRubberband.js +0 -113
  284. package/dist/LinearGenomeView/components/OverviewRubberbandHoverTooltip.d.ts +0 -10
  285. package/dist/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js +0 -28
  286. package/dist/LinearGenomeView/components/OverviewScalebar.d.ts +0 -7
  287. package/dist/LinearGenomeView/components/OverviewScalebar.js +0 -146
  288. package/dist/LinearGenomeView/components/OverviewScalebarPolygon.d.ts +0 -8
  289. package/dist/LinearGenomeView/components/OverviewScalebarPolygon.js +0 -41
  290. package/dist/LinearGenomeView/components/OverviewScalebarTickLabels.d.ts +0 -10
  291. package/dist/LinearGenomeView/components/OverviewScalebarTickLabels.js +0 -37
  292. package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.d.ts +0 -8
  293. package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js +0 -18
  294. package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.d.ts +0 -3
  295. package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +0 -56
  296. package/dist/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.d.ts +0 -3
  297. package/dist/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.js +0 -11
  298. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +0 -16
  299. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js +0 -127
  300. package/dist/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +0 -10
  301. package/dist/LinearGenomeView/components/RefNameAutocomplete/util.js +0 -53
  302. package/dist/LinearGenomeView/components/RegionWidthEditorDialog.d.ts +0 -6
  303. package/dist/LinearGenomeView/components/RegionWidthEditorDialog.js +0 -30
  304. package/dist/LinearGenomeView/components/Rubberband.d.ts +0 -7
  305. package/dist/LinearGenomeView/components/Rubberband.js +0 -35
  306. package/dist/LinearGenomeView/components/RubberbandSpan.d.ts +0 -15
  307. package/dist/LinearGenomeView/components/RubberbandSpan.js +0 -39
  308. package/dist/LinearGenomeView/components/RubberbandTooltip.d.ts +0 -5
  309. package/dist/LinearGenomeView/components/RubberbandTooltip.js +0 -20
  310. package/dist/LinearGenomeView/components/Scalebar.d.ts +0 -10
  311. package/dist/LinearGenomeView/components/Scalebar.js +0 -40
  312. package/dist/LinearGenomeView/components/ScalebarCoordinateLabels.d.ts +0 -6
  313. package/dist/LinearGenomeView/components/ScalebarCoordinateLabels.js +0 -29
  314. package/dist/LinearGenomeView/components/ScalebarCoordinateTicks.d.ts +0 -6
  315. package/dist/LinearGenomeView/components/ScalebarCoordinateTicks.js +0 -38
  316. package/dist/LinearGenomeView/components/ScalebarRefNameLabels.d.ts +0 -6
  317. package/dist/LinearGenomeView/components/ScalebarRefNameLabels.js +0 -46
  318. package/dist/LinearGenomeView/components/SearchBox.d.ts +0 -6
  319. package/dist/LinearGenomeView/components/SearchBox.js +0 -88
  320. package/dist/LinearGenomeView/components/SearchResultsDialog.d.ts +0 -9
  321. package/dist/LinearGenomeView/components/SearchResultsDialog.js +0 -15
  322. package/dist/LinearGenomeView/components/SearchResultsTable.d.ts +0 -8
  323. package/dist/LinearGenomeView/components/SearchResultsTable.js +0 -74
  324. package/dist/LinearGenomeView/components/SequenceSearchDialog.d.ts +0 -8
  325. package/dist/LinearGenomeView/components/SequenceSearchDialog.js +0 -67
  326. package/dist/LinearGenomeView/components/TrackContainer.d.ts +0 -8
  327. package/dist/LinearGenomeView/components/TrackContainer.js +0 -51
  328. package/dist/LinearGenomeView/components/TrackLabel.d.ts +0 -7
  329. package/dist/LinearGenomeView/components/TrackLabel.js +0 -49
  330. package/dist/LinearGenomeView/components/TrackLabelContainer.d.ts +0 -8
  331. package/dist/LinearGenomeView/components/TrackLabelContainer.js +0 -31
  332. package/dist/LinearGenomeView/components/TrackLabelDragHandle.d.ts +0 -8
  333. package/dist/LinearGenomeView/components/TrackLabelDragHandle.js +0 -32
  334. package/dist/LinearGenomeView/components/TrackLabelMenu.d.ts +0 -5
  335. package/dist/LinearGenomeView/components/TrackLabelMenu.js +0 -93
  336. package/dist/LinearGenomeView/components/TrackRenderingContainer.d.ts +0 -9
  337. package/dist/LinearGenomeView/components/TrackRenderingContainer.js +0 -50
  338. package/dist/LinearGenomeView/components/TracksContainer.d.ts +0 -7
  339. package/dist/LinearGenomeView/components/TracksContainer.js +0 -84
  340. package/dist/LinearGenomeView/components/VerticalGuide.d.ts +0 -7
  341. package/dist/LinearGenomeView/components/VerticalGuide.js +0 -31
  342. package/dist/LinearGenomeView/components/fetchSequence.d.ts +0 -4
  343. package/dist/LinearGenomeView/components/fetchSequence.js +0 -29
  344. package/dist/LinearGenomeView/components/useRangeSelect.d.ts +0 -59
  345. package/dist/LinearGenomeView/components/useRangeSelect.js +0 -131
  346. package/dist/LinearGenomeView/components/useSideScroll.d.ts +0 -6
  347. package/dist/LinearGenomeView/components/useSideScroll.js +0 -60
  348. package/dist/LinearGenomeView/components/useWheelScroll.d.ts +0 -7
  349. package/dist/LinearGenomeView/components/useWheelScroll.js +0 -62
  350. package/dist/LinearGenomeView/components/util.d.ts +0 -25
  351. package/dist/LinearGenomeView/components/util.js +0 -49
  352. package/dist/LinearGenomeView/consts.d.ts +0 -7
  353. package/dist/LinearGenomeView/consts.js +0 -10
  354. package/dist/LinearGenomeView/index.d.ts +0 -3
  355. package/dist/LinearGenomeView/index.js +0 -53
  356. package/dist/LinearGenomeView/model.d.ts +0 -268
  357. package/dist/LinearGenomeView/model.js +0 -1109
  358. package/dist/LinearGenomeView/svgcomponents/SVGBackground.d.ts +0 -5
  359. package/dist/LinearGenomeView/svgcomponents/SVGBackground.js +0 -10
  360. package/dist/LinearGenomeView/svgcomponents/SVGHeader.d.ts +0 -7
  361. package/dist/LinearGenomeView/svgcomponents/SVGHeader.js +0 -47
  362. package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.d.ts +0 -6
  363. package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +0 -42
  364. package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.js +0 -8
  365. package/dist/LinearGenomeView/svgcomponents/SVGRuler.d.ts +0 -7
  366. package/dist/LinearGenomeView/svgcomponents/SVGRuler.js +0 -39
  367. package/dist/LinearGenomeView/svgcomponents/SVGScalebar.d.ts +0 -7
  368. package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js +0 -17
  369. package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts +0 -7
  370. package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js +0 -14
  371. package/dist/LinearGenomeView/svgcomponents/SVGTracks.d.ts +0 -21
  372. package/dist/LinearGenomeView/svgcomponents/SVGTracks.js +0 -32
  373. package/dist/LinearGenomeView/svgcomponents/util.d.ts +0 -8
  374. package/dist/LinearGenomeView/svgcomponents/util.js +0 -8
  375. package/dist/LinearGenomeView/types.d.ts +0 -43
  376. package/dist/LinearGenomeView/types.js +0 -2
  377. package/dist/LinearGenomeView/util.d.ts +0 -26
  378. package/dist/LinearGenomeView/util.js +0 -138
  379. package/dist/index.d.ts +0 -353
  380. package/dist/index.js +0 -120
  381. package/dist/searchUtils.d.ts +0 -26
  382. package/dist/searchUtils.js +0 -80
  383. package/esm/BaseLinearDisplay/components/BlockLoadingMessage.d.ts +0 -6
  384. package/esm/BaseLinearDisplay/components/BlockLoadingMessage.js +0 -24
  385. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +0 -311
  386. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js +0 -286
  387. package/esm/LinearBasicDisplay/components/AddFiltersDialog.d.ts +0 -9
  388. package/esm/LinearBasicDisplay/components/SetMaxHeightDialog.d.ts +0 -8
  389. package/esm/LinearGenomeView/components/ScalebarCoordinateTicks.d.ts +0 -6
  390. package/esm/LinearGenomeView/components/ScalebarCoordinateTicks.js +0 -36
  391. /package/{dist/LinearBasicDisplay → esm/LinearFeatureDisplay}/components/AddFiltersDialog.d.ts +0 -0
  392. /package/{dist/LinearBasicDisplay → esm/LinearFeatureDisplay}/components/SetMaxHeightDialog.d.ts +0 -0
@@ -1,325 +0,0 @@
1
- "use strict";
2
- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
- if (k2 === undefined) k2 = k;
4
- var desc = Object.getOwnPropertyDescriptor(m, k);
5
- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
- desc = { enumerable: true, get: function() { return m[k]; } };
7
- }
8
- Object.defineProperty(o, k2, desc);
9
- }) : (function(o, m, k, k2) {
10
- if (k2 === undefined) k2 = k;
11
- o[k2] = m[k];
12
- }));
13
- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
- Object.defineProperty(o, "default", { enumerable: true, value: v });
15
- }) : function(o, v) {
16
- o["default"] = v;
17
- });
18
- var __importStar = (this && this.__importStar) || (function () {
19
- var ownKeys = function(o) {
20
- ownKeys = Object.getOwnPropertyNames || function (o) {
21
- var ar = [];
22
- for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
23
- return ar;
24
- };
25
- return ownKeys(o);
26
- };
27
- return function (mod) {
28
- if (mod && mod.__esModule) return mod;
29
- var result = {};
30
- if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
31
- __setModuleDefault(result, mod);
32
- return result;
33
- };
34
- })();
35
- var __importDefault = (this && this.__importDefault) || function (mod) {
36
- return (mod && mod.__esModule) ? mod : { "default": mod };
37
- };
38
- Object.defineProperty(exports, "__esModule", { value: true });
39
- exports.BaseLinearDisplay = void 0;
40
- const react_1 = require("react");
41
- const configuration_1 = require("@jbrowse/core/configuration");
42
- const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
43
- const util_1 = require("@jbrowse/core/util");
44
- const compositeMap_1 = __importDefault(require("@jbrowse/core/util/compositeMap"));
45
- const tracks_1 = require("@jbrowse/core/util/tracks");
46
- const CenterFocusStrong_1 = __importDefault(require("@mui/icons-material/CenterFocusStrong"));
47
- const ContentCopy_1 = __importDefault(require("@mui/icons-material/ContentCopy"));
48
- const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
49
- const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
50
- const mobx_1 = require("mobx");
51
- const mobx_state_tree_1 = require("mobx-state-tree");
52
- const FeatureDensityMixin_1 = __importDefault(require("./FeatureDensityMixin"));
53
- const TrackHeightMixin_1 = __importDefault(require("./TrackHeightMixin"));
54
- const configSchema_1 = __importDefault(require("./configSchema"));
55
- const serverSideRenderedBlock_1 = __importDefault(require("./serverSideRenderedBlock"));
56
- const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../components/Tooltip'))));
57
- function stateModelFactory() {
58
- return mobx_state_tree_1.types
59
- .compose('BaseLinearDisplay', models_1.BaseDisplay, (0, TrackHeightMixin_1.default)(), (0, FeatureDensityMixin_1.default)(), mobx_state_tree_1.types.model({
60
- blockState: mobx_state_tree_1.types.map(serverSideRenderedBlock_1.default),
61
- configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
62
- }))
63
- .volatile(() => ({
64
- featureIdUnderMouse: undefined,
65
- contextMenuFeature: undefined,
66
- }))
67
- .views(self => ({
68
- get DisplayMessageComponent() {
69
- return undefined;
70
- },
71
- get blockType() {
72
- return 'staticBlocks';
73
- },
74
- get blockDefinitions() {
75
- const view = (0, util_1.getContainingView)(self);
76
- if (!view.initialized) {
77
- throw new Error('view not initialized yet');
78
- }
79
- return view[this.blockType];
80
- },
81
- }))
82
- .views(self => ({
83
- get renderDelay() {
84
- return 50;
85
- },
86
- get TooltipComponent() {
87
- return Tooltip;
88
- },
89
- get selectedFeatureId() {
90
- if ((0, mobx_state_tree_1.isAlive)(self)) {
91
- const { selection } = (0, util_1.getSession)(self);
92
- if ((0, util_1.isFeature)(selection)) {
93
- return selection.id();
94
- }
95
- }
96
- return undefined;
97
- },
98
- copyInfoToClipboard(feature) {
99
- const { uniqueId, ...rest } = feature.toJSON();
100
- const session = (0, util_1.getSession)(self);
101
- (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
102
- session.notify('Copied to clipboard', 'success');
103
- },
104
- }))
105
- .views(self => ({
106
- get features() {
107
- const featureMaps = [];
108
- for (const block of self.blockState.values()) {
109
- if (block.features) {
110
- featureMaps.push(block.features);
111
- }
112
- }
113
- return new compositeMap_1.default(featureMaps);
114
- },
115
- get featureUnderMouse() {
116
- const feat = self.featureIdUnderMouse;
117
- return feat ? this.features.get(feat) : undefined;
118
- },
119
- getFeatureOverlapping(blockKey, x, y) {
120
- var _a, _b;
121
- return (_b = (_a = self.blockState.get(blockKey)) === null || _a === void 0 ? void 0 : _a.layout) === null || _b === void 0 ? void 0 : _b.getByCoord(x, y);
122
- },
123
- getFeatureByID(blockKey, id) {
124
- var _a, _b;
125
- return (_b = (_a = self.blockState.get(blockKey)) === null || _a === void 0 ? void 0 : _a.layout) === null || _b === void 0 ? void 0 : _b.getByID(id);
126
- },
127
- searchFeatureByID(id) {
128
- var _a;
129
- let ret;
130
- for (const block of self.blockState.values()) {
131
- const val = (_a = block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
132
- if (val) {
133
- ret = val;
134
- }
135
- }
136
- return ret;
137
- },
138
- }))
139
- .actions(self => ({
140
- addBlock(key, block) {
141
- self.blockState.set(key, serverSideRenderedBlock_1.default.create({
142
- key,
143
- region: block.toRegion(),
144
- }));
145
- },
146
- deleteBlock(key) {
147
- self.blockState.delete(key);
148
- },
149
- selectFeature(feature) {
150
- const session = (0, util_1.getSession)(self);
151
- if ((0, util_1.isSessionModelWithWidgets)(session)) {
152
- const { rpcManager } = session;
153
- const sessionId = (0, tracks_1.getRpcSessionId)(self);
154
- const track = (0, util_1.getContainingTrack)(self);
155
- const view = (0, util_1.getContainingView)(self);
156
- const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
157
- (async () => {
158
- try {
159
- const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
160
- adapterConfig,
161
- });
162
- session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
163
- featureData: feature.toJSON(),
164
- view,
165
- track,
166
- descriptions,
167
- }));
168
- }
169
- catch (e) {
170
- console.error(e);
171
- (0, util_1.getSession)(e).notifyError(`${e}`, e);
172
- }
173
- })();
174
- }
175
- if ((0, util_1.isSelectionContainer)(session)) {
176
- session.setSelection(feature);
177
- }
178
- },
179
- navToFeature(feature) {
180
- const view = (0, util_1.getContainingView)(self);
181
- view.navTo({
182
- refName: feature.get('refName'),
183
- start: feature.get('start'),
184
- end: feature.get('end'),
185
- });
186
- },
187
- clearFeatureSelection() {
188
- (0, util_1.getSession)(self).clearSelection();
189
- },
190
- setFeatureIdUnderMouse(feature) {
191
- self.featureIdUnderMouse = feature;
192
- },
193
- setContextMenuFeature(feature) {
194
- self.contextMenuFeature = feature;
195
- },
196
- }))
197
- .actions(self => {
198
- const { reload: superReload } = self;
199
- return {
200
- async reload() {
201
- self.setError();
202
- self.setCurrStatsBpPerPx(0);
203
- self.clearFeatureDensityStats();
204
- for (const val of self.blockState.values()) {
205
- val.doReload();
206
- }
207
- superReload();
208
- },
209
- };
210
- })
211
- .views(self => ({
212
- trackMenuItems() {
213
- return [];
214
- },
215
- contextMenuItems() {
216
- const feat = self.contextMenuFeature;
217
- return feat
218
- ? [
219
- {
220
- label: 'Open feature details',
221
- icon: MenuOpen_1.default,
222
- onClick: () => {
223
- self.selectFeature(feat);
224
- },
225
- },
226
- {
227
- label: 'Zoom to feature',
228
- icon: CenterFocusStrong_1.default,
229
- onClick: () => {
230
- self.navToFeature(feat);
231
- },
232
- },
233
- {
234
- label: 'Copy info to clipboard',
235
- icon: ContentCopy_1.default,
236
- onClick: () => {
237
- self.copyInfoToClipboard(feat);
238
- },
239
- },
240
- ]
241
- : [];
242
- },
243
- renderProps() {
244
- return {
245
- ...(0, tracks_1.getParentRenderProps)(self),
246
- notReady: !self.featureDensityStatsReady,
247
- rpcDriverName: self.rpcDriverName,
248
- displayModel: self,
249
- onFeatureClick(_, featureId) {
250
- const f = featureId || self.featureIdUnderMouse;
251
- if (!f) {
252
- self.clearFeatureSelection();
253
- }
254
- else {
255
- const feature = self.features.get(f);
256
- if (feature) {
257
- self.selectFeature(feature);
258
- }
259
- }
260
- },
261
- onClick() {
262
- self.clearFeatureSelection();
263
- },
264
- onFeatureContextMenu(_, featureId) {
265
- const f = featureId || self.featureIdUnderMouse;
266
- if (!f) {
267
- self.clearFeatureSelection();
268
- }
269
- else {
270
- self.setContextMenuFeature(self.features.get(f));
271
- }
272
- },
273
- onMouseMove(_, featureId) {
274
- self.setFeatureIdUnderMouse(featureId);
275
- },
276
- onMouseLeave(_) {
277
- self.setFeatureIdUnderMouse(undefined);
278
- },
279
- onContextMenu() {
280
- self.setContextMenuFeature(undefined);
281
- self.clearFeatureSelection();
282
- },
283
- };
284
- },
285
- }))
286
- .actions(self => ({
287
- async renderSvg(opts) {
288
- const { renderBaseLinearDisplaySvg } = await Promise.resolve().then(() => __importStar(require('./renderSvg')));
289
- return renderBaseLinearDisplaySvg(self, opts);
290
- },
291
- afterAttach() {
292
- (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
293
- const blocksPresent = {};
294
- const view = (0, util_1.getContainingView)(self);
295
- if (!view.initialized) {
296
- return;
297
- }
298
- for (const block of self.blockDefinitions.contentBlocks) {
299
- blocksPresent[block.key] = true;
300
- if (!self.blockState.has(block.key)) {
301
- self.addBlock(block.key, block);
302
- }
303
- }
304
- for (const key of self.blockState.keys()) {
305
- if (!blocksPresent[key]) {
306
- self.deleteBlock(key);
307
- }
308
- }
309
- }));
310
- },
311
- }))
312
- .preProcessSnapshot(snap => {
313
- if (!snap) {
314
- return snap;
315
- }
316
- const { height, ...rest } = snap;
317
- return { heightPreConfig: height, ...rest };
318
- })
319
- .postProcessSnapshot(snap => {
320
- const r = snap;
321
- const { blockState, ...rest } = r;
322
- return rest;
323
- });
324
- }
325
- exports.BaseLinearDisplay = stateModelFactory();
@@ -1,32 +0,0 @@
1
- import type { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
2
- import type { Region } from '@jbrowse/core/util/types';
3
- export default function FeatureDensityMixin(): import("mobx-state-tree").IModelType<{
4
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
5
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
6
- }, {
7
- featureDensityStatsP: undefined | Promise<FeatureDensityStats>;
8
- featureDensityStats: undefined | FeatureDensityStats;
9
- currStatsBpPerPx: number;
10
- } & {
11
- readonly currentBytesRequested: number;
12
- readonly currentFeatureScreenDensity: number;
13
- readonly maxFeatureScreenDensity: any;
14
- readonly featureDensityStatsReady: boolean;
15
- readonly maxAllowableBytes: number;
16
- } & {
17
- afterAttach(): void;
18
- } & {
19
- setCurrStatsBpPerPx(n: number): void;
20
- setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
21
- getFeatureDensityStats(): Promise<FeatureDensityStats>;
22
- setFeatureDensityStatsP(arg: any): void;
23
- setFeatureDensityStats(featureDensityStats?: FeatureDensityStats): void;
24
- clearFeatureDensityStats(): void;
25
- } & {
26
- readonly regionTooLarge: boolean;
27
- readonly regionTooLargeReason: string;
28
- } & {
29
- readonly statsReadyAndRegionNotTooLarge: boolean;
30
- regionCannotBeRenderedText(_region: Region): "" | "Force load to see features";
31
- regionCannotBeRendered(_region: Region): import("react/jsx-runtime").JSX.Element | null;
32
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -1,122 +0,0 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.default = FeatureDensityMixin;
7
- const jsx_runtime_1 = require("react/jsx-runtime");
8
- const configuration_1 = require("@jbrowse/core/configuration");
9
- const util_1 = require("@jbrowse/core/util");
10
- const mobx_1 = require("mobx");
11
- const mobx_state_tree_1 = require("mobx-state-tree");
12
- const autorunFeatureDensityStats_1 = __importDefault(require("./autorunFeatureDensityStats"));
13
- const util_2 = require("./util");
14
- const TooLargeMessage_1 = __importDefault(require("../components/TooLargeMessage"));
15
- function FeatureDensityMixin() {
16
- return mobx_state_tree_1.types
17
- .model({
18
- userBpPerPxLimit: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
19
- userByteSizeLimit: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
20
- })
21
- .volatile(() => ({
22
- featureDensityStatsP: undefined,
23
- featureDensityStats: undefined,
24
- currStatsBpPerPx: 0,
25
- }))
26
- .views(self => ({
27
- get currentBytesRequested() {
28
- var _a;
29
- return ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
30
- },
31
- get currentFeatureScreenDensity() {
32
- var _a;
33
- const view = (0, util_1.getContainingView)(self);
34
- return (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
35
- },
36
- get maxFeatureScreenDensity() {
37
- return (0, configuration_1.getConf)(self, 'maxFeatureScreenDensity');
38
- },
39
- get featureDensityStatsReady() {
40
- const view = (0, util_1.getContainingView)(self);
41
- return (self.currStatsBpPerPx === view.bpPerPx &&
42
- (!!self.featureDensityStats || !!self.userBpPerPxLimit));
43
- },
44
- get maxAllowableBytes() {
45
- var _a;
46
- return (self.userByteSizeLimit ||
47
- ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
48
- (0, configuration_1.getConf)(self, 'fetchSizeLimit'));
49
- },
50
- }))
51
- .actions(self => ({
52
- afterAttach() {
53
- (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => (0, autorunFeatureDensityStats_1.default)(self)));
54
- },
55
- }))
56
- .actions(self => ({
57
- setCurrStatsBpPerPx(n) {
58
- self.currStatsBpPerPx = n;
59
- },
60
- setFeatureDensityStatsLimit(stats) {
61
- const view = (0, util_1.getContainingView)(self);
62
- if (stats === null || stats === void 0 ? void 0 : stats.bytes) {
63
- self.userByteSizeLimit = stats.bytes;
64
- }
65
- else {
66
- self.userBpPerPxLimit = view.bpPerPx;
67
- }
68
- },
69
- getFeatureDensityStats() {
70
- if (!self.featureDensityStatsP) {
71
- self.featureDensityStatsP = (0, util_2.getFeatureDensityStatsPre)(self).catch((e) => {
72
- if ((0, mobx_state_tree_1.isAlive)(self)) {
73
- this.setFeatureDensityStatsP(undefined);
74
- }
75
- throw e;
76
- });
77
- }
78
- return self.featureDensityStatsP;
79
- },
80
- setFeatureDensityStatsP(arg) {
81
- self.featureDensityStatsP = arg;
82
- },
83
- setFeatureDensityStats(featureDensityStats) {
84
- self.featureDensityStats = featureDensityStats;
85
- },
86
- clearFeatureDensityStats() {
87
- self.featureDensityStatsP = undefined;
88
- self.featureDensityStats = undefined;
89
- },
90
- }))
91
- .views(self => ({
92
- get regionTooLarge() {
93
- const view = (0, util_1.getContainingView)(self);
94
- if (!self.featureDensityStatsReady ||
95
- view.dynamicBlocks.totalBp < 20000) {
96
- return false;
97
- }
98
- return (self.currentBytesRequested > self.maxAllowableBytes ||
99
- (self.userBpPerPxLimit
100
- ? view.bpPerPx > self.userBpPerPxLimit
101
- : self.currentFeatureScreenDensity > self.maxFeatureScreenDensity));
102
- },
103
- get regionTooLargeReason() {
104
- const req = self.currentBytesRequested;
105
- const max = self.maxAllowableBytes;
106
- return req && req > max
107
- ? `Requested too much data (${(0, util_2.getDisplayStr)(req)})`
108
- : '';
109
- },
110
- }))
111
- .views(self => ({
112
- get statsReadyAndRegionNotTooLarge() {
113
- return self.featureDensityStatsReady && !self.regionTooLarge;
114
- },
115
- regionCannotBeRenderedText(_region) {
116
- return self.regionTooLarge ? 'Force load to see features' : '';
117
- },
118
- regionCannotBeRendered(_region) {
119
- return self.regionTooLarge ? ((0, jsx_runtime_1.jsx)(TooLargeMessage_1.default, { model: self })) : null;
120
- },
121
- }));
122
- }
@@ -1,11 +0,0 @@
1
- export default function TrackHeightMixin(): import("mobx-state-tree").IModelType<{
2
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
3
- }, {
4
- scrollTop: number;
5
- } & {
6
- readonly height: number;
7
- } & {
8
- setScrollTop(scrollTop: number): void;
9
- setHeight(displayHeight: number): number;
10
- resizeHeight(distance: number): number;
11
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -1,35 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.default = TrackHeightMixin;
4
- const configuration_1 = require("@jbrowse/core/configuration");
5
- const mobx_state_tree_1 = require("mobx-state-tree");
6
- const minDisplayHeight = 20;
7
- function TrackHeightMixin() {
8
- return mobx_state_tree_1.types
9
- .model({
10
- heightPreConfig: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.refinement('displayHeight', mobx_state_tree_1.types.number, n => n >= minDisplayHeight)),
11
- })
12
- .volatile(() => ({
13
- scrollTop: 0,
14
- }))
15
- .views(self => ({
16
- get height() {
17
- var _a;
18
- return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'height');
19
- },
20
- }))
21
- .actions(self => ({
22
- setScrollTop(scrollTop) {
23
- self.scrollTop = scrollTop;
24
- },
25
- setHeight(displayHeight) {
26
- self.heightPreConfig = Math.max(displayHeight, minDisplayHeight);
27
- return self.height;
28
- },
29
- resizeHeight(distance) {
30
- const oldHeight = self.height;
31
- const newHeight = this.setHeight(self.height + distance);
32
- return newHeight - oldHeight;
33
- },
34
- }));
35
- }
@@ -1,2 +0,0 @@
1
- import type { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
2
- export default function autorunFeatureDensityStats(self: BaseLinearDisplayModel): Promise<void>;
@@ -1,33 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.default = autorunFeatureDensityStats;
4
- const util_1 = require("@jbrowse/core/util");
5
- const mobx_state_tree_1 = require("mobx-state-tree");
6
- async function autorunFeatureDensityStats(self) {
7
- var _a;
8
- try {
9
- const view = (0, util_1.getContainingView)(self);
10
- if (!view.initialized ||
11
- !view.staticBlocks.contentBlocks.length ||
12
- view.bpPerPx === self.currStatsBpPerPx ||
13
- self.error) {
14
- return;
15
- }
16
- if (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
17
- self.setCurrStatsBpPerPx(view.bpPerPx);
18
- return;
19
- }
20
- self.clearFeatureDensityStats();
21
- self.setCurrStatsBpPerPx(view.bpPerPx);
22
- const stats = await self.getFeatureDensityStats();
23
- if ((0, mobx_state_tree_1.isAlive)(self)) {
24
- self.setFeatureDensityStats(stats);
25
- }
26
- }
27
- catch (e) {
28
- console.error(e);
29
- if ((0, mobx_state_tree_1.isAlive)(self) && !(0, util_1.isAbortException)(e)) {
30
- self.setError(e);
31
- }
32
- }
33
- }
@@ -1,29 +0,0 @@
1
- declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
- maxFeatureScreenDensity: {
3
- type: string;
4
- description: string;
5
- defaultValue: number;
6
- };
7
- fetchSizeLimit: {
8
- type: string;
9
- defaultValue: number;
10
- description: string;
11
- };
12
- height: {
13
- type: string;
14
- defaultValue: number;
15
- description: string;
16
- };
17
- mouseover: {
18
- type: string;
19
- description: string;
20
- defaultValue: string;
21
- contextVariable: string[];
22
- };
23
- jexlFilters: {
24
- type: string;
25
- description: string;
26
- defaultValue: never[];
27
- };
28
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
29
- export default baseLinearDisplayConfigSchema;
@@ -1,35 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- const configuration_1 = require("@jbrowse/core/configuration");
4
- function x() { }
5
- const baseLinearDisplayConfigSchema = (0, configuration_1.ConfigurationSchema)('BaseLinearDisplay', {
6
- maxFeatureScreenDensity: {
7
- type: 'number',
8
- description: 'maximum features per pixel that is displayed in the view, used if byte size estimates not available',
9
- defaultValue: 0.3,
10
- },
11
- fetchSizeLimit: {
12
- type: 'number',
13
- defaultValue: 1000000,
14
- description: "maximum data to attempt to download for a given track, used if adapter doesn't specify one",
15
- },
16
- height: {
17
- type: 'number',
18
- defaultValue: 100,
19
- description: 'default height for the track',
20
- },
21
- mouseover: {
22
- type: 'string',
23
- description: 'text to display when the cursor hovers over a feature',
24
- defaultValue: `jexl:get(feature,'name')`,
25
- contextVariable: ['feature'],
26
- },
27
- jexlFilters: {
28
- type: 'stringArray',
29
- description: 'default set of jexl filters to apply to a track. note: these do not use the jexl prefix because they have a deferred evaluation system',
30
- defaultValue: [],
31
- },
32
- }, {
33
- explicitIdentifier: 'displayId',
34
- });
35
- exports.default = baseLinearDisplayConfigSchema;
@@ -1,7 +0,0 @@
1
- import type { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
2
- import type { ExportSvgOptions } from '../../LinearGenomeView/types';
3
- import type { ThemeOptions } from '@mui/material';
4
- export declare function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
5
- overrideHeight: number;
6
- theme?: ThemeOptions;
7
- }): Promise<import("react/jsx-runtime").JSX.Element>;