@jbrowse/plugin-linear-genome-view 2.5.0 → 2.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (279) hide show
  1. package/dist/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +1 -1
  2. package/dist/BaseLinearDisplay/components/Block.d.ts +3 -3
  3. package/dist/BaseLinearDisplay/components/BlockMsg.d.ts +1 -1
  4. package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts +3 -2
  5. package/dist/BaseLinearDisplay/components/TooLargeMessage.d.ts +2 -1
  6. package/dist/BaseLinearDisplay/components/Tooltip.d.ts +2 -1
  7. package/dist/BaseLinearDisplay/index.d.ts +5 -2
  8. package/dist/BaseLinearDisplay/index.js +7 -1
  9. package/dist/BaseLinearDisplay/index.js.map +1 -1
  10. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +62 -142
  11. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +34 -355
  12. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
  13. package/dist/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +99 -0
  14. package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js +190 -0
  15. package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js.map +1 -0
  16. package/dist/BaseLinearDisplay/models/TrackHeightMixin.d.ts +30 -0
  17. package/dist/BaseLinearDisplay/models/TrackHeightMixin.js +56 -0
  18. package/dist/BaseLinearDisplay/models/TrackHeightMixin.js.map +1 -0
  19. package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts +2 -0
  20. package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.js +42 -0
  21. package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.js.map +1 -0
  22. package/dist/BaseLinearDisplay/models/configSchema.js +1 -0
  23. package/dist/BaseLinearDisplay/models/configSchema.js.map +1 -1
  24. package/dist/BaseLinearDisplay/models/renderSvg.d.ts +8 -0
  25. package/dist/BaseLinearDisplay/models/renderSvg.js +83 -0
  26. package/dist/BaseLinearDisplay/models/renderSvg.js.map +1 -0
  27. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +20 -16
  28. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
  29. package/dist/BasicTrack/configSchema.js +1 -0
  30. package/dist/BasicTrack/configSchema.js.map +1 -1
  31. package/dist/FeatureTrack/configSchema.d.ts +1 -3
  32. package/dist/FeatureTrack/configSchema.js +1 -0
  33. package/dist/FeatureTrack/configSchema.js.map +1 -1
  34. package/dist/LinearBareDisplay/configSchema.d.ts +1 -0
  35. package/dist/LinearBareDisplay/configSchema.js +1 -0
  36. package/dist/LinearBareDisplay/configSchema.js.map +1 -1
  37. package/dist/LinearBareDisplay/model.d.ts +52 -39
  38. package/dist/LinearBareDisplay/model.js +1 -0
  39. package/dist/LinearBareDisplay/model.js.map +1 -1
  40. package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts +2 -1
  41. package/dist/LinearBasicDisplay/configSchema.d.ts +1 -0
  42. package/dist/LinearBasicDisplay/configSchema.js +1 -0
  43. package/dist/LinearBasicDisplay/configSchema.js.map +1 -1
  44. package/dist/LinearBasicDisplay/model.d.ts +67 -66
  45. package/dist/LinearBasicDisplay/model.js +1 -0
  46. package/dist/LinearBasicDisplay/model.js.map +1 -1
  47. package/dist/LinearGenomeView/components/CenterLine.d.ts +2 -1
  48. package/dist/LinearGenomeView/components/Cytobands.d.ts +2 -1
  49. package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts +2 -1
  50. package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts +2 -1
  51. package/dist/LinearGenomeView/components/Gridlines.d.ts +2 -1
  52. package/dist/LinearGenomeView/components/Header.d.ts +2 -1
  53. package/dist/LinearGenomeView/components/ImportForm.d.ts +2 -1
  54. package/dist/LinearGenomeView/components/LinearGenomeView.d.ts +2 -1
  55. package/dist/LinearGenomeView/components/LinearGenomeView.js +28 -4
  56. package/dist/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
  57. package/dist/LinearGenomeView/components/MiniControls.d.ts +3 -2
  58. package/dist/LinearGenomeView/components/MiniControls.js +20 -40
  59. package/dist/LinearGenomeView/components/MiniControls.js.map +1 -1
  60. package/dist/LinearGenomeView/components/OverviewRubberband.d.ts +1 -1
  61. package/dist/LinearGenomeView/components/OverviewScalebar.d.ts +2 -2
  62. package/dist/LinearGenomeView/components/OverviewScalebar.js +10 -4
  63. package/dist/LinearGenomeView/components/OverviewScalebar.js.map +1 -1
  64. package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.d.ts +10 -0
  65. package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js +22 -0
  66. package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js.map +1 -0
  67. package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.d.ts +5 -0
  68. package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +52 -0
  69. package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js.map +1 -0
  70. package/dist/LinearGenomeView/components/{HelpDialog.d.ts → RefNameAutocomplete/HelpDialog.d.ts} +2 -1
  71. package/dist/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.js.map +1 -0
  72. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +18 -0
  73. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js +111 -0
  74. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js.map +1 -0
  75. package/dist/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +12 -0
  76. package/dist/LinearGenomeView/components/RefNameAutocomplete/util.js +59 -0
  77. package/dist/LinearGenomeView/components/RefNameAutocomplete/util.js.map +1 -0
  78. package/dist/LinearGenomeView/components/Rubberband.d.ts +1 -1
  79. package/dist/LinearGenomeView/components/RubberbandSpan.d.ts +2 -1
  80. package/dist/LinearGenomeView/components/SearchBox.d.ts +2 -1
  81. package/dist/LinearGenomeView/components/SearchResultsDialog.d.ts +2 -1
  82. package/dist/LinearGenomeView/components/SearchResultsTable.d.ts +2 -1
  83. package/dist/LinearGenomeView/components/SequenceSearchDialog.d.ts +2 -1
  84. package/dist/LinearGenomeView/components/TrackContainer.d.ts +3 -3
  85. package/dist/LinearGenomeView/components/TrackContainer.js +12 -68
  86. package/dist/LinearGenomeView/components/TrackContainer.js.map +1 -1
  87. package/dist/LinearGenomeView/components/TrackLabel.js +6 -10
  88. package/dist/LinearGenomeView/components/TrackLabel.js.map +1 -1
  89. package/dist/LinearGenomeView/components/TrackLabelContainer.d.ts +9 -0
  90. package/dist/LinearGenomeView/components/TrackLabelContainer.js +32 -0
  91. package/dist/LinearGenomeView/components/TrackLabelContainer.js.map +1 -0
  92. package/dist/LinearGenomeView/components/TrackRenderingContainer.d.ts +10 -0
  93. package/dist/LinearGenomeView/components/TrackRenderingContainer.js +74 -0
  94. package/dist/LinearGenomeView/components/TrackRenderingContainer.js.map +1 -0
  95. package/dist/LinearGenomeView/components/TracksContainer.d.ts +1 -1
  96. package/dist/LinearGenomeView/components/TracksContainer.js +2 -2
  97. package/dist/LinearGenomeView/components/TracksContainer.js.map +1 -1
  98. package/dist/LinearGenomeView/components/VerticalGuide.d.ts +2 -1
  99. package/dist/LinearGenomeView/components/ZoomControls.d.ts +2 -1
  100. package/dist/LinearGenomeView/model.d.ts +13 -12
  101. package/dist/LinearGenomeView/model.js +25 -25
  102. package/dist/LinearGenomeView/model.js.map +1 -1
  103. package/dist/LinearGenomeView/svgcomponents/SVGBackground.d.ts +2 -1
  104. package/dist/LinearGenomeView/svgcomponents/SVGHeader.d.ts +3 -4
  105. package/dist/LinearGenomeView/svgcomponents/SVGHeader.js +7 -2
  106. package/dist/LinearGenomeView/svgcomponents/SVGHeader.js.map +1 -1
  107. package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +1 -1
  108. package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map +1 -1
  109. package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts +2 -1
  110. package/dist/LinearGenomeView/svgcomponents/SVGRuler.d.ts +2 -1
  111. package/dist/LinearGenomeView/svgcomponents/SVGScalebar.d.ts +2 -1
  112. package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts +2 -1
  113. package/dist/LinearGenomeView/svgcomponents/SVGTracks.d.ts +2 -1
  114. package/dist/LinearGenomeView/util.d.ts +2 -2
  115. package/dist/index.d.ts +160 -134
  116. package/dist/index.js +6 -3
  117. package/dist/index.js.map +1 -1
  118. package/esm/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +1 -1
  119. package/esm/BaseLinearDisplay/components/Block.d.ts +3 -3
  120. package/esm/BaseLinearDisplay/components/BlockMsg.d.ts +1 -1
  121. package/esm/BaseLinearDisplay/components/LinearBlocks.d.ts +3 -2
  122. package/esm/BaseLinearDisplay/components/TooLargeMessage.d.ts +2 -1
  123. package/esm/BaseLinearDisplay/components/Tooltip.d.ts +2 -1
  124. package/esm/BaseLinearDisplay/index.d.ts +5 -2
  125. package/esm/BaseLinearDisplay/index.js +3 -0
  126. package/esm/BaseLinearDisplay/index.js.map +1 -1
  127. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +62 -142
  128. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js +36 -334
  129. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
  130. package/esm/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +99 -0
  131. package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js +184 -0
  132. package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js.map +1 -0
  133. package/esm/BaseLinearDisplay/models/TrackHeightMixin.d.ts +30 -0
  134. package/esm/BaseLinearDisplay/models/TrackHeightMixin.js +53 -0
  135. package/esm/BaseLinearDisplay/models/TrackHeightMixin.js.map +1 -0
  136. package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts +2 -0
  137. package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js +39 -0
  138. package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js.map +1 -0
  139. package/esm/BaseLinearDisplay/models/configSchema.js +1 -0
  140. package/esm/BaseLinearDisplay/models/configSchema.js.map +1 -1
  141. package/esm/BaseLinearDisplay/models/renderSvg.d.ts +8 -0
  142. package/esm/BaseLinearDisplay/models/renderSvg.js +54 -0
  143. package/esm/BaseLinearDisplay/models/renderSvg.js.map +1 -0
  144. package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js +20 -16
  145. package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
  146. package/esm/BasicTrack/configSchema.js +1 -0
  147. package/esm/BasicTrack/configSchema.js.map +1 -1
  148. package/esm/FeatureTrack/configSchema.d.ts +1 -3
  149. package/esm/FeatureTrack/configSchema.js +1 -0
  150. package/esm/FeatureTrack/configSchema.js.map +1 -1
  151. package/esm/LinearBareDisplay/configSchema.d.ts +1 -0
  152. package/esm/LinearBareDisplay/configSchema.js +1 -0
  153. package/esm/LinearBareDisplay/configSchema.js.map +1 -1
  154. package/esm/LinearBareDisplay/model.d.ts +52 -39
  155. package/esm/LinearBareDisplay/model.js +1 -0
  156. package/esm/LinearBareDisplay/model.js.map +1 -1
  157. package/esm/LinearBasicDisplay/components/SetMaxHeight.d.ts +2 -1
  158. package/esm/LinearBasicDisplay/configSchema.d.ts +1 -0
  159. package/esm/LinearBasicDisplay/configSchema.js +1 -0
  160. package/esm/LinearBasicDisplay/configSchema.js.map +1 -1
  161. package/esm/LinearBasicDisplay/model.d.ts +67 -66
  162. package/esm/LinearBasicDisplay/model.js +1 -0
  163. package/esm/LinearBasicDisplay/model.js.map +1 -1
  164. package/esm/LinearGenomeView/components/CenterLine.d.ts +2 -1
  165. package/esm/LinearGenomeView/components/Cytobands.d.ts +2 -1
  166. package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts +2 -1
  167. package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts +2 -1
  168. package/esm/LinearGenomeView/components/Gridlines.d.ts +2 -1
  169. package/esm/LinearGenomeView/components/Header.d.ts +2 -1
  170. package/esm/LinearGenomeView/components/ImportForm.d.ts +2 -1
  171. package/esm/LinearGenomeView/components/LinearGenomeView.d.ts +2 -1
  172. package/esm/LinearGenomeView/components/LinearGenomeView.js +4 -3
  173. package/esm/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
  174. package/esm/LinearGenomeView/components/MiniControls.d.ts +3 -2
  175. package/esm/LinearGenomeView/components/MiniControls.js +20 -17
  176. package/esm/LinearGenomeView/components/MiniControls.js.map +1 -1
  177. package/esm/LinearGenomeView/components/OverviewRubberband.d.ts +1 -1
  178. package/esm/LinearGenomeView/components/OverviewScalebar.d.ts +2 -2
  179. package/esm/LinearGenomeView/components/OverviewScalebar.js +10 -4
  180. package/esm/LinearGenomeView/components/OverviewScalebar.js.map +1 -1
  181. package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.d.ts +10 -0
  182. package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js +16 -0
  183. package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js.map +1 -0
  184. package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.d.ts +5 -0
  185. package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +23 -0
  186. package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js.map +1 -0
  187. package/esm/LinearGenomeView/components/{HelpDialog.d.ts → RefNameAutocomplete/HelpDialog.d.ts} +2 -1
  188. package/esm/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.js.map +1 -0
  189. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +18 -0
  190. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js +83 -0
  191. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js.map +1 -0
  192. package/esm/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +12 -0
  193. package/esm/LinearGenomeView/components/RefNameAutocomplete/util.js +50 -0
  194. package/esm/LinearGenomeView/components/RefNameAutocomplete/util.js.map +1 -0
  195. package/esm/LinearGenomeView/components/Rubberband.d.ts +1 -1
  196. package/esm/LinearGenomeView/components/RubberbandSpan.d.ts +2 -1
  197. package/esm/LinearGenomeView/components/SearchBox.d.ts +2 -1
  198. package/esm/LinearGenomeView/components/SearchResultsDialog.d.ts +2 -1
  199. package/esm/LinearGenomeView/components/SearchResultsTable.d.ts +2 -1
  200. package/esm/LinearGenomeView/components/SequenceSearchDialog.d.ts +2 -1
  201. package/esm/LinearGenomeView/components/TrackContainer.d.ts +3 -3
  202. package/esm/LinearGenomeView/components/TrackContainer.js +13 -69
  203. package/esm/LinearGenomeView/components/TrackContainer.js.map +1 -1
  204. package/esm/LinearGenomeView/components/TrackLabel.js +6 -10
  205. package/esm/LinearGenomeView/components/TrackLabel.js.map +1 -1
  206. package/esm/LinearGenomeView/components/TrackLabelContainer.d.ts +9 -0
  207. package/esm/LinearGenomeView/components/TrackLabelContainer.js +27 -0
  208. package/esm/LinearGenomeView/components/TrackLabelContainer.js.map +1 -0
  209. package/esm/LinearGenomeView/components/TrackRenderingContainer.d.ts +10 -0
  210. package/esm/LinearGenomeView/components/TrackRenderingContainer.js +49 -0
  211. package/esm/LinearGenomeView/components/TrackRenderingContainer.js.map +1 -0
  212. package/esm/LinearGenomeView/components/TracksContainer.d.ts +1 -1
  213. package/esm/LinearGenomeView/components/TracksContainer.js +2 -2
  214. package/esm/LinearGenomeView/components/TracksContainer.js.map +1 -1
  215. package/esm/LinearGenomeView/components/VerticalGuide.d.ts +2 -1
  216. package/esm/LinearGenomeView/components/ZoomControls.d.ts +2 -1
  217. package/esm/LinearGenomeView/model.d.ts +13 -12
  218. package/esm/LinearGenomeView/model.js +21 -21
  219. package/esm/LinearGenomeView/model.js.map +1 -1
  220. package/esm/LinearGenomeView/svgcomponents/SVGBackground.d.ts +2 -1
  221. package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts +3 -4
  222. package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +7 -2
  223. package/esm/LinearGenomeView/svgcomponents/SVGHeader.js.map +1 -1
  224. package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +1 -1
  225. package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map +1 -1
  226. package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts +2 -1
  227. package/esm/LinearGenomeView/svgcomponents/SVGRuler.d.ts +2 -1
  228. package/esm/LinearGenomeView/svgcomponents/SVGScalebar.d.ts +2 -1
  229. package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts +2 -1
  230. package/esm/LinearGenomeView/svgcomponents/SVGTracks.d.ts +2 -1
  231. package/esm/LinearGenomeView/util.d.ts +2 -2
  232. package/esm/index.d.ts +160 -134
  233. package/esm/index.js +1 -1
  234. package/esm/index.js.map +1 -1
  235. package/package.json +2 -2
  236. package/src/BaseLinearDisplay/index.ts +5 -1
  237. package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +46 -407
  238. package/src/BaseLinearDisplay/models/FeatureDensityMixin.tsx +213 -0
  239. package/src/BaseLinearDisplay/models/TrackHeightMixin.tsx +59 -0
  240. package/src/BaseLinearDisplay/models/autorunFeatureDensityStats.ts +46 -0
  241. package/src/BaseLinearDisplay/models/configSchema.ts +1 -0
  242. package/src/BaseLinearDisplay/models/renderSvg.tsx +101 -0
  243. package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +21 -19
  244. package/src/BasicTrack/configSchema.ts +1 -0
  245. package/src/FeatureTrack/configSchema.ts +1 -0
  246. package/src/LinearBareDisplay/configSchema.ts +1 -0
  247. package/src/LinearBareDisplay/model.ts +1 -0
  248. package/src/LinearBasicDisplay/configSchema.ts +1 -0
  249. package/src/LinearBasicDisplay/model.ts +1 -0
  250. package/src/LinearGenomeView/components/LinearGenomeView.test.tsx +3 -3
  251. package/src/LinearGenomeView/components/LinearGenomeView.tsx +6 -3
  252. package/src/LinearGenomeView/components/MiniControls.tsx +37 -38
  253. package/src/LinearGenomeView/components/OverviewScalebar.tsx +11 -5
  254. package/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx +53 -0
  255. package/src/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.tsx +44 -0
  256. package/src/LinearGenomeView/components/RefNameAutocomplete/index.tsx +160 -0
  257. package/src/LinearGenomeView/components/RefNameAutocomplete/util.ts +65 -0
  258. package/src/LinearGenomeView/components/TrackContainer.tsx +16 -104
  259. package/src/LinearGenomeView/components/TrackLabel.tsx +7 -27
  260. package/src/LinearGenomeView/components/TrackLabelContainer.tsx +48 -0
  261. package/src/LinearGenomeView/components/TrackRenderingContainer.tsx +96 -0
  262. package/src/LinearGenomeView/components/TracksContainer.tsx +2 -2
  263. package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap +3 -3
  264. package/src/LinearGenomeView/model.ts +29 -28
  265. package/src/LinearGenomeView/svgcomponents/SVGHeader.tsx +8 -6
  266. package/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx +1 -1
  267. package/src/index.ts +11 -5
  268. package/dist/LinearGenomeView/components/HelpDialog.js.map +0 -1
  269. package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts +0 -23
  270. package/dist/LinearGenomeView/components/RefNameAutocomplete.js +0 -189
  271. package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map +0 -1
  272. package/esm/LinearGenomeView/components/HelpDialog.js.map +0 -1
  273. package/esm/LinearGenomeView/components/RefNameAutocomplete.d.ts +0 -23
  274. package/esm/LinearGenomeView/components/RefNameAutocomplete.js +0 -161
  275. package/esm/LinearGenomeView/components/RefNameAutocomplete.js.map +0 -1
  276. package/src/LinearGenomeView/components/RefNameAutocomplete.tsx +0 -321
  277. /package/dist/LinearGenomeView/components/{HelpDialog.js → RefNameAutocomplete/HelpDialog.js} +0 -0
  278. /package/esm/LinearGenomeView/components/{HelpDialog.js → RefNameAutocomplete/HelpDialog.js} +0 -0
  279. /package/src/LinearGenomeView/components/{HelpDialog.tsx → RefNameAutocomplete/HelpDialog.tsx} +0 -0
@@ -0,0 +1,184 @@
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+ /* eslint-disable @typescript-eslint/no-explicit-any */
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+ import React from 'react';
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+ import { getConf } from '@jbrowse/core/configuration';
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+ import { getContainingView } from '@jbrowse/core/util';
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+ import { autorun } from 'mobx';
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+ import { addDisposer, isAlive, types } from 'mobx-state-tree';
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+ import TooLargeMessage from '../components/TooLargeMessage';
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+ import { getDisplayStr, getFeatureDensityStatsPre } from './util';
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+ import autorunFeatureDensityStats from './autorunFeatureDensityStats';
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+ /**
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+ * #stateModel FeatureDensityMixin
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+ * #category display
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+ */
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+ export default function FeatureDensityMixin() {
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+ return types
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+ .model({
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+ /**
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+ * #property
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+ */
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+ userBpPerPxLimit: types.maybe(types.number),
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+ /**
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+ * #property
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+ */
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+ userByteSizeLimit: types.maybe(types.number),
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+ })
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+ .volatile(() => ({
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+ featureDensityStatsP: undefined,
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+ featureDensityStats: undefined,
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+ currStatsBpPerPx: 0,
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+ }))
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+ .views(self => ({
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+ /**
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+ * #getter
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+ */
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+ get currentBytesRequested() {
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+ var _a;
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+ return ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
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+ },
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+ /**
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+ * #getter
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+ */
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+ get currentFeatureScreenDensity() {
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+ var _a;
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+ const view = getContainingView(self);
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+ return (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
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+ },
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+ /**
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+ * #getter
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+ */
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+ get maxFeatureScreenDensity() {
51
+ // @ts-expect-error
52
+ return getConf(self, 'maxFeatureScreenDensity');
53
+ },
54
+ /**
55
+ * #getter
56
+ */
57
+ get featureDensityStatsReady() {
58
+ const view = getContainingView(self);
59
+ return (self.currStatsBpPerPx === view.bpPerPx &&
60
+ (!!self.featureDensityStats || !!self.userBpPerPxLimit));
61
+ },
62
+ /**
63
+ * #getter
64
+ */
65
+ get maxAllowableBytes() {
66
+ var _a;
67
+ return (self.userByteSizeLimit ||
68
+ ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
69
+ // @ts-expect-error
70
+ getConf(self, 'fetchSizeLimit'));
71
+ },
72
+ }))
73
+ .actions(self => ({
74
+ afterAttach() {
75
+ addDisposer(self, autorun(() => autorunFeatureDensityStats(self)));
76
+ },
77
+ }))
78
+ .actions(self => ({
79
+ /**
80
+ * #action
81
+ */
82
+ setCurrStatsBpPerPx(n) {
83
+ self.currStatsBpPerPx = n;
84
+ },
85
+ /**
86
+ * #action
87
+ */
88
+ setFeatureDensityStatsLimit(stats) {
89
+ const view = getContainingView(self);
90
+ if (stats === null || stats === void 0 ? void 0 : stats.bytes) {
91
+ self.userByteSizeLimit = stats.bytes;
92
+ }
93
+ else {
94
+ self.userBpPerPxLimit = view.bpPerPx;
95
+ }
96
+ },
97
+ /**
98
+ * #action
99
+ */
100
+ async getFeatureDensityStats() {
101
+ if (!self.featureDensityStatsP) {
102
+ self.featureDensityStatsP = getFeatureDensityStatsPre(self).catch(e => {
103
+ if (isAlive(self)) {
104
+ this.setFeatureDensityStatsP(undefined);
105
+ }
106
+ throw e;
107
+ });
108
+ }
109
+ return self.featureDensityStatsP;
110
+ },
111
+ /**
112
+ * #action
113
+ */
114
+ setFeatureDensityStatsP(arg) {
115
+ self.featureDensityStatsP = arg;
116
+ },
117
+ /**
118
+ * #action
119
+ */
120
+ setFeatureDensityStats(featureDensityStats) {
121
+ self.featureDensityStats = featureDensityStats;
122
+ },
123
+ /**
124
+ * #action
125
+ */
126
+ clearFeatureDensityStats() {
127
+ self.featureDensityStatsP = undefined;
128
+ self.featureDensityStats = undefined;
129
+ },
130
+ }))
131
+ .views(self => ({
132
+ /**
133
+ * #getter
134
+ * region is too large if:
135
+ * - stats are ready
136
+ * - region is greater than 20kb (don't warn when zoomed in less than that)
137
+ * - and bytes is greater than max allowed bytes or density greater than max
138
+ * density
139
+ */
140
+ get regionTooLarge() {
141
+ const view = getContainingView(self);
142
+ if (!self.featureDensityStatsReady ||
143
+ view.dynamicBlocks.totalBp < 20000) {
144
+ return false;
145
+ }
146
+ return (self.currentBytesRequested > self.maxAllowableBytes ||
147
+ (self.userBpPerPxLimit
148
+ ? view.bpPerPx > self.userBpPerPxLimit
149
+ : self.currentFeatureScreenDensity > self.maxFeatureScreenDensity));
150
+ },
151
+ /**
152
+ * #getter
153
+ * only shows a message of bytes requested is defined, the feature density
154
+ * based stats don't produce any helpful message besides to zoom in
155
+ */
156
+ get regionTooLargeReason() {
157
+ const req = self.currentBytesRequested;
158
+ const max = self.maxAllowableBytes;
159
+ return req && req > max
160
+ ? `Requested too much data (${getDisplayStr(req)})`
161
+ : '';
162
+ },
163
+ }))
164
+ .views(self => ({
165
+ /**
166
+ * #method
167
+ */
168
+ regionCannotBeRenderedText(_region) {
169
+ return self.regionTooLarge ? 'Force load to see features' : '';
170
+ },
171
+ /**
172
+ * #method
173
+ * @param region -
174
+ * @returns falsy if the region is fine to try rendering. Otherwise,
175
+ * return a react node + string of text.
176
+ * string of text describes why it cannot be rendered
177
+ * react node allows user to force load at current setting
178
+ */
179
+ regionCannotBeRendered(_region) {
180
+ return self.regionTooLarge ? (React.createElement(TooLargeMessage, { model: self })) : null;
181
+ },
182
+ }));
183
+ }
184
+ //# sourceMappingURL=FeatureDensityMixin.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"FeatureDensityMixin.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/FeatureDensityMixin.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAGtD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAI7D,OAAO,eAAe,MAAM,+BAA+B,CAAA;AAC3D,OAAO,EAAE,aAAa,EAAE,yBAAyB,EAAE,MAAM,QAAQ,CAAA;AACjE,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AAIrE;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,mBAAmB;IACzC,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,gBAAgB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC3C;;WAEG;QAEH,iBAAiB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC7C,CAAC;SACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,oBAAoB,EAAE,SAEU;QAChC,mBAAmB,EAAE,SAA4C;QACjE,gBAAgB,EAAE,CAAC;KACpB,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,qBAAqB;;YACvB,OAAO,CAAA,MAAA,IAAI,CAAC,mBAAmB,0CAAE,KAAK,KAAI,CAAC,CAAA;QAC7C,CAAC;QAED;;WAEG;QACH,IAAI,2BAA2B;;YAC7B,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;YAC3C,OAAO,CAAC,CAAA,MAAA,IAAI,CAAC,mBAAmB,0CAAE,cAAc,KAAI,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAA;QACvE,CAAC;QAED;;WAEG;QACH,IAAI,uBAAuB;YACzB,mBAAmB;YACnB,OAAO,OAAO,CAAC,IAAI,EAAE,yBAAyB,CAAC,CAAA;QACjD,CAAC;QACD;;WAEG;QACH,IAAI,wBAAwB;YAC1B,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;YACpC,OAAO,CACL,IAAI,CAAC,gBAAgB,KAAK,IAAI,CAAC,OAAO;gBACtC,CAAC,CAAC,CAAC,IAAI,CAAC,mBAAmB,IAAI,CAAC,CAAC,IAAI,CAAC,gBAAgB,CAAC,CACxD,CAAA;QACH,CAAC;QAED;;WAEG;QACH,IAAI,iBAAiB;;YACnB,OAAO,CACL,IAAI,CAAC,iBAAiB;iBACtB,MAAA,IAAI,CAAC,mBAAmB,0CAAE,cAAc,CAAA;gBACxC,mBAAmB;gBAClB,OAAO,CAAC,IAAI,EAAE,gBAAgB,CAAY,CAC5C,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE,CAAC,0BAA0B,CAAC,IAAW,CAAC,CAAC,CACvD,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,mBAAmB,CAAC,CAAS;YAC3B,IAAI,CAAC,gBAAgB,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD;;WAEG;QACH,2BAA2B,CAAC,KAA2B;YACrD,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;YAC3C,IAAI,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,EAAE;gBAChB,IAAI,CAAC,iBAAiB,GAAG,KAAK,CAAC,KAAK,CAAA;aACrC;iBAAM;gBACL,IAAI,CAAC,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAA;aACrC;QACH,CAAC;QACD;;WAEG;QACH,KAAK,CAAC,sBAAsB;YAC1B,IAAI,CAAC,IAAI,CAAC,oBAAoB,EAAE;gBAC9B,IAAI,CAAC,oBAAoB,GAAG,yBAAyB,CACnD,IAAW,CACZ,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACV,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE;wBACjB,IAAI,CAAC,uBAAuB,CAAC,SAAS,CAAC,CAAA;qBACxC;oBACD,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;aACH;YACD,OAAO,IAAI,CAAC,oBAAoB,CAAA;QAClC,CAAC;QAED;;WAEG;QACH,uBAAuB,CAAC,GAAQ;YAC9B,IAAI,CAAC,oBAAoB,GAAG,GAAG,CAAA;QACjC,CAAC;QAED;;WAEG;QACH,sBAAsB,CAAC,mBAAyC;YAC9D,IAAI,CAAC,mBAAmB,GAAG,mBAAmB,CAAA;QAChD,CAAC;QACD;;WAEG;QACH,wBAAwB;YACtB,IAAI,CAAC,oBAAoB,GAAG,SAAS,CAAA;YACrC,IAAI,CAAC,mBAAmB,GAAG,SAAS,CAAA;QACtC,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;;;;;;WAOG;QACH,IAAI,cAAc;YAChB,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;YAC3C,IACE,CAAC,IAAI,CAAC,wBAAwB;gBAC9B,IAAI,CAAC,aAAa,CAAC,OAAO,GAAG,KAAM,EACnC;gBACA,OAAO,KAAK,CAAA;aACb;YACD,OAAO,CACL,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,iBAAiB;gBACnD,CAAC,IAAI,CAAC,gBAAgB;oBACpB,CAAC,CAAC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,gBAAgB;oBACtC,CAAC,CAAC,IAAI,CAAC,2BAA2B,GAAG,IAAI,CAAC,uBAAuB,CAAC,CACrE,CAAA;QACH,CAAC;QAED;;;;WAIG;QACH,IAAI,oBAAoB;YACtB,MAAM,GAAG,GAAG,IAAI,CAAC,qBAAqB,CAAA;YACtC,MAAM,GAAG,GAAG,IAAI,CAAC,iBAAiB,CAAA;YAElC,OAAO,GAAG,IAAI,GAAG,GAAG,GAAG;gBACrB,CAAC,CAAC,4BAA4B,aAAa,CAAC,GAAG,CAAC,GAAG;gBACnD,CAAC,CAAC,EAAE,CAAA;QACR,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,0BAA0B,CAAC,OAAe;YACxC,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,4BAA4B,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,CAAC;QAED;;;;;;;WAOG;QACH,sBAAsB,CAAC,OAAe;YACpC,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAC3B,oBAAC,eAAe,IAAC,KAAK,EAAE,IAAW,GAAI,CACxC,CAAC,CAAC,CAAC,IAAI,CAAA;QACV,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
@@ -0,0 +1,30 @@
1
+ /**
2
+ * #stateModel TrackHeightMixin
3
+ * #category display
4
+ */
5
+ export default function TrackHeightMixin(): import("mobx-state-tree").IModelType<{
6
+ /**
7
+ * #property
8
+ */
9
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
10
+ }, {
11
+ /**
12
+ * #property
13
+ */
14
+ scrollTop: number;
15
+ } & {
16
+ readonly height: number;
17
+ } & {
18
+ /**
19
+ * #action
20
+ */
21
+ setScrollTop(scrollTop: number): void;
22
+ /**
23
+ * #action
24
+ */
25
+ setHeight(displayHeight: number): number;
26
+ /**
27
+ * #action
28
+ */
29
+ resizeHeight(distance: number): number;
30
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
@@ -0,0 +1,53 @@
1
+ import { getConf } from '@jbrowse/core/configuration';
2
+ import { types } from 'mobx-state-tree';
3
+ const minDisplayHeight = 20;
4
+ /**
5
+ * #stateModel TrackHeightMixin
6
+ * #category display
7
+ */
8
+ export default function TrackHeightMixin() {
9
+ return types
10
+ .model({
11
+ /**
12
+ * #property
13
+ */
14
+ heightPreConfig: types.maybe(types.refinement('displayHeight', types.number, n => n >= minDisplayHeight)),
15
+ })
16
+ .volatile(() => ({
17
+ /**
18
+ * #property
19
+ */
20
+ scrollTop: 0,
21
+ }))
22
+ .views(self => ({
23
+ get height() {
24
+ var _a;
25
+ // @ts-expect-error
26
+ return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : getConf(self, 'height');
27
+ },
28
+ }))
29
+ .actions(self => ({
30
+ /**
31
+ * #action
32
+ */
33
+ setScrollTop(scrollTop) {
34
+ self.scrollTop = scrollTop;
35
+ },
36
+ /**
37
+ * #action
38
+ */
39
+ setHeight(displayHeight) {
40
+ self.heightPreConfig = Math.max(displayHeight, minDisplayHeight);
41
+ return self.height;
42
+ },
43
+ /**
44
+ * #action
45
+ */
46
+ resizeHeight(distance) {
47
+ const oldHeight = self.height;
48
+ const newHeight = this.setHeight(self.height + distance);
49
+ return newHeight - oldHeight;
50
+ },
51
+ }));
52
+ }
53
+ //# sourceMappingURL=TrackHeightMixin.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"TrackHeightMixin.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/TrackHeightMixin.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,gBAAgB;IACtC,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,eAAe,EAAE,KAAK,CAAC,KAAK,CAC1B,KAAK,CAAC,UAAU,CACd,eAAe,EACf,KAAK,CAAC,MAAM,EACZ,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,gBAAgB,CAC3B,CACF;KACF,CAAC;SACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf;;WAEG;QACH,SAAS,EAAE,CAAC;KACb,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,IAAI,MAAM;;YACR,mBAAmB;YACnB,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAK,OAAO,CAAC,IAAI,EAAE,QAAQ,CAAY,CAAA;QACpE,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,SAAiB;YAC5B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,SAAS,CAAC,aAAqB;YAC7B,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,aAAa,EAAE,gBAAgB,CAAC,CAAA;YAChE,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,QAAgB;YAC3B,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAA;YAC7B,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;YACxD,OAAO,SAAS,GAAG,SAAS,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
@@ -0,0 +1,2 @@
1
+ import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
2
+ export default function autorunFeatureDensityStats(self: BaseLinearDisplayModel): Promise<void>;
@@ -0,0 +1,39 @@
1
+ import { getContainingView, isAbortException } from '@jbrowse/core/util';
2
+ import { isAlive } from 'mobx-state-tree';
3
+ // stats estimation autorun calls getFeatureDensityStats against the data
4
+ // adapter which by default uses featureDensity, but can also respond with a
5
+ // byte size estimate and fetch size limit (data adapter can define what is too
6
+ // much data)
7
+ export default async function autorunFeatureDensityStats(self) {
8
+ var _a;
9
+ try {
10
+ const view = getContainingView(self);
11
+ // extra check for contentBlocks.length
12
+ // https://github.com/GMOD/jbrowse-components/issues/2694
13
+ if (!view.initialized ||
14
+ !view.staticBlocks.contentBlocks.length ||
15
+ view.bpPerPx === self.currStatsBpPerPx ||
16
+ self.error) {
17
+ return;
18
+ }
19
+ // don't re-estimate featureDensity even if zoom level changes,
20
+ // jbrowse1-style assume it's sort of representative
21
+ if (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
22
+ self.setCurrStatsBpPerPx(view.bpPerPx);
23
+ return;
24
+ }
25
+ self.clearFeatureDensityStats();
26
+ self.setCurrStatsBpPerPx(view.bpPerPx);
27
+ const stats = await self.getFeatureDensityStats();
28
+ if (isAlive(self)) {
29
+ self.setFeatureDensityStats(stats);
30
+ }
31
+ }
32
+ catch (e) {
33
+ if (!isAbortException(e) && isAlive(self)) {
34
+ console.error(e);
35
+ self.setError(e);
36
+ }
37
+ }
38
+ }
39
+ //# sourceMappingURL=autorunFeatureDensityStats.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"autorunFeatureDensityStats.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/autorunFeatureDensityStats.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAExE,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAGzC,yEAAyE;AACzE,4EAA4E;AAC5E,+EAA+E;AAC/E,aAAa;AACb,MAAM,CAAC,OAAO,CAAC,KAAK,UAAU,0BAA0B,CACtD,IAA4B;;IAE5B,IAAI;QACF,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;QAE7D,uCAAuC;QACvC,yDAAyD;QACzD,IACE,CAAC,IAAI,CAAC,WAAW;YACjB,CAAC,IAAI,CAAC,YAAY,CAAC,aAAa,CAAC,MAAM;YACvC,IAAI,CAAC,OAAO,KAAK,IAAI,CAAC,gBAAgB;YACtC,IAAI,CAAC,KAAK,EACV;YACA,OAAM;SACP;QAED,+DAA+D;QAC/D,oDAAoD;QACpD,IAAI,CAAA,MAAA,IAAI,CAAC,mBAAmB,0CAAE,cAAc,MAAK,SAAS,EAAE;YAC1D,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACtC,OAAM;SACP;QAED,IAAI,CAAC,wBAAwB,EAAE,CAAA;QAC/B,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,sBAAsB,EAAE,CAAA;QACjD,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE;YACjB,IAAI,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAA;SACnC;KACF;IAAC,OAAO,CAAC,EAAE;QACV,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE;YACzC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;SACjB;KACF;AACH,CAAC"}
@@ -1,6 +1,7 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
2
  /**
3
3
  * #config BaseLinearDisplay
4
+ * #category display
4
5
  * `BaseLinearDisplay` is a "base" config that is extended by classes like
5
6
  * `LinearBasicDisplay` (used for feature tracks, etc) and `LinearBareDisplay`
6
7
  * (more stripped down than even the basic display, not commonly used)
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,6BAA6B,GAAG,mBAAmB,CACvD,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,GAAG;QACjB,WAAW,EAAE,8BAA8B;KAC5C;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uDAAuD;QACpE,YAAY,EAAE,0BAA0B;QAExC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AAED,eAAe,6BAA6B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;;GAMG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,6BAA6B,GAAG,mBAAmB,CACvD,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,GAAG;QACjB,WAAW,EAAE,8BAA8B;KAC5C;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uDAAuD;QACpE,YAAY,EAAE,0BAA0B;QAExC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AAED,eAAe,6BAA6B,CAAA"}
@@ -0,0 +1,8 @@
1
+ import React from 'react';
2
+ import { ThemeOptions } from '@mui/material';
3
+ import { ExportSvgOptions } from '../../LinearGenomeView';
4
+ import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
5
+ export default function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
6
+ overrideHeight: number;
7
+ theme: ThemeOptions;
8
+ }): Promise<React.JSX.Element>;
@@ -0,0 +1,54 @@
1
+ import React from 'react';
2
+ import { getContainingView, getViewParams, ReactRendering, } from '@jbrowse/core/util';
3
+ import BlockState, { renderBlockData } from './serverSideRenderedBlock';
4
+ import { getId } from './util';
5
+ export default async function renderBaseLinearDisplaySvg(self, opts) {
6
+ const { height, id } = self;
7
+ const { overrideHeight } = opts;
8
+ const view = getContainingView(self);
9
+ const { offsetPx: viewOffsetPx, roundedDynamicBlocks, width } = view;
10
+ const renderings = await Promise.all(roundedDynamicBlocks.map(async (block) => {
11
+ const blockState = BlockState.create({
12
+ key: block.key,
13
+ region: block,
14
+ });
15
+ // regionCannotBeRendered can return jsx so look for plaintext
16
+ // version, or just get the default if none available
17
+ const cannotBeRenderedReason = self.regionCannotBeRenderedText(block) ||
18
+ self.regionCannotBeRendered(block);
19
+ if (cannotBeRenderedReason) {
20
+ return [
21
+ block,
22
+ {
23
+ reactElement: (React.createElement(React.Fragment, null,
24
+ React.createElement("rect", { x: 0, y: 0, width: width, height: 20, fill: "#aaa" }),
25
+ React.createElement("text", { x: 0, y: 15 }, cannotBeRenderedReason))),
26
+ },
27
+ ];
28
+ }
29
+ const { rpcManager, renderArgs, renderProps, rendererType } = renderBlockData(blockState, self);
30
+ return [
31
+ block,
32
+ await rendererType.renderInClient(rpcManager, {
33
+ ...renderArgs,
34
+ ...renderProps,
35
+ viewParams: getViewParams(self, true),
36
+ exportSVG: opts,
37
+ theme: opts.theme || renderProps.theme,
38
+ }),
39
+ ];
40
+ }));
41
+ return (React.createElement(React.Fragment, null, renderings.map(([block, rendering], index) => {
42
+ const { offsetPx, widthPx } = block;
43
+ const offset = offsetPx - viewOffsetPx;
44
+ const clipid = getId(id, index);
45
+ return (React.createElement(React.Fragment, { key: `frag-${index}` },
46
+ React.createElement("defs", null,
47
+ React.createElement("clipPath", { id: clipid },
48
+ React.createElement("rect", { x: 0, y: 0, width: widthPx, height: overrideHeight || height }))),
49
+ React.createElement("g", { transform: `translate(${offset} 0)` },
50
+ React.createElement("g", { clipPath: `url(#${clipid})` },
51
+ React.createElement(ReactRendering, { rendering: rendering })))));
52
+ })));
53
+ }
54
+ //# sourceMappingURL=renderSvg.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EACL,iBAAiB,EACjB,aAAa,EACb,cAAc,GACf,MAAM,oBAAoB,CAAA;AAI3B,OAAO,UAAU,EAAE,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AACvE,OAAO,EAAE,KAAK,EAAE,MAAM,QAAQ,CAAA;AAI9B,MAAM,CAAC,OAAO,CAAC,KAAK,UAAU,0BAA0B,CACtD,IAA4B,EAC5B,IAGC;IAED,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC7D,MAAM,EAAE,QAAQ,EAAE,YAAY,EAAE,oBAAoB,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;IACpE,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAClC,oBAAoB,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACrC,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,MAAM,EAAE,KAAK;SACd,CAAC,CAAA;QAEF,8DAA8D;QAC9D,qDAAqD;QACrD,MAAM,sBAAsB,GAC1B,IAAI,CAAC,0BAA0B,CAAC,KAAK,CAAC;YACtC,IAAI,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAA;QAEpC,IAAI,sBAAsB,EAAE;YAC1B,OAAO;gBACL,KAAK;gBACL;oBACE,YAAY,EAAE,CACZ;wBACE,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAC,MAAM,GAAG;wBAC1D,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,IACd,sBAAsB,CAClB,CACN,CACJ;iBACF;aACO,CAAA;SACX;QAED,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,YAAY,EAAE,GACzD,eAAe,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;QAEnC,OAAO;YACL,KAAK;YACL,MAAM,YAAY,CAAC,cAAc,CAAC,UAAU,EAAE;gBAC5C,GAAG,UAAU;gBACb,GAAG,WAAW;gBACd,UAAU,EAAE,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC;gBACrC,SAAS,EAAE,IAAI;gBACf,KAAK,EAAE,IAAI,CAAC,KAAK,IAAI,WAAW,CAAC,KAAK;aACvC,CAAC;SACM,CAAA;IACZ,CAAC,CAAC,CACH,CAAA;IAED,OAAO,CACL,0CACG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,SAAS,CAAC,EAAE,KAAK,EAAE,EAAE;QAC5C,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACnC,MAAM,MAAM,GAAG,QAAQ,GAAG,YAAY,CAAA;QACtC,MAAM,MAAM,GAAG,KAAK,CAAC,EAAE,EAAE,KAAK,CAAC,CAAA;QAE/B,OAAO,CACL,oBAAC,KAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,QAAQ,KAAK,EAAE;YAClC;gBACE,kCAAU,EAAE,EAAE,MAAM;oBAClB,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,OAAO,EACd,MAAM,EAAE,cAAc,IAAI,MAAM,GAChC,CACO,CACN;YACP,2BAAG,SAAS,EAAE,aAAa,MAAM,KAAK;gBACpC,2BAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;oBAC5B,oBAAC,cAAc,IAAC,SAAS,EAAE,SAAS,GAAI,CACtC,CACF,CACW,CAClB,CAAA;IACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC"}
@@ -128,22 +128,26 @@ const blockState = types
128
128
  getParent(self, 2).reload();
129
129
  },
130
130
  beforeDestroy() {
131
- if (renderInProgress && !renderInProgress.signal.aborted) {
132
- renderInProgress.abort();
133
- }
134
- const display = getContainingDisplay(self);
135
- const { rpcManager } = getSession(self);
136
- const { rendererType } = display;
137
- const { renderArgs } = renderBlockData(cast(self));
138
- // renderArgs can be undefined if an error occurred in this block
139
- if (renderArgs) {
140
- rendererType
141
- .freeResourcesInClient(rpcManager, JSON.parse(JSON.stringify(renderArgs)))
142
- .catch((e) => {
143
- // just console.error if it's something while it's being destroyed
144
- console.warn('Error while destroying block', e);
145
- });
146
- }
131
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
132
+ ;
133
+ (async () => {
134
+ try {
135
+ if (renderInProgress && !renderInProgress.signal.aborted) {
136
+ renderInProgress.abort();
137
+ }
138
+ const display = getContainingDisplay(self);
139
+ const { rpcManager } = getSession(self);
140
+ const { rendererType } = display;
141
+ const { renderArgs } = renderBlockData(cast(self));
142
+ // renderArgs can be undefined if an error occurred in this block
143
+ if (renderArgs) {
144
+ await rendererType.freeResourcesInClient(rpcManager, JSON.parse(JSON.stringify(renderArgs)));
145
+ }
146
+ }
147
+ catch (e) {
148
+ console.error('Error while destroying block', e);
149
+ }
150
+ })();
147
151
  },
148
152
  };
149
153
  });
@@ -1 +1 @@
1
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@@ -2,6 +2,7 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
2
  import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
3
3
  /**
4
4
  * #config BasicTrack
5
+ * #category track
5
6
  * synonym for FeatureTrack
6
7
  */
7
8
  function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BasicTrack/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,mBAAmB,CACjB,YAAY,EACZ,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;IACvD,kBAAkB,EAAE,SAAS;CAC9B,CACF,CAAA;AACH,eAAe,YAAY,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BasicTrack/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,mBAAmB,CACjB,YAAY,EACZ,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;IACvD,kBAAkB,EAAE,SAAS;CAC9B,CACF,CAAA;AACH,eAAe,YAAY,CAAA"}
@@ -7,9 +7,7 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
7
7
  };
8
8
  assemblyNames: {
9
9
  description: string;
10
- type: string; /**
11
- * #baseConfiguration
12
- */
10
+ type: string;
13
11
  defaultValue: string[];
14
12
  };
15
13
  description: {
@@ -2,6 +2,7 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
2
  import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
3
3
  /**
4
4
  * #config FeatureTrack
5
+ * #category track
5
6
  * used for basic gene and feature tracks, generally used with LinearBasicDisplay
6
7
  */
7
8
  function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FeatureTrack/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,mBAAmB,CACjB,cAAc,EACd,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;IACvD;;OAEG;IACH,kBAAkB,EAAE,SAAS;CAC9B,CACF,CAAA;AAEH,eAAe,YAAY,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FeatureTrack/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,mBAAmB,CACjB,cAAc,EACd,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;IACvD;;OAEG;IACH,kBAAkB,EAAE,SAAS;CAC9B,CACF,CAAA;AAEH,eAAe,YAAY,CAAA"}
@@ -1,6 +1,7 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
2
  /**
3
3
  * #config LinearBareDisplay
4
+ * #category display
4
5
  */
5
6
  declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
6
7
  /**
@@ -2,6 +2,7 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
2
  import { baseLinearDisplayConfigSchema } from '../BaseLinearDisplay';
3
3
  /**
4
4
  * #config LinearBareDisplay
5
+ * #category display
5
6
  */
6
7
  function configSchemaFactory(pluginManager) {
7
8
  return ConfigurationSchema('LinearBareDisplay', {
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,sBAAsB,CAAA;AAEpE;;GAEG;AACH,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,mBAAmB,EACnB;QACE;;WAEG;QACH,QAAQ,EAAE,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC;KAC9D,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,OAAO,EAAE,mBAAmB,EAAE,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,sBAAsB,CAAA;AAEpE;;;GAGG;AACH,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,mBAAmB,EACnB;QACE;;WAEG;QACH,QAAQ,EAAE,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC;KAC9D,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,OAAO,EAAE,mBAAmB,EAAE,CAAA"}