@jbrowse/plugin-wiggle 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 (407) hide show
  1. package/esm/BigWigAdapter/BigWigAdapter.d.ts +14 -1
  2. package/esm/BigWigAdapter/BigWigAdapter.js +118 -22
  3. package/esm/BigWigAdapter/configSchema.d.ts +2 -2
  4. package/esm/BigWigAdapter/configSchema.js +1 -1
  5. package/esm/BigWigAdapter/index.js +2 -2
  6. package/esm/CreateMultiWiggleExtension/ConfirmDialog.js +1 -1
  7. package/esm/CreateMultiWiggleExtension/index.js +2 -2
  8. package/esm/DensityRenderer/DensityRenderer.d.ts +5 -6
  9. package/esm/DensityRenderer/DensityRenderer.js +6 -5
  10. package/esm/DensityRenderer/configSchema.d.ts +3 -3
  11. package/esm/DensityRenderer/configSchema.js +1 -1
  12. package/esm/DensityRenderer/index.js +11 -9
  13. package/esm/DensityRenderer/makeImageData.d.ts +3 -0
  14. package/esm/DensityRenderer/makeImageData.js +13 -0
  15. package/esm/DensityRenderer/renderDensity.d.ts +3 -0
  16. package/esm/DensityRenderer/renderDensity.js +18 -0
  17. package/esm/LinePlotRenderer/LinePlotRenderer.d.ts +5 -7
  18. package/esm/LinePlotRenderer/LinePlotRenderer.js +6 -15
  19. package/esm/LinePlotRenderer/configSchema.d.ts +4 -4
  20. package/esm/LinePlotRenderer/configSchema.js +1 -1
  21. package/esm/LinePlotRenderer/index.js +4 -4
  22. package/esm/LinePlotRenderer/makeImageData.d.ts +3 -0
  23. package/esm/LinePlotRenderer/makeImageData.js +13 -0
  24. package/esm/LinePlotRenderer/renderLinePlot.d.ts +3 -0
  25. package/esm/LinePlotRenderer/renderLinePlot.js +23 -0
  26. package/esm/LinearWiggleDisplay/components/Tooltip.d.ts +2 -2
  27. package/esm/LinearWiggleDisplay/components/Tooltip.js +10 -6
  28. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +1 -1
  29. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.js +2 -2
  30. package/esm/LinearWiggleDisplay/configSchema.d.ts +9 -9
  31. package/esm/LinearWiggleDisplay/configSchema.js +2 -2
  32. package/esm/LinearWiggleDisplay/index.d.ts +3 -3
  33. package/esm/LinearWiggleDisplay/index.js +6 -6
  34. package/esm/LinearWiggleDisplay/model.d.ts +1130 -92
  35. package/esm/LinearWiggleDisplay/model.js +58 -18
  36. package/esm/LinearWiggleDisplay/renderSvg.d.ts +1 -1
  37. package/esm/LinearWiggleDisplay/renderSvg.js +3 -2
  38. package/esm/MultiDensityRenderer/MultiDensityRenderer.d.ts +5 -7
  39. package/esm/MultiDensityRenderer/MultiDensityRenderer.js +6 -24
  40. package/esm/MultiDensityRenderer/configSchema.d.ts +3 -3
  41. package/esm/MultiDensityRenderer/configSchema.js +1 -1
  42. package/esm/MultiDensityRenderer/index.js +4 -4
  43. package/esm/MultiDensityRenderer/makeImageData.d.ts +3 -0
  44. package/esm/MultiDensityRenderer/makeImageData.js +7 -0
  45. package/esm/MultiDensityRenderer/renderMultiDensity.d.ts +3 -0
  46. package/esm/MultiDensityRenderer/renderMultiDensity.js +37 -0
  47. package/esm/MultiLineRenderer/MultiLineRenderer.d.ts +5 -7
  48. package/esm/MultiLineRenderer/MultiLineRenderer.js +6 -17
  49. package/esm/MultiLineRenderer/configSchema.d.ts +5 -5
  50. package/esm/MultiLineRenderer/configSchema.js +2 -2
  51. package/esm/MultiLineRenderer/index.js +4 -4
  52. package/esm/MultiLineRenderer/makeImageData.d.ts +3 -0
  53. package/esm/MultiLineRenderer/makeImageData.js +7 -0
  54. package/esm/MultiLineRenderer/renderMultiLine.d.ts +3 -0
  55. package/esm/MultiLineRenderer/renderMultiLine.js +34 -0
  56. package/esm/MultiLinearWiggleDisplay/components/ColorLegend.d.ts +2 -2
  57. package/esm/MultiLinearWiggleDisplay/components/ColorLegend.js +11 -5
  58. package/esm/MultiLinearWiggleDisplay/components/FullHeightScaleBar.d.ts +1 -1
  59. package/esm/MultiLinearWiggleDisplay/components/FullHeightScaleBar.js +4 -4
  60. package/esm/MultiLinearWiggleDisplay/components/IndividualScaleBars.d.ts +1 -1
  61. package/esm/MultiLinearWiggleDisplay/components/IndividualScaleBars.js +5 -5
  62. package/esm/MultiLinearWiggleDisplay/components/LegendItem.d.ts +3 -3
  63. package/esm/MultiLinearWiggleDisplay/components/LegendItem.js +2 -4
  64. package/esm/MultiLinearWiggleDisplay/components/LegendItemText.d.ts +12 -0
  65. package/esm/MultiLinearWiggleDisplay/components/LegendItemText.js +11 -0
  66. package/esm/MultiLinearWiggleDisplay/components/RectBg.d.ts +1 -1
  67. package/esm/MultiLinearWiggleDisplay/components/RectBg.js +4 -3
  68. package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.d.ts +2 -2
  69. package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.js +3 -3
  70. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +1 -1
  71. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +4 -34
  72. package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.d.ts +1 -1
  73. package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js +3 -3
  74. package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts +2 -4
  75. package/esm/MultiLinearWiggleDisplay/components/Tooltip.js +15 -12
  76. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.d.ts +1 -1
  77. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.js +3 -3
  78. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.d.ts +1 -1
  79. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.js +13 -6
  80. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.d.ts +1 -1
  81. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js +24 -21
  82. package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts +2 -1
  83. package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +1 -1
  84. package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +2 -2
  85. package/esm/MultiLinearWiggleDisplay/components/YScaleBars.d.ts +2 -2
  86. package/esm/MultiLinearWiggleDisplay/components/YScaleBars.js +5 -16
  87. package/esm/MultiLinearWiggleDisplay/components/YScaleBarsWrapper.d.ts +7 -0
  88. package/esm/MultiLinearWiggleDisplay/components/YScaleBarsWrapper.js +15 -0
  89. package/esm/MultiLinearWiggleDisplay/components/types.d.ts +10 -0
  90. package/esm/MultiLinearWiggleDisplay/components/types.js +1 -0
  91. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialog.d.ts +31 -0
  92. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialog.js +45 -0
  93. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogBulkEditPanel.d.ts +10 -0
  94. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogBulkEditPanel.js +81 -0
  95. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogHelpfulTips.d.ts +1 -0
  96. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogHelpfulTips.js +4 -0
  97. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogRowPalettizer.d.ts +10 -0
  98. package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogRowPalettizer.js +39 -0
  99. package/esm/MultiLinearWiggleDisplay/components/util.d.ts +5 -9
  100. package/esm/MultiLinearWiggleDisplay/configSchema.d.ts +9 -9
  101. package/esm/MultiLinearWiggleDisplay/configSchema.js +2 -2
  102. package/esm/MultiLinearWiggleDisplay/index.js +3 -3
  103. package/esm/MultiLinearWiggleDisplay/model.d.ts +3628 -93
  104. package/esm/MultiLinearWiggleDisplay/model.js +80 -50
  105. package/esm/MultiLinearWiggleDisplay/renderSvg.d.ts +1 -1
  106. package/esm/MultiLinearWiggleDisplay/renderSvg.js +3 -2
  107. package/esm/MultiLinearWiggleDisplay/types.d.ts +1 -0
  108. package/esm/MultiLinearWiggleDisplay/util.d.ts +0 -1
  109. package/esm/MultiLinearWiggleDisplay/util.js +1 -7
  110. package/esm/MultiQuantitativeTrack/configSchema.d.ts +16 -11
  111. package/esm/MultiQuantitativeTrack/index.js +13 -2
  112. package/esm/MultiRowLineRenderer/MultiRowLineRenderer.d.ts +5 -7
  113. package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js +6 -29
  114. package/esm/MultiRowLineRenderer/configSchema.d.ts +5 -5
  115. package/esm/MultiRowLineRenderer/configSchema.js +2 -2
  116. package/esm/MultiRowLineRenderer/index.js +4 -4
  117. package/esm/MultiRowLineRenderer/makeImageData.d.ts +3 -0
  118. package/esm/MultiRowLineRenderer/makeImageData.js +7 -0
  119. package/esm/MultiRowLineRenderer/renderMultiRowLine.d.ts +3 -0
  120. package/esm/MultiRowLineRenderer/renderMultiRowLine.js +44 -0
  121. package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.d.ts +5 -7
  122. package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +6 -29
  123. package/esm/MultiRowXYPlotRenderer/configSchema.d.ts +5 -5
  124. package/esm/MultiRowXYPlotRenderer/configSchema.js +2 -2
  125. package/esm/MultiRowXYPlotRenderer/index.js +4 -4
  126. package/esm/MultiRowXYPlotRenderer/makeImageData.d.ts +3 -0
  127. package/esm/MultiRowXYPlotRenderer/makeImageData.js +7 -0
  128. package/esm/MultiRowXYPlotRenderer/renderMultiRowXYPlot.d.ts +3 -0
  129. package/esm/MultiRowXYPlotRenderer/renderMultiRowXYPlot.js +42 -0
  130. package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +7 -1
  131. package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js +81 -26
  132. package/esm/MultiWiggleAdapter/configSchema.d.ts +2 -2
  133. package/esm/MultiWiggleAdapter/index.js +2 -2
  134. package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts +1 -1
  135. package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +4 -5
  136. package/esm/MultiWiggleAddTrackWorkflow/index.js +2 -2
  137. package/esm/MultiWiggleRendering.d.ts +7 -7
  138. package/esm/MultiWiggleRendering.js +9 -7
  139. package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts +5 -7
  140. package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js +6 -20
  141. package/esm/MultiXYPlotRenderer/configSchema.d.ts +5 -5
  142. package/esm/MultiXYPlotRenderer/configSchema.js +2 -2
  143. package/esm/MultiXYPlotRenderer/index.js +4 -4
  144. package/esm/MultiXYPlotRenderer/makeImageData.d.ts +3 -0
  145. package/esm/MultiXYPlotRenderer/makeImageData.js +7 -0
  146. package/esm/MultiXYPlotRenderer/renderMultiXYPlot.d.ts +3 -0
  147. package/esm/MultiXYPlotRenderer/renderMultiXYPlot.js +35 -0
  148. package/esm/QuantitativeTrack/configSchema.d.ts +16 -11
  149. package/esm/QuantitativeTrack/index.js +13 -2
  150. package/esm/SVGErrorBox.d.ts +5 -0
  151. package/esm/SVGErrorBox.js +4 -0
  152. package/esm/Tooltip.d.ts +1 -3
  153. package/esm/Tooltip.js +7 -7
  154. package/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.d.ts +2 -10
  155. package/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.js +3 -15
  156. package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts +1 -1
  157. package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.js +2 -5
  158. package/esm/WiggleRPC/MultiWiggleGetSources.js +1 -4
  159. package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +1 -4
  160. package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +10 -0
  161. package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +26 -5
  162. package/esm/WiggleRPC/executeClusterScoreMatrix.d.ts +6 -0
  163. package/esm/WiggleRPC/executeClusterScoreMatrix.js +15 -0
  164. package/esm/WiggleRPC/getScoreMatrix.d.ts +1 -1
  165. package/esm/WiggleRPC/getScoreMatrix.js +9 -6
  166. package/esm/WiggleRPC/rpcMethods.d.ts +5 -5
  167. package/esm/WiggleRPC/rpcMethods.js +5 -5
  168. package/esm/WiggleRPC/types.d.ts +1 -1
  169. package/esm/WiggleRendering.d.ts +2 -3
  170. package/esm/WiggleRendering.js +16 -3
  171. package/esm/XYPlotRenderer/XYPlotRenderer.d.ts +5 -6
  172. package/esm/XYPlotRenderer/XYPlotRenderer.js +6 -20
  173. package/esm/XYPlotRenderer/configSchema.d.ts +5 -5
  174. package/esm/XYPlotRenderer/configSchema.js +2 -2
  175. package/esm/XYPlotRenderer/index.d.ts +3 -3
  176. package/esm/XYPlotRenderer/index.js +14 -12
  177. package/esm/XYPlotRenderer/makeImageData.d.ts +3 -0
  178. package/esm/XYPlotRenderer/makeImageData.js +13 -0
  179. package/esm/XYPlotRenderer/renderXYPlot.d.ts +3 -0
  180. package/esm/XYPlotRenderer/renderXYPlot.js +23 -0
  181. package/esm/configSchema.d.ts +3 -3
  182. package/esm/configSchema.js +1 -1
  183. package/esm/drawDensity.d.ts +4 -2
  184. package/esm/drawDensity.js +25 -15
  185. package/esm/drawLine.d.ts +5 -3
  186. package/esm/drawLine.js +118 -41
  187. package/esm/drawXY.d.ts +4 -2
  188. package/esm/drawXY.js +75 -36
  189. package/esm/getMultiWiggleSourcesAutorun.d.ts +4 -2
  190. package/esm/getMultiWiggleSourcesAutorun.js +7 -2
  191. package/esm/getQuantitativeStats.d.ts +4 -2
  192. package/esm/getQuantitativeStats.js +18 -7
  193. package/esm/getQuantitativeStatsAutorun.d.ts +3 -2
  194. package/esm/getQuantitativeStatsAutorun.js +3 -3
  195. package/esm/index.d.ts +15 -19
  196. package/esm/index.js +31 -37
  197. package/esm/multiRendererHelper.d.ts +7 -0
  198. package/esm/multiRendererHelper.js +12 -0
  199. package/esm/saveTrackFormats/bedGraph.d.ts +4 -0
  200. package/esm/saveTrackFormats/bedGraph.js +11 -0
  201. package/esm/shared/SharedWiggleConfigSchema.d.ts +5 -5
  202. package/esm/shared/SharedWiggleConfigSchema.js +1 -1
  203. package/esm/shared/SharedWiggleMixin.d.ts +1083 -120
  204. package/esm/shared/SharedWiggleMixin.js +48 -26
  205. package/esm/shared/YScaleBar.d.ts +1 -1
  206. package/esm/shared/YScaleBar.js +16 -4
  207. package/esm/shared/axisPropsFromTickScale.d.ts +7 -0
  208. package/esm/shared/axisPropsFromTickScale.js +12 -0
  209. package/esm/svgExportUtil.d.ts +9 -0
  210. package/esm/svgExportUtil.js +6 -0
  211. package/esm/types.d.ts +24 -0
  212. package/esm/types.js +1 -0
  213. package/esm/util.d.ts +35 -1
  214. package/esm/util.js +61 -2
  215. package/package.json +35 -38
  216. package/dist/BigWigAdapter/BigWigAdapter.d.ts +0 -25
  217. package/dist/BigWigAdapter/BigWigAdapter.js +0 -81
  218. package/dist/BigWigAdapter/configSchema.d.ts +0 -20
  219. package/dist/BigWigAdapter/configSchema.js +0 -37
  220. package/dist/BigWigAdapter/index.d.ts +0 -2
  221. package/dist/BigWigAdapter/index.js +0 -54
  222. package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts +0 -8
  223. package/dist/CreateMultiWiggleExtension/ConfirmDialog.js +0 -26
  224. package/dist/CreateMultiWiggleExtension/index.d.ts +0 -2
  225. package/dist/CreateMultiWiggleExtension/index.js +0 -95
  226. package/dist/DensityRenderer/DensityRenderer.d.ts +0 -7
  227. package/dist/DensityRenderer/DensityRenderer.js +0 -46
  228. package/dist/DensityRenderer/configSchema.d.ts +0 -37
  229. package/dist/DensityRenderer/configSchema.js +0 -13
  230. package/dist/DensityRenderer/index.d.ts +0 -2
  231. package/dist/DensityRenderer/index.js +0 -17
  232. package/dist/GuessAdapter/index.d.ts +0 -2
  233. package/dist/GuessAdapter/index.js +0 -25
  234. package/dist/LinePlotRenderer/LinePlotRenderer.d.ts +0 -8
  235. package/dist/LinePlotRenderer/LinePlotRenderer.js +0 -56
  236. package/dist/LinePlotRenderer/configSchema.d.ts +0 -43
  237. package/dist/LinePlotRenderer/configSchema.js +0 -19
  238. package/dist/LinePlotRenderer/index.d.ts +0 -2
  239. package/dist/LinePlotRenderer/index.js +0 -17
  240. package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +0 -12
  241. package/dist/LinearWiggleDisplay/components/SetColorDialog.js +0 -31
  242. package/dist/LinearWiggleDisplay/components/Tooltip.d.ts +0 -15
  243. package/dist/LinearWiggleDisplay/components/Tooltip.js +0 -32
  244. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -5
  245. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js +0 -28
  246. package/dist/LinearWiggleDisplay/configSchema.d.ts +0 -78
  247. package/dist/LinearWiggleDisplay/configSchema.js +0 -29
  248. package/dist/LinearWiggleDisplay/index.d.ts +0 -5
  249. package/dist/LinearWiggleDisplay/index.js +0 -65
  250. package/dist/LinearWiggleDisplay/model.d.ts +0 -419
  251. package/dist/LinearWiggleDisplay/model.js +0 -262
  252. package/dist/LinearWiggleDisplay/renderSvg.d.ts +0 -3
  253. package/dist/LinearWiggleDisplay/renderSvg.js +0 -16
  254. package/dist/MultiDensityRenderer/MultiDensityRenderer.d.ts +0 -8
  255. package/dist/MultiDensityRenderer/MultiDensityRenderer.js +0 -65
  256. package/dist/MultiDensityRenderer/configSchema.d.ts +0 -37
  257. package/dist/MultiDensityRenderer/configSchema.js +0 -13
  258. package/dist/MultiDensityRenderer/index.d.ts +0 -2
  259. package/dist/MultiDensityRenderer/index.js +0 -17
  260. package/dist/MultiLineRenderer/MultiLineRenderer.d.ts +0 -8
  261. package/dist/MultiLineRenderer/MultiLineRenderer.js +0 -58
  262. package/dist/MultiLineRenderer/configSchema.d.ts +0 -49
  263. package/dist/MultiLineRenderer/configSchema.js +0 -26
  264. package/dist/MultiLineRenderer/index.d.ts +0 -2
  265. package/dist/MultiLineRenderer/index.js +0 -17
  266. package/dist/MultiLinearWiggleDisplay/components/ColorLegend.d.ts +0 -7
  267. package/dist/MultiLinearWiggleDisplay/components/ColorLegend.js +0 -18
  268. package/dist/MultiLinearWiggleDisplay/components/FullHeightScaleBar.d.ts +0 -7
  269. package/dist/MultiLinearWiggleDisplay/components/FullHeightScaleBar.js +0 -17
  270. package/dist/MultiLinearWiggleDisplay/components/IndividualScaleBars.d.ts +0 -7
  271. package/dist/MultiLinearWiggleDisplay/components/IndividualScaleBars.js +0 -15
  272. package/dist/MultiLinearWiggleDisplay/components/LegendItem.d.ts +0 -11
  273. package/dist/MultiLinearWiggleDisplay/components/LegendItem.js +0 -19
  274. package/dist/MultiLinearWiggleDisplay/components/RectBg.d.ts +0 -8
  275. package/dist/MultiLinearWiggleDisplay/components/RectBg.js +0 -9
  276. package/dist/MultiLinearWiggleDisplay/components/ScoreLegend.d.ts +0 -5
  277. package/dist/MultiLinearWiggleDisplay/components/ScoreLegend.js +0 -19
  278. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +0 -9
  279. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +0 -42
  280. package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.d.ts +0 -7
  281. package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.js +0 -130
  282. package/dist/MultiLinearWiggleDisplay/components/Tooltip.d.ts +0 -18
  283. package/dist/MultiLinearWiggleDisplay/components/Tooltip.js +0 -35
  284. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.d.ts +0 -6
  285. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.js +0 -29
  286. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.d.ts +0 -7
  287. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.js +0 -79
  288. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.d.ts +0 -7
  289. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js +0 -145
  290. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts +0 -7
  291. package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.js +0 -2
  292. package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -5
  293. package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +0 -14
  294. package/dist/MultiLinearWiggleDisplay/components/YScaleBars.d.ts +0 -7
  295. package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js +0 -28
  296. package/dist/MultiLinearWiggleDisplay/components/util.d.ts +0 -13
  297. package/dist/MultiLinearWiggleDisplay/components/util.js +0 -45
  298. package/dist/MultiLinearWiggleDisplay/configSchema.d.ts +0 -84
  299. package/dist/MultiLinearWiggleDisplay/configSchema.js +0 -44
  300. package/dist/MultiLinearWiggleDisplay/index.d.ts +0 -2
  301. package/dist/MultiLinearWiggleDisplay/index.js +0 -57
  302. package/dist/MultiLinearWiggleDisplay/model.d.ts +0 -436
  303. package/dist/MultiLinearWiggleDisplay/model.js +0 -413
  304. package/dist/MultiLinearWiggleDisplay/renderSvg.d.ts +0 -3
  305. package/dist/MultiLinearWiggleDisplay/renderSvg.js +0 -15
  306. package/dist/MultiLinearWiggleDisplay/types.d.ts +0 -14
  307. package/dist/MultiLinearWiggleDisplay/types.js +0 -2
  308. package/dist/MultiLinearWiggleDisplay/util.d.ts +0 -1
  309. package/dist/MultiLinearWiggleDisplay/util.js +0 -10
  310. package/dist/MultiQuantitativeTrack/configSchema.d.ts +0 -80
  311. package/dist/MultiQuantitativeTrack/configSchema.js +0 -11
  312. package/dist/MultiQuantitativeTrack/index.d.ts +0 -2
  313. package/dist/MultiQuantitativeTrack/index.js +0 -20
  314. package/dist/MultiRowLineRenderer/MultiRowLineRenderer.d.ts +0 -8
  315. package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js +0 -70
  316. package/dist/MultiRowLineRenderer/configSchema.d.ts +0 -49
  317. package/dist/MultiRowLineRenderer/configSchema.js +0 -26
  318. package/dist/MultiRowLineRenderer/index.d.ts +0 -2
  319. package/dist/MultiRowLineRenderer/index.js +0 -17
  320. package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.d.ts +0 -8
  321. package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +0 -70
  322. package/dist/MultiRowXYPlotRenderer/configSchema.d.ts +0 -57
  323. package/dist/MultiRowXYPlotRenderer/configSchema.js +0 -34
  324. package/dist/MultiRowXYPlotRenderer/index.d.ts +0 -2
  325. package/dist/MultiRowXYPlotRenderer/index.js +0 -17
  326. package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +0 -30
  327. package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js +0 -85
  328. package/dist/MultiWiggleAdapter/configSchema.d.ts +0 -13
  329. package/dist/MultiWiggleAdapter/configSchema.js +0 -17
  330. package/dist/MultiWiggleAdapter/index.d.ts +0 -2
  331. package/dist/MultiWiggleAdapter/index.js +0 -57
  332. package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts +0 -5
  333. package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +0 -89
  334. package/dist/MultiWiggleAddTrackWorkflow/index.d.ts +0 -2
  335. package/dist/MultiWiggleAddTrackWorkflow/index.js +0 -46
  336. package/dist/MultiWiggleRendering.d.ts +0 -19
  337. package/dist/MultiWiggleRendering.js +0 -81
  338. package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts +0 -8
  339. package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js +0 -61
  340. package/dist/MultiXYPlotRenderer/configSchema.d.ts +0 -57
  341. package/dist/MultiXYPlotRenderer/configSchema.js +0 -34
  342. package/dist/MultiXYPlotRenderer/index.d.ts +0 -2
  343. package/dist/MultiXYPlotRenderer/index.js +0 -17
  344. package/dist/QuantitativeTrack/configSchema.d.ts +0 -80
  345. package/dist/QuantitativeTrack/configSchema.js +0 -11
  346. package/dist/QuantitativeTrack/index.d.ts +0 -2
  347. package/dist/QuantitativeTrack/index.js +0 -20
  348. package/dist/Tooltip.d.ts +0 -18
  349. package/dist/Tooltip.js +0 -34
  350. package/dist/WiggleBaseRenderer.d.ts +0 -57
  351. package/dist/WiggleBaseRenderer.js +0 -42
  352. package/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.d.ts +0 -14
  353. package/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.js +0 -31
  354. package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts +0 -6
  355. package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.js +0 -22
  356. package/dist/WiggleRPC/MultiWiggleGetSources.d.ts +0 -14
  357. package/dist/WiggleRPC/MultiWiggleGetSources.js +0 -22
  358. package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +0 -12
  359. package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +0 -22
  360. package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +0 -13
  361. package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +0 -22
  362. package/dist/WiggleRPC/getScoreMatrix.d.ts +0 -6
  363. package/dist/WiggleRPC/getScoreMatrix.js +0 -35
  364. package/dist/WiggleRPC/rpcMethods.d.ts +0 -5
  365. package/dist/WiggleRPC/rpcMethods.js +0 -21
  366. package/dist/WiggleRPC/type.d.ts +0 -0
  367. package/dist/WiggleRPC/type.js +0 -1
  368. package/dist/WiggleRPC/types.d.ts +0 -13
  369. package/dist/WiggleRPC/types.js +0 -2
  370. package/dist/WiggleRendering.d.ts +0 -14
  371. package/dist/WiggleRendering.js +0 -35
  372. package/dist/XYPlotRenderer/XYPlotRenderer.d.ts +0 -7
  373. package/dist/XYPlotRenderer/XYPlotRenderer.js +0 -61
  374. package/dist/XYPlotRenderer/configSchema.d.ts +0 -57
  375. package/dist/XYPlotRenderer/configSchema.js +0 -34
  376. package/dist/XYPlotRenderer/index.d.ts +0 -5
  377. package/dist/XYPlotRenderer/index.js +0 -24
  378. package/dist/configSchema.d.ts +0 -37
  379. package/dist/configSchema.js +0 -47
  380. package/dist/drawDensity.d.ts +0 -18
  381. package/dist/drawDensity.js +0 -81
  382. package/dist/drawLine.d.ts +0 -20
  383. package/dist/drawLine.js +0 -77
  384. package/dist/drawXY.d.ts +0 -21
  385. package/dist/drawXY.js +0 -191
  386. package/dist/getMultiWiggleSourcesAutorun.d.ts +0 -17
  387. package/dist/getMultiWiggleSourcesAutorun.js +0 -38
  388. package/dist/getQuantitativeStats.d.ts +0 -13
  389. package/dist/getQuantitativeStats.js +0 -70
  390. package/dist/getQuantitativeStatsAutorun.d.ts +0 -13
  391. package/dist/getQuantitativeStatsAutorun.js +0 -35
  392. package/dist/index.d.ts +0 -91
  393. package/dist/index.js +0 -112
  394. package/dist/shared/SetMinMaxDialog.d.ts +0 -10
  395. package/dist/shared/SetMinMaxDialog.js +0 -26
  396. package/dist/shared/SharedWiggleConfigSchema.d.ts +0 -66
  397. package/dist/shared/SharedWiggleConfigSchema.js +0 -56
  398. package/dist/shared/SharedWiggleMixin.d.ts +0 -405
  399. package/dist/shared/SharedWiggleMixin.js +0 -343
  400. package/dist/shared/YScaleBar.d.ts +0 -9
  401. package/dist/shared/YScaleBar.js +0 -12
  402. package/dist/util.d.ts +0 -24
  403. package/dist/util.js +0 -105
  404. package/esm/WiggleBaseRenderer.d.ts +0 -57
  405. package/esm/WiggleBaseRenderer.js +0 -36
  406. package/esm/WiggleRPC/type.d.ts +0 -0
  407. package/esm/WiggleRPC/type.js +0 -1
package/dist/drawLine.js DELETED
@@ -1,77 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.drawLine = drawLine;
4
- const configuration_1 = require("@jbrowse/core/configuration");
5
- const util_1 = require("@jbrowse/core/util");
6
- const stopToken_1 = require("@jbrowse/core/util/stopToken");
7
- const util_2 = require("./util");
8
- const fudgeFactor = 0.3;
9
- const clipHeight = 2;
10
- function drawLine(ctx, props) {
11
- const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, stopToken, } = props;
12
- const region = regions[0];
13
- const width = (region.end - region.start) / bpPerPx;
14
- const height = unadjustedHeight - offset * 2;
15
- const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
16
- const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
17
- const domain = scale.domain();
18
- const niceMin = domain[0];
19
- const niceMax = domain[1];
20
- const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
21
- let lastVal;
22
- let prevLeftPx = Number.NEGATIVE_INFINITY;
23
- const reducedFeatures = [];
24
- let start = performance.now();
25
- for (const feature of features.values()) {
26
- if (performance.now() - start > 400) {
27
- (0, stopToken_1.checkStopToken)(stopToken);
28
- start = performance.now();
29
- }
30
- const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
31
- if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
32
- reducedFeatures.push(feature);
33
- prevLeftPx = leftPx;
34
- }
35
- const score = feature.get('score');
36
- const lowClipping = score < niceMin;
37
- const highClipping = score > niceMax;
38
- const w = rightPx - leftPx + fudgeFactor;
39
- const c = colorCallback(feature, score);
40
- ctx.beginPath();
41
- ctx.strokeStyle = c;
42
- const startPos = lastVal !== undefined ? lastVal : score;
43
- if (!region.reversed) {
44
- ctx.moveTo(leftPx, toY(startPos));
45
- ctx.lineTo(leftPx, toY(score));
46
- ctx.lineTo(rightPx, toY(score));
47
- }
48
- else {
49
- ctx.moveTo(rightPx, toY(startPos));
50
- ctx.lineTo(rightPx, toY(score));
51
- ctx.lineTo(leftPx, toY(score));
52
- }
53
- ctx.stroke();
54
- lastVal = score;
55
- if (highClipping) {
56
- ctx.fillStyle = clipColor;
57
- ctx.fillRect(leftPx, offset, w, clipHeight);
58
- }
59
- else if (lowClipping && scaleOpts.scaleType !== 'log') {
60
- ctx.fillStyle = clipColor;
61
- ctx.fillRect(leftPx, height - clipHeight, w, height);
62
- }
63
- }
64
- if (displayCrossHatches) {
65
- ctx.lineWidth = 1;
66
- ctx.strokeStyle = 'rgba(200,200,200,0.5)';
67
- for (const tick of values) {
68
- ctx.beginPath();
69
- ctx.moveTo(0, Math.round(toY(tick)));
70
- ctx.lineTo(width, Math.round(toY(tick)));
71
- ctx.stroke();
72
- }
73
- }
74
- return {
75
- reducedFeatures,
76
- };
77
- }
package/dist/drawXY.d.ts DELETED
@@ -1,21 +0,0 @@
1
- import type { ScaleOpts } from './util';
2
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
- import type { Feature, Region } from '@jbrowse/core/util';
4
- export declare function drawXY(ctx: CanvasRenderingContext2D, props: {
5
- stopToken?: string;
6
- features: Map<string, Feature> | Feature[];
7
- bpPerPx: number;
8
- regions: Region[];
9
- scaleOpts: ScaleOpts;
10
- height: number;
11
- ticks: {
12
- values: number[];
13
- };
14
- config: AnyConfigurationModel;
15
- displayCrossHatches: boolean;
16
- inverted: boolean;
17
- offset?: number;
18
- colorCallback: (f: Feature, score: number) => string;
19
- }): {
20
- reducedFeatures: Feature[];
21
- };
package/dist/drawXY.js DELETED
@@ -1,191 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.drawXY = drawXY;
4
- const configuration_1 = require("@jbrowse/core/configuration");
5
- const util_1 = require("@jbrowse/core/util");
6
- const colord_1 = require("@jbrowse/core/util/colord");
7
- const stopToken_1 = require("@jbrowse/core/util/stopToken");
8
- const util_2 = require("./util");
9
- function lighten(color, amount) {
10
- const hslColor = color.toHsl();
11
- const l = hslColor.l * (1 + amount);
12
- return (0, colord_1.colord)({
13
- ...hslColor,
14
- l: (0, util_1.clamp)(l, 0, 100),
15
- });
16
- }
17
- function darken(color, amount) {
18
- const hslColor = color.toHsl();
19
- const l = hslColor.l * (1 - amount);
20
- return (0, colord_1.colord)({
21
- ...hslColor,
22
- l: (0, util_1.clamp)(l, 0, 100),
23
- });
24
- }
25
- const fudgeFactor = 0.3;
26
- const clipHeight = 2;
27
- function drawXY(ctx, props) {
28
- const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, inverted, stopToken, } = props;
29
- const region = regions[0];
30
- const width = (region.end - region.start) / bpPerPx;
31
- const height = unadjustedHeight - offset * 2;
32
- const filled = (0, configuration_1.readConfObject)(config, 'filled');
33
- const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
34
- const summaryScoreMode = (0, configuration_1.readConfObject)(config, 'summaryScoreMode');
35
- const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
36
- const minSize = (0, configuration_1.readConfObject)(config, 'minSize');
37
- const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height], inverted });
38
- const originY = (0, util_2.getOrigin)(scaleOpts.scaleType);
39
- const domain = scale.domain();
40
- const niceMin = domain[0];
41
- const niceMax = domain[1];
42
- const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
43
- const toOrigin = (n) => toY(originY) - toY(n);
44
- const getHeight = (n) => (filled ? toOrigin(n) : Math.max(minSize, 1));
45
- let hasClipping = false;
46
- let prevLeftPx = Number.NEGATIVE_INFINITY;
47
- const reducedFeatures = [];
48
- const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
49
- let start = performance.now();
50
- if (summaryScoreMode === 'whiskers') {
51
- let lastCol;
52
- let lastMix;
53
- start = performance.now();
54
- for (const feature of features.values()) {
55
- if (performance.now() - start > 400) {
56
- (0, stopToken_1.checkStopToken)(stopToken);
57
- start = performance.now();
58
- }
59
- const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
60
- if (feature.get('summary')) {
61
- const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
62
- const max = feature.get('maxScore');
63
- const c = colorCallback(feature, max);
64
- const effectiveC = crossingOrigin
65
- ? c
66
- : c === lastCol
67
- ? lastMix
68
- : (lastMix = lighten((0, colord_1.colord)(c), 0.4).toHex());
69
- (0, util_2.fillRectCtx)(leftPx, toY(max), w, getHeight(max), ctx, effectiveC);
70
- lastCol = c;
71
- }
72
- }
73
- lastMix = undefined;
74
- lastCol = undefined;
75
- start = performance.now();
76
- for (const feature of features.values()) {
77
- if (performance.now() - start > 400) {
78
- (0, stopToken_1.checkStopToken)(stopToken);
79
- start = performance.now();
80
- }
81
- const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
82
- const score = feature.get('score');
83
- const max = feature.get('maxScore');
84
- const min = feature.get('minScore');
85
- const summary = feature.get('summary');
86
- const c = colorCallback(feature, score);
87
- const effectiveC = crossingOrigin && summary
88
- ? c === lastCol
89
- ? lastMix
90
- : (lastMix = (0, colord_1.colord)(colorCallback(feature, max))
91
- .mix((0, colord_1.colord)(colorCallback(feature, min)))
92
- .toString())
93
- : c;
94
- const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
95
- if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
96
- rightPx - leftPx > 1) {
97
- reducedFeatures.push(feature);
98
- prevLeftPx = leftPx;
99
- }
100
- hasClipping = hasClipping || score < niceMin || score > niceMax;
101
- (0, util_2.fillRectCtx)(leftPx, toY(score), w, getHeight(score), ctx, effectiveC);
102
- lastCol = c;
103
- }
104
- lastMix = undefined;
105
- lastCol = undefined;
106
- start = performance.now();
107
- for (const feature of features.values()) {
108
- if (performance.now() - start > 400) {
109
- (0, stopToken_1.checkStopToken)(stopToken);
110
- start = performance.now();
111
- }
112
- const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
113
- if (feature.get('summary')) {
114
- const min = feature.get('minScore');
115
- const c = colorCallback(feature, min);
116
- const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
117
- const effectiveC = crossingOrigin
118
- ? c
119
- : c === lastCol
120
- ? lastMix
121
- : (lastMix = darken((0, colord_1.colord)(c), 0.4).toHex());
122
- (0, util_2.fillRectCtx)(leftPx, toY(min), w, getHeight(min), ctx, effectiveC);
123
- lastCol = c;
124
- }
125
- }
126
- }
127
- else {
128
- start = performance.now();
129
- for (const feature of features.values()) {
130
- if (performance.now() - start > 400) {
131
- (0, stopToken_1.checkStopToken)(stopToken);
132
- start = performance.now();
133
- }
134
- const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
135
- if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
136
- rightPx - leftPx > 1) {
137
- reducedFeatures.push(feature);
138
- prevLeftPx = leftPx;
139
- }
140
- const score = feature.get('score');
141
- const c = colorCallback(feature, score);
142
- hasClipping = hasClipping || score < niceMin || score > niceMax;
143
- const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
144
- if (summaryScoreMode === 'max') {
145
- const s = feature.get('summary') ? feature.get('maxScore') : score;
146
- (0, util_2.fillRectCtx)(leftPx, toY(s), w, getHeight(s), ctx, c);
147
- }
148
- else if (summaryScoreMode === 'min') {
149
- const s = feature.get('summary') ? feature.get('minScore') : score;
150
- (0, util_2.fillRectCtx)(leftPx, toY(s), w, getHeight(s), ctx, c);
151
- }
152
- else {
153
- (0, util_2.fillRectCtx)(leftPx, toY(score), w, getHeight(score), ctx, c);
154
- }
155
- }
156
- }
157
- ctx.save();
158
- if (hasClipping) {
159
- ctx.fillStyle = clipColor;
160
- start = performance.now();
161
- for (const feature of features.values()) {
162
- if (performance.now() - start > 400) {
163
- (0, stopToken_1.checkStopToken)(stopToken);
164
- start = performance.now();
165
- }
166
- const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
167
- const w = rightPx - leftPx + fudgeFactor;
168
- const score = feature.get('score');
169
- if (score > niceMax) {
170
- (0, util_2.fillRectCtx)(leftPx, offset, w, clipHeight, ctx);
171
- }
172
- else if (score < niceMin && scaleOpts.scaleType !== 'log') {
173
- (0, util_2.fillRectCtx)(leftPx, unadjustedHeight, w, clipHeight, ctx);
174
- }
175
- }
176
- }
177
- ctx.restore();
178
- if (displayCrossHatches) {
179
- ctx.lineWidth = 1;
180
- ctx.strokeStyle = 'rgba(200,200,200,0.5)';
181
- for (const tick of ticks.values) {
182
- ctx.beginPath();
183
- ctx.moveTo(0, Math.round(toY(tick)));
184
- ctx.lineTo(width, Math.round(toY(tick)));
185
- ctx.stroke();
186
- }
187
- }
188
- return {
189
- reducedFeatures,
190
- };
191
- }
@@ -1,17 +0,0 @@
1
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
- export interface Source {
3
- name: string;
4
- color?: string;
5
- group?: string;
6
- }
7
- export declare function getMultiWiggleSourcesAutorun(self: {
8
- quantitativeStatsReady: boolean;
9
- configuration: AnyConfigurationModel;
10
- adapterConfig: AnyConfigurationModel;
11
- autoscaleType: string;
12
- adapterProps: () => Record<string, unknown>;
13
- setSourcesLoading: (aborter: string) => void;
14
- setError: (error: unknown) => void;
15
- setMessage: (str: string) => void;
16
- setSources: (sources: Source[]) => void;
17
- }): void;
@@ -1,38 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.getMultiWiggleSourcesAutorun = getMultiWiggleSourcesAutorun;
4
- const util_1 = require("@jbrowse/core/util");
5
- const aborting_1 = require("@jbrowse/core/util/aborting");
6
- const stopToken_1 = require("@jbrowse/core/util/stopToken");
7
- const tracks_1 = require("@jbrowse/core/util/tracks");
8
- const mobx_1 = require("mobx");
9
- const mobx_state_tree_1 = require("mobx-state-tree");
10
- function getMultiWiggleSourcesAutorun(self) {
11
- (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
12
- try {
13
- const view = (0, util_1.getContainingView)(self);
14
- if (!view.initialized) {
15
- return;
16
- }
17
- const { rpcManager } = (0, util_1.getSession)(self);
18
- const { adapterConfig } = self;
19
- const token = (0, stopToken_1.createStopToken)();
20
- self.setSourcesLoading(token);
21
- const sessionId = (0, tracks_1.getRpcSessionId)(self);
22
- const sources = (await rpcManager.call(sessionId, 'MultiWiggleGetSources', {
23
- regions: view.staticBlocks.contentBlocks,
24
- sessionId,
25
- adapterConfig,
26
- }));
27
- if ((0, mobx_state_tree_1.isAlive)(self)) {
28
- self.setSources(sources);
29
- }
30
- }
31
- catch (e) {
32
- if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
33
- console.error(e);
34
- (0, util_1.getSession)(self).notifyError(`${e}`, e);
35
- }
36
- }
37
- }));
38
- }
@@ -1,13 +0,0 @@
1
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
- import type { QuantitativeStats } from '@jbrowse/core/util/stats';
3
- export declare function getQuantitativeStats(self: {
4
- adapterConfig: AnyConfigurationModel;
5
- configuration: AnyConfigurationModel;
6
- autoscaleType: string;
7
- setMessage: (str: string) => void;
8
- }, opts: {
9
- headers?: Record<string, string>;
10
- stopToken?: string;
11
- filters: string[];
12
- currStatsBpPerPx: number;
13
- }): Promise<QuantitativeStats>;
@@ -1,70 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.getQuantitativeStats = getQuantitativeStats;
4
- const configuration_1 = require("@jbrowse/core/configuration");
5
- const util_1 = require("@jbrowse/core/util");
6
- const tracks_1 = require("@jbrowse/core/util/tracks");
7
- const mobx_state_tree_1 = require("mobx-state-tree");
8
- async function getQuantitativeStats(self, opts) {
9
- const { rpcManager } = (0, util_1.getSession)(self);
10
- const numStdDev = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
11
- const { adapterConfig, autoscaleType } = self;
12
- const sessionId = (0, tracks_1.getRpcSessionId)(self);
13
- const { currStatsBpPerPx } = opts;
14
- const params = {
15
- sessionId,
16
- adapterConfig,
17
- statusCallback: (message) => {
18
- if ((0, mobx_state_tree_1.isAlive)(self)) {
19
- self.setMessage(message);
20
- }
21
- },
22
- ...opts,
23
- };
24
- if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
25
- const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
26
- const { scoreMin, scoreMean, scoreStdDev } = results;
27
- return autoscaleType === 'globalsd'
28
- ? {
29
- ...results,
30
- scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
31
- scoreMax: scoreMean + numStdDev * scoreStdDev,
32
- currStatsBpPerPx,
33
- }
34
- : {
35
- ...results,
36
- currStatsBpPerPx,
37
- };
38
- }
39
- if (autoscaleType === 'local' || autoscaleType === 'localsd') {
40
- const { dynamicBlocks, bpPerPx } = (0, util_1.getContainingView)(self);
41
- const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
42
- ...params,
43
- regions: dynamicBlocks.contentBlocks.map(region => {
44
- const { start, end } = region;
45
- return {
46
- ...JSON.parse(JSON.stringify(region)),
47
- start: Math.floor(start),
48
- end: Math.ceil(end),
49
- };
50
- }),
51
- bpPerPx,
52
- }));
53
- const { scoreMin, scoreMean, scoreStdDev } = results;
54
- return autoscaleType === 'localsd'
55
- ? {
56
- ...results,
57
- scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
58
- scoreMax: scoreMean + numStdDev * scoreStdDev,
59
- currStatsBpPerPx,
60
- }
61
- : {
62
- ...results,
63
- currStatsBpPerPx,
64
- };
65
- }
66
- if (autoscaleType === 'zscale') {
67
- return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
68
- }
69
- throw new Error(`invalid autoscaleType '${autoscaleType}'`);
70
- }
@@ -1,13 +0,0 @@
1
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
- import type { QuantitativeStats } from '@jbrowse/core/util/stats';
3
- export declare function getQuantitativeStatsAutorun(self: {
4
- quantitativeStatsReady: boolean;
5
- configuration: AnyConfigurationModel;
6
- adapterConfig: AnyConfigurationModel;
7
- autoscaleType: string;
8
- adapterProps: () => Record<string, unknown>;
9
- setStatsLoading: (token: string) => void;
10
- setError: (error: unknown) => void;
11
- setMessage: (str: string) => void;
12
- updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;
13
- }): void;
@@ -1,35 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.getQuantitativeStatsAutorun = getQuantitativeStatsAutorun;
4
- const util_1 = require("@jbrowse/core/util");
5
- const stopToken_1 = require("@jbrowse/core/util/stopToken");
6
- const mobx_1 = require("mobx");
7
- const mobx_state_tree_1 = require("mobx-state-tree");
8
- const getQuantitativeStats_1 = require("./getQuantitativeStats");
9
- function getQuantitativeStatsAutorun(self) {
10
- (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
11
- try {
12
- if (self.quantitativeStatsReady) {
13
- const view = (0, util_1.getContainingView)(self);
14
- const stopToken = (0, stopToken_1.createStopToken)();
15
- self.setStatsLoading(stopToken);
16
- const statsRegion = JSON.stringify(view.dynamicBlocks);
17
- const wiggleStats = await (0, getQuantitativeStats_1.getQuantitativeStats)(self, {
18
- stopToken,
19
- filters: [],
20
- currStatsBpPerPx: view.bpPerPx,
21
- ...self.adapterProps(),
22
- });
23
- if ((0, mobx_state_tree_1.isAlive)(self)) {
24
- self.updateQuantitativeStats(wiggleStats, statsRegion);
25
- }
26
- }
27
- }
28
- catch (e) {
29
- if ((0, mobx_state_tree_1.isAlive)(self) && !(0, util_1.isAbortException)(e)) {
30
- console.error(e);
31
- self.setError(e);
32
- }
33
- }
34
- }, { delay: 1000 }));
35
- }
package/dist/index.d.ts DELETED
@@ -1,91 +0,0 @@
1
- import Plugin from '@jbrowse/core/Plugin';
2
- import { modelFactory as linearWiggleDisplayModelFactory } from './LinearWiggleDisplay';
3
- import WiggleBaseRenderer from './WiggleBaseRenderer';
4
- import { XYPlotRenderer } from './XYPlotRenderer';
5
- import * as utils from './util';
6
- import type PluginManager from '@jbrowse/core/PluginManager';
7
- export default class WigglePlugin extends Plugin {
8
- name: string;
9
- install(pm: PluginManager): void;
10
- exports: {
11
- LinearWiggleDisplayReactComponent: (props: {
12
- model: import("./LinearWiggleDisplay/model").WiggleDisplayModel;
13
- }) => import("react/jsx-runtime").JSX.Element;
14
- XYPlotRendererReactComponent: (props: {
15
- regions: import("@jbrowse/core/util").Region[];
16
- features: Map<string, import("@jbrowse/core/util").Feature>;
17
- bpPerPx: number;
18
- width: number;
19
- height: number;
20
- blockKey: string;
21
- onMouseLeave?: (event: React.MouseEvent) => void;
22
- onMouseMove?: (event: React.MouseEvent, arg?: string) => void;
23
- onFeatureClick?: (event: React.MouseEvent, arg?: string) => void;
24
- }) => import("react/jsx-runtime").JSX.Element;
25
- XYPlotRenderer: typeof XYPlotRenderer;
26
- WiggleBaseRenderer: typeof WiggleBaseRenderer;
27
- linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
28
- xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
29
- filled: {
30
- type: string;
31
- defaultValue: boolean;
32
- };
33
- displayCrossHatches: {
34
- type: string;
35
- description: string;
36
- defaultValue: boolean;
37
- };
38
- summaryScoreMode: {
39
- type: string;
40
- model: import("mobx-state-tree").ISimpleType<string>;
41
- description: string;
42
- defaultValue: string;
43
- };
44
- minSize: {
45
- type: string;
46
- defaultValue: number;
47
- };
48
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
49
- color: {
50
- type: string;
51
- description: string;
52
- defaultValue: string;
53
- contextVariable: string[];
54
- };
55
- posColor: {
56
- type: string;
57
- description: string;
58
- defaultValue: string;
59
- contextVariable: string[];
60
- };
61
- negColor: {
62
- type: string;
63
- description: string;
64
- defaultValue: string;
65
- contextVariable: string[];
66
- };
67
- clipColor: {
68
- type: string;
69
- description: string;
70
- defaultValue: string;
71
- };
72
- bicolorPivot: {
73
- type: string;
74
- model: import("mobx-state-tree").ISimpleType<string>;
75
- description: string;
76
- defaultValue: string;
77
- };
78
- bicolorPivotValue: {
79
- type: string;
80
- defaultValue: number;
81
- description: string;
82
- };
83
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
84
- utils: typeof utils;
85
- };
86
- }
87
- export * from './util';
88
- export { default as WiggleRendering } from './WiggleRendering';
89
- export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
90
- export type { TooltipContentsComponent } from './Tooltip';
91
- export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';