@jbrowse/plugin-variants 3.7.0 → 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 (539) hide show
  1. package/esm/ChordVariantDisplay/components/ChordVariantDisplay.d.ts +11 -0
  2. package/esm/ChordVariantDisplay/components/ChordVariantDisplay.js +16 -0
  3. package/esm/ChordVariantDisplay/components/DisplayError.d.ts +9 -0
  4. package/esm/ChordVariantDisplay/components/DisplayError.js +7 -0
  5. package/esm/ChordVariantDisplay/components/Loading.d.ts +8 -0
  6. package/esm/ChordVariantDisplay/components/Loading.js +28 -0
  7. package/esm/ChordVariantDisplay/index.js +4 -4
  8. package/esm/ChordVariantDisplay/models/configSchema.d.ts +4 -5
  9. package/esm/ChordVariantDisplay/models/configSchema.js +10 -5
  10. package/esm/ChordVariantDisplay/models/renderReaction.d.ts +30 -0
  11. package/esm/ChordVariantDisplay/models/renderReaction.js +48 -0
  12. package/esm/ChordVariantDisplay/models/renderSvg.d.ts +6 -0
  13. package/esm/ChordVariantDisplay/models/renderSvg.js +12 -0
  14. package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +535 -46
  15. package/esm/ChordVariantDisplay/models/stateModelFactory.js +146 -8
  16. package/esm/LinearVariantDisplay/configSchema.d.ts +5 -5
  17. package/esm/LinearVariantDisplay/configSchema.js +2 -2
  18. package/esm/LinearVariantDisplay/index.js +6 -4
  19. package/esm/LinearVariantDisplay/model.d.ts +1086 -103
  20. package/esm/LinearVariantDisplay/model.js +10 -26
  21. package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts +1 -1
  22. package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js +8 -18
  23. package/esm/MultiLinearVariantDisplay/configSchema.d.ts +6 -44
  24. package/esm/MultiLinearVariantDisplay/configSchema.js +2 -2
  25. package/esm/MultiLinearVariantDisplay/index.js +4 -3
  26. package/esm/MultiLinearVariantDisplay/model.d.ts +1031 -125
  27. package/esm/MultiLinearVariantDisplay/model.js +3 -23
  28. package/esm/MultiLinearVariantDisplay/renderSvg.d.ts +1 -1
  29. package/esm/MultiLinearVariantDisplay/renderSvg.js +4 -4
  30. package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +8 -2
  31. package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js +26 -23
  32. package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts +1 -1
  33. package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js +9 -20
  34. package/esm/MultiLinearVariantMatrixDisplay/configSchema.d.ts +6 -6
  35. package/esm/MultiLinearVariantMatrixDisplay/configSchema.js +1 -1
  36. package/esm/MultiLinearVariantMatrixDisplay/index.js +5 -4
  37. package/esm/MultiLinearVariantMatrixDisplay/model.d.ts +1110 -131
  38. package/esm/MultiLinearVariantMatrixDisplay/model.js +22 -48
  39. package/esm/MultiLinearVariantMatrixDisplay/renderSvg.d.ts +1 -1
  40. package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js +3 -3
  41. package/esm/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.d.ts +4 -35
  42. package/esm/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.js +19 -33
  43. package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts +12 -1
  44. package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js +48 -22
  45. package/esm/MultiLinearVariantMatrixRenderer/configSchema.d.ts +1 -1
  46. package/esm/MultiLinearVariantMatrixRenderer/index.js +4 -4
  47. package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts +10 -2
  48. package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js +155 -135
  49. package/esm/MultiLinearVariantMatrixRenderer/types.d.ts +2 -14
  50. package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts +3 -60
  51. package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.js +9 -18
  52. package/esm/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.d.ts +7 -6
  53. package/esm/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.js +30 -26
  54. package/esm/MultiLinearVariantRenderer/configSchema.d.ts +1 -1
  55. package/esm/MultiLinearVariantRenderer/index.js +4 -4
  56. package/esm/MultiLinearVariantRenderer/makeImageData.d.ts +14 -11
  57. package/esm/MultiLinearVariantRenderer/makeImageData.js +127 -110
  58. package/esm/MultiLinearVariantRenderer/types.d.ts +3 -20
  59. package/esm/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js +1 -1
  60. package/esm/SplitVcfTabixAdapter/configSchema.d.ts +2 -2
  61. package/esm/SplitVcfTabixAdapter/index.d.ts +1 -1
  62. package/esm/SplitVcfTabixAdapter/index.js +3 -3
  63. package/esm/StructuralVariantChordRenderer/Chord.d.ts +1 -1
  64. package/esm/StructuralVariantChordRenderer/Chord.js +41 -58
  65. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +3 -3
  66. package/esm/StructuralVariantChordRenderer/ReactComponent.js +3 -3
  67. package/esm/StructuralVariantChordRenderer/configSchema.d.ts +2 -2
  68. package/esm/StructuralVariantChordRenderer/index.js +3 -3
  69. package/esm/Tooltip.js +2 -2
  70. package/esm/VariantFeatureWidget/AltFormatter.js +1 -1
  71. package/esm/VariantFeatureWidget/Formatter.js +2 -2
  72. package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakpointSplitViewChoiceDialog.d.ts +1 -0
  73. package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakpointSplitViewChoiceDialog.js +1 -0
  74. package/esm/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendPanel.d.ts +1 -1
  75. package/esm/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendPanel.js +8 -23
  76. package/esm/VariantFeatureWidget/VariantConsequence/VariantConsequenceDataGrid.js +1 -1
  77. package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts +1 -1
  78. package/esm/VariantFeatureWidget/VariantFeatureWidget.js +16 -29
  79. package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.d.ts +5 -2
  80. package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js +68 -59
  81. package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleFilters.js +13 -2
  82. package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.d.ts +1 -1
  83. package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js +72 -30
  84. package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts +2 -2
  85. package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js +49 -26
  86. package/esm/VariantFeatureWidget/VariantSampleGrid/types.d.ts +3 -5
  87. package/esm/VariantFeatureWidget/configSchema.d.ts +1 -1
  88. package/esm/VariantFeatureWidget/index.js +3 -3
  89. package/esm/VariantFeatureWidget/stateModelFactory.d.ts +39 -39
  90. package/esm/VariantFeatureWidget/stateModelFactory.js +1 -1
  91. package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts +2 -7
  92. package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.js +3 -14
  93. package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts +4 -2
  94. package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js +2 -5
  95. package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts +2 -2
  96. package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js +34 -19
  97. package/esm/VariantRPC/MultiVariantGetSources.js +2 -6
  98. package/esm/VariantRPC/executeClusterGenotypeMatrix.d.ts +22 -0
  99. package/esm/VariantRPC/executeClusterGenotypeMatrix.js +19 -0
  100. package/esm/VariantRPC/getGenotypeMatrix.d.ts +18 -3
  101. package/esm/VariantRPC/getGenotypeMatrix.js +23 -40
  102. package/esm/VariantRPC/types.d.ts +10 -24
  103. package/esm/VariantTrack/configSchema.d.ts +16 -11
  104. package/esm/VariantTrack/index.js +13 -2
  105. package/esm/VariantTrack/saveTrackFormats/vcf.d.ts +4 -0
  106. package/esm/VariantTrack/saveTrackFormats/vcf.js +15 -0
  107. package/esm/VcfAdapter/VcfAdapter.d.ts +6 -3
  108. package/esm/VcfAdapter/VcfAdapter.js +36 -24
  109. package/esm/VcfAdapter/configSchema.d.ts +2 -2
  110. package/esm/VcfAdapter/index.js +3 -2
  111. package/esm/VcfExtensionPoints/index.d.ts +2 -0
  112. package/esm/{extensionPoints.js → VcfExtensionPoints/index.js} +1 -1
  113. package/esm/VcfFeature/index.js +20 -8
  114. package/esm/VcfFeature/util.d.ts +0 -1
  115. package/esm/VcfFeature/util.js +70 -188
  116. package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts +2 -0
  117. package/esm/VcfTabixAdapter/VcfTabixAdapter.js +28 -3
  118. package/esm/VcfTabixAdapter/configSchema.d.ts +5 -5
  119. package/esm/VcfTabixAdapter/configSchema.js +1 -1
  120. package/esm/VcfTabixAdapter/index.d.ts +1 -1
  121. package/esm/VcfTabixAdapter/index.js +4 -3
  122. package/esm/d3-hierarchy2/accessors.d.ts +2 -0
  123. package/esm/d3-hierarchy2/accessors.js +8 -0
  124. package/esm/d3-hierarchy2/array.d.ts +2 -0
  125. package/esm/d3-hierarchy2/array.js +15 -0
  126. package/esm/d3-hierarchy2/cluster.d.ts +8 -0
  127. package/esm/d3-hierarchy2/cluster.js +63 -0
  128. package/esm/d3-hierarchy2/constant.d.ts +2 -0
  129. package/esm/d3-hierarchy2/constant.js +8 -0
  130. package/esm/d3-hierarchy2/hierarchy/ancestors.d.ts +1 -0
  131. package/esm/d3-hierarchy2/hierarchy/ancestors.js +7 -0
  132. package/esm/d3-hierarchy2/hierarchy/count.d.ts +1 -0
  133. package/esm/d3-hierarchy2/hierarchy/count.js +12 -0
  134. package/esm/d3-hierarchy2/hierarchy/descendants.d.ts +1 -0
  135. package/esm/d3-hierarchy2/hierarchy/descendants.js +3 -0
  136. package/esm/d3-hierarchy2/hierarchy/each.d.ts +1 -0
  137. package/esm/d3-hierarchy2/hierarchy/each.js +7 -0
  138. package/esm/d3-hierarchy2/hierarchy/eachAfter.d.ts +1 -0
  139. package/esm/d3-hierarchy2/hierarchy/eachAfter.js +15 -0
  140. package/esm/d3-hierarchy2/hierarchy/eachBefore.d.ts +1 -0
  141. package/esm/d3-hierarchy2/hierarchy/eachBefore.js +12 -0
  142. package/esm/d3-hierarchy2/hierarchy/find.d.ts +1 -0
  143. package/esm/d3-hierarchy2/hierarchy/find.js +8 -0
  144. package/esm/d3-hierarchy2/hierarchy/index.d.ts +3 -0
  145. package/esm/d3-hierarchy2/hierarchy/index.js +78 -0
  146. package/esm/d3-hierarchy2/hierarchy/iterator.d.ts +1 -0
  147. package/esm/d3-hierarchy2/hierarchy/iterator.js +14 -0
  148. package/esm/d3-hierarchy2/hierarchy/leaves.d.ts +1 -0
  149. package/esm/d3-hierarchy2/hierarchy/leaves.js +9 -0
  150. package/esm/d3-hierarchy2/hierarchy/links.d.ts +1 -0
  151. package/esm/d3-hierarchy2/hierarchy/links.js +9 -0
  152. package/esm/d3-hierarchy2/hierarchy/path.d.ts +1 -0
  153. package/esm/d3-hierarchy2/hierarchy/path.js +26 -0
  154. package/esm/d3-hierarchy2/hierarchy/sort.d.ts +1 -0
  155. package/esm/d3-hierarchy2/hierarchy/sort.js +7 -0
  156. package/esm/d3-hierarchy2/hierarchy/sum.d.ts +1 -0
  157. package/esm/d3-hierarchy2/hierarchy/sum.js +8 -0
  158. package/esm/d3-hierarchy2/index.d.ts +15 -0
  159. package/esm/d3-hierarchy2/index.js +15 -0
  160. package/esm/d3-hierarchy2/lcg.d.ts +1 -0
  161. package/esm/d3-hierarchy2/lcg.js +7 -0
  162. package/esm/d3-hierarchy2/pack/enclose.d.ts +10 -0
  163. package/esm/d3-hierarchy2/pack/enclose.js +84 -0
  164. package/esm/d3-hierarchy2/pack/index.d.ts +7 -0
  165. package/esm/d3-hierarchy2/pack/index.js +68 -0
  166. package/esm/d3-hierarchy2/pack/siblings.d.ts +2 -0
  167. package/esm/d3-hierarchy2/pack/siblings.js +94 -0
  168. package/esm/d3-hierarchy2/partition.d.ts +6 -0
  169. package/esm/d3-hierarchy2/partition.js +42 -0
  170. package/esm/d3-hierarchy2/stratify.d.ts +9 -0
  171. package/esm/d3-hierarchy2/stratify.js +115 -0
  172. package/esm/d3-hierarchy2/tree.d.ts +8 -0
  173. package/esm/d3-hierarchy2/tree.js +153 -0
  174. package/esm/d3-hierarchy2/treemap/binary.d.ts +1 -0
  175. package/esm/d3-hierarchy2/treemap/binary.js +36 -0
  176. package/esm/d3-hierarchy2/treemap/dice.d.ts +1 -0
  177. package/esm/d3-hierarchy2/treemap/dice.js +7 -0
  178. package/esm/d3-hierarchy2/treemap/index.d.ts +17 -0
  179. package/esm/d3-hierarchy2/treemap/index.js +72 -0
  180. package/esm/d3-hierarchy2/treemap/resquarify.d.ts +5 -0
  181. package/esm/d3-hierarchy2/treemap/resquarify.js +28 -0
  182. package/esm/d3-hierarchy2/treemap/round.d.ts +1 -0
  183. package/esm/d3-hierarchy2/treemap/round.js +6 -0
  184. package/esm/d3-hierarchy2/treemap/slice.d.ts +1 -0
  185. package/esm/d3-hierarchy2/treemap/slice.js +7 -0
  186. package/esm/d3-hierarchy2/treemap/sliceDice.d.ts +1 -0
  187. package/esm/d3-hierarchy2/treemap/sliceDice.js +5 -0
  188. package/esm/d3-hierarchy2/treemap/squarify.d.ts +11 -0
  189. package/esm/d3-hierarchy2/treemap/squarify.js +46 -0
  190. package/esm/index.d.ts +1 -1
  191. package/esm/index.js +19 -22
  192. package/esm/shared/MultiVariantBaseModel.d.ts +1103 -117
  193. package/esm/shared/MultiVariantBaseModel.js +231 -65
  194. package/esm/shared/SharedVariantConfigSchema.d.ts +2 -40
  195. package/esm/shared/SharedVariantConfigSchema.js +1 -46
  196. package/esm/shared/components/AddFiltersDialog.d.ts +2 -3
  197. package/esm/shared/components/AddFiltersDialog.js +20 -28
  198. package/esm/shared/components/{ui/SetColorDialog.d.ts → BaseSetColorDialog.d.ts} +2 -1
  199. package/esm/shared/components/BaseSetColorDialog.js +61 -0
  200. package/esm/shared/components/ClearTreeWarningDialog.d.ts +4 -0
  201. package/esm/shared/components/ClearTreeWarningDialog.js +9 -0
  202. package/esm/shared/components/MAFFilterDialog.d.ts +2 -3
  203. package/esm/shared/components/MAFFilterDialog.js +4 -8
  204. package/esm/shared/components/MultiVariantBaseDisplayComponent.d.ts +1 -1
  205. package/esm/shared/components/MultiVariantBaseDisplayComponent.js +8 -17
  206. package/esm/shared/components/MultiVariantClusterDialog/ClusterDialog.d.ts +1 -1
  207. package/esm/shared/components/MultiVariantClusterDialog/ClusterDialog.js +3 -3
  208. package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.d.ts +1 -1
  209. package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.js +9 -14
  210. package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogManual.d.ts +1 -1
  211. package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogManual.js +11 -15
  212. package/esm/shared/components/MultiVariantClusterDialog/types.d.ts +3 -2
  213. package/esm/shared/components/MultiVariantColorLegend.d.ts +1 -1
  214. package/esm/shared/components/MultiVariantColorLegend.js +22 -12
  215. package/esm/shared/components/MultiVariantCrosshairs.d.ts +4 -2
  216. package/esm/shared/components/MultiVariantCrosshairs.js +31 -23
  217. package/esm/shared/components/MultiVariantLegendBar.d.ts +4 -4
  218. package/esm/shared/components/MultiVariantLegendBar.js +24 -22
  219. package/esm/shared/components/MultiVariantLegendBarWrapper.d.ts +7 -0
  220. package/esm/shared/components/MultiVariantLegendBarWrapper.js +18 -0
  221. package/esm/shared/components/MultiVariantTooltip.d.ts +5 -6
  222. package/esm/shared/components/MultiVariantTooltip.js +35 -17
  223. package/esm/shared/components/ScrollableVariantContainer.d.ts +8 -0
  224. package/esm/shared/components/ScrollableVariantContainer.js +23 -0
  225. package/esm/shared/components/SetColorDialog.d.ts +3 -2
  226. package/esm/shared/components/SetColorDialog.js +2 -2
  227. package/esm/shared/components/SetColorDialogBulkEditPanel.d.ts +7 -8
  228. package/esm/shared/components/SetColorDialogBulkEditPanel.js +24 -54
  229. package/esm/shared/components/SetColorDialogRowPalettizer.js +13 -23
  230. package/esm/shared/components/SetRowHeightDialog.d.ts +2 -3
  231. package/esm/shared/components/SourcesDataGrid.d.ts +1 -1
  232. package/esm/shared/components/SourcesDataGrid.js +1 -1
  233. package/esm/shared/components/SourcesGrid.d.ts +1 -1
  234. package/esm/shared/components/SourcesGrid.js +2 -2
  235. package/esm/shared/components/SourcesGridHeader.d.ts +1 -1
  236. package/esm/shared/components/SourcesGridHeader.js +1 -1
  237. package/esm/shared/components/SvgTree.d.ts +5 -0
  238. package/esm/shared/components/SvgTree.js +19 -0
  239. package/esm/shared/components/TreeSidebar.d.ts +5 -0
  240. package/esm/shared/components/TreeSidebar.js +121 -0
  241. package/esm/shared/components/types.d.ts +43 -0
  242. package/esm/shared/components/types.js +1 -0
  243. package/esm/shared/constants.d.ts +8 -2
  244. package/esm/shared/constants.js +11 -2
  245. package/esm/shared/drawAlleleCount.d.ts +2 -1
  246. package/esm/shared/drawAlleleCount.js +50 -16
  247. package/esm/shared/drawPhased.js +11 -12
  248. package/{dist → esm/shared}/getMultiVariantFeaturesAutorun.d.ts +5 -4
  249. package/esm/{getMultiVariantFeaturesAutorun.js → shared/getMultiVariantFeaturesAutorun.js} +9 -2
  250. package/esm/{getMultiVariantSourcesAutorun.d.ts → shared/getMultiVariantSourcesAutorun.d.ts} +4 -3
  251. package/esm/{getMultiVariantSourcesAutorun.js → shared/getMultiVariantSourcesAutorun.js} +10 -2
  252. package/esm/shared/getSources.d.ts +1 -1
  253. package/esm/shared/getSources.js +2 -2
  254. package/esm/shared/hooks/useMouseTracking.d.ts +6 -0
  255. package/esm/shared/hooks/useMouseTracking.js +34 -0
  256. package/esm/shared/makeSidebarSvg.d.ts +9 -0
  257. package/esm/shared/makeSidebarSvg.js +9 -0
  258. package/esm/shared/minorAlleleFrequencyUtils.d.ts +6 -5
  259. package/esm/shared/minorAlleleFrequencyUtils.js +37 -38
  260. package/esm/shared/setupMultiVariantAutoruns.d.ts +2 -0
  261. package/esm/shared/setupMultiVariantAutoruns.js +8 -0
  262. package/esm/shared/treeDrawingAutorun.d.ts +16 -0
  263. package/esm/shared/treeDrawingAutorun.js +71 -0
  264. package/esm/shared/types.d.ts +15 -0
  265. package/package.json +38 -39
  266. package/dist/ChordVariantDisplay/index.d.ts +0 -2
  267. package/dist/ChordVariantDisplay/index.js +0 -25
  268. package/dist/ChordVariantDisplay/models/configSchema.d.ts +0 -12
  269. package/dist/ChordVariantDisplay/models/configSchema.js +0 -15
  270. package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +0 -115
  271. package/dist/ChordVariantDisplay/models/stateModelFactory.js +0 -35
  272. package/dist/LinearVariantDisplay/configSchema.d.ts +0 -34
  273. package/dist/LinearVariantDisplay/configSchema.js +0 -12
  274. package/dist/LinearVariantDisplay/index.d.ts +0 -2
  275. package/dist/LinearVariantDisplay/index.js +0 -24
  276. package/dist/LinearVariantDisplay/model.d.ts +0 -278
  277. package/dist/LinearVariantDisplay/model.js +0 -37
  278. package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts +0 -5
  279. package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.js +0 -29
  280. package/dist/MultiLinearVariantDisplay/configSchema.d.ts +0 -80
  281. package/dist/MultiLinearVariantDisplay/configSchema.js +0 -30
  282. package/dist/MultiLinearVariantDisplay/index.d.ts +0 -2
  283. package/dist/MultiLinearVariantDisplay/index.js +0 -57
  284. package/dist/MultiLinearVariantDisplay/model.d.ts +0 -422
  285. package/dist/MultiLinearVariantDisplay/model.js +0 -82
  286. package/dist/MultiLinearVariantDisplay/renderSvg.d.ts +0 -3
  287. package/dist/MultiLinearVariantDisplay/renderSvg.js +0 -15
  288. package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +0 -6
  289. package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js +0 -83
  290. package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts +0 -5
  291. package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js +0 -31
  292. package/dist/MultiLinearVariantMatrixDisplay/configSchema.d.ts +0 -37
  293. package/dist/MultiLinearVariantMatrixDisplay/configSchema.js +0 -22
  294. package/dist/MultiLinearVariantMatrixDisplay/index.d.ts +0 -2
  295. package/dist/MultiLinearVariantMatrixDisplay/index.js +0 -24
  296. package/dist/MultiLinearVariantMatrixDisplay/model.d.ts +0 -431
  297. package/dist/MultiLinearVariantMatrixDisplay/model.js +0 -125
  298. package/dist/MultiLinearVariantMatrixDisplay/renderSvg.d.ts +0 -3
  299. package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js +0 -17
  300. package/dist/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.d.ts +0 -37
  301. package/dist/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.js +0 -87
  302. package/dist/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts +0 -8
  303. package/dist/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js +0 -41
  304. package/dist/MultiLinearVariantMatrixRenderer/configSchema.d.ts +0 -2
  305. package/dist/MultiLinearVariantMatrixRenderer/configSchema.js +0 -6
  306. package/dist/MultiLinearVariantMatrixRenderer/index.d.ts +0 -2
  307. package/dist/MultiLinearVariantMatrixRenderer/index.js +0 -20
  308. package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts +0 -14
  309. package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js +0 -154
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  523. package/esm/VariantFeatureWidget/VariantSampleGrid/util.d.ts +0 -1
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  525. package/esm/extensionPoints.d.ts +0 -2
  526. package/esm/getMultiVariantFeaturesAutorun.d.ts +0 -18
  527. package/esm/shared/SharedVariantMixin.d.ts +0 -325
  528. package/esm/shared/SharedVariantMixin.js +0 -55
  529. package/esm/shared/components/ui/SetColorDialog.js +0 -45
  530. package/esm/shared/components/ui/SetColorDialogBulkEditPanel.d.ts +0 -10
  531. package/esm/shared/components/ui/SetColorDialogBulkEditPanel.js +0 -81
  532. package/esm/shared/components/ui/SetColorDialogHelpfulTips.d.ts +0 -1
  533. package/esm/shared/components/ui/SetColorDialogHelpfulTips.js +0 -4
  534. package/esm/shared/components/ui/SetColorDialogRowPalettizer.d.ts +0 -10
  535. package/esm/shared/components/ui/SetColorDialogRowPalettizer.js +0 -38
  536. package/esm/shared/findSecondLargestNumber.d.ts +0 -0
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  538. package/esm/shared/util.d.ts +0 -2
  539. package/esm/shared/util.js +0 -17
@@ -1,48 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.getMultiVariantFeaturesAutorun = getMultiVariantFeaturesAutorun;
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 getMultiVariantFeaturesAutorun(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 || !self.statsReadyAndRegionNotTooLarge) {
15
- return;
16
- }
17
- const stopToken = (0, stopToken_1.createStopToken)();
18
- self.setSimplifiedFeaturesLoading(stopToken);
19
- const { rpcManager } = (0, util_1.getSession)(self);
20
- const { lengthCutoffFilter, sources, minorAlleleFrequencyFilter, adapterConfig, } = self;
21
- if (sources) {
22
- const sessionId = (0, tracks_1.getRpcSessionId)(self);
23
- const { sampleInfo, hasPhased, features } = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
24
- regions: view.dynamicBlocks.contentBlocks,
25
- sources,
26
- minorAlleleFrequencyFilter,
27
- lengthCutoffFilter,
28
- sessionId,
29
- adapterConfig,
30
- stopToken,
31
- }));
32
- if ((0, mobx_state_tree_1.isAlive)(self)) {
33
- self.setHasPhased(hasPhased);
34
- self.setSampleInfo(sampleInfo);
35
- self.setFeatures(features.map(f => new util_1.SimpleFeature(f)));
36
- }
37
- }
38
- }
39
- catch (e) {
40
- console.error(e);
41
- if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
42
- (0, util_1.getSession)(self).notifyError(`${e}`, e);
43
- }
44
- }
45
- }, {
46
- delay: 1000,
47
- }));
48
- }
@@ -1,11 +0,0 @@
1
- import type { Source } from './shared/types';
2
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
- export declare function getMultiVariantSourcesAutorun(self: {
4
- configuration: AnyConfigurationModel;
5
- adapterConfig: AnyConfigurationModel;
6
- adapterProps: () => Record<string, unknown>;
7
- setSourcesLoading: (aborter: string) => void;
8
- setError: (error: unknown) => void;
9
- setMessage: (str: string) => void;
10
- setSources: (sources: Source[]) => void;
11
- }): void;
@@ -1,38 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.getMultiVariantSourcesAutorun = getMultiVariantSourcesAutorun;
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 getMultiVariantSourcesAutorun(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 stopToken = (0, stopToken_1.createStopToken)();
20
- self.setSourcesLoading(stopToken);
21
- const sessionId = (0, tracks_1.getRpcSessionId)(self);
22
- const sources = (await rpcManager.call(sessionId, 'MultiVariantGetSources', {
23
- sessionId,
24
- adapterConfig,
25
- stopToken,
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
- }, { delay: 1000 }));
38
- }
package/dist/index.d.ts DELETED
@@ -1,7 +0,0 @@
1
- import Plugin from '@jbrowse/core/Plugin';
2
- import type PluginManager from '@jbrowse/core/PluginManager';
3
- export default class VariantsPlugin extends Plugin {
4
- name: string;
5
- install(pluginManager: PluginManager): void;
6
- }
7
- export { default as VcfFeature } from './VcfFeature';
package/dist/index.js DELETED
@@ -1,52 +0,0 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.VcfFeature = void 0;
7
- const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
8
- const ChordVariantDisplay_1 = __importDefault(require("./ChordVariantDisplay"));
9
- const LinearVariantDisplay_1 = __importDefault(require("./LinearVariantDisplay"));
10
- const MultiLinearVariantDisplay_1 = __importDefault(require("./MultiLinearVariantDisplay"));
11
- const MultiLinearVariantMatrixDisplay_1 = __importDefault(require("./MultiLinearVariantMatrixDisplay"));
12
- const MultiLinearVariantMatrixRenderer_1 = __importDefault(require("./MultiLinearVariantMatrixRenderer"));
13
- const MultiLinearVariantRenderer_1 = __importDefault(require("./MultiLinearVariantRenderer"));
14
- const SplitVcfTabixAdapter_1 = __importDefault(require("./SplitVcfTabixAdapter"));
15
- const StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
16
- const VariantFeatureWidget_1 = __importDefault(require("./VariantFeatureWidget"));
17
- const MultiVariantClusterGenotypeMatrix_1 = require("./VariantRPC/MultiVariantClusterGenotypeMatrix");
18
- const MultiVariantGetGenotypeMatrix_1 = require("./VariantRPC/MultiVariantGetGenotypeMatrix");
19
- const MultiVariantGetSimplifiedFeatures_1 = require("./VariantRPC/MultiVariantGetSimplifiedFeatures");
20
- const MultiVariantGetSources_1 = require("./VariantRPC/MultiVariantGetSources");
21
- const VariantTrack_1 = __importDefault(require("./VariantTrack"));
22
- const VcfAdapter_1 = __importDefault(require("./VcfAdapter"));
23
- const VcfTabixAdapter_1 = __importDefault(require("./VcfTabixAdapter"));
24
- const extensionPoints_1 = __importDefault(require("./extensionPoints"));
25
- class VariantsPlugin extends Plugin_1.default {
26
- constructor() {
27
- super(...arguments);
28
- this.name = 'VariantsPlugin';
29
- }
30
- install(pluginManager) {
31
- (0, VcfAdapter_1.default)(pluginManager);
32
- (0, VcfTabixAdapter_1.default)(pluginManager);
33
- (0, SplitVcfTabixAdapter_1.default)(pluginManager);
34
- (0, VariantFeatureWidget_1.default)(pluginManager);
35
- (0, VariantTrack_1.default)(pluginManager);
36
- (0, extensionPoints_1.default)(pluginManager);
37
- (0, LinearVariantDisplay_1.default)(pluginManager);
38
- (0, MultiLinearVariantMatrixDisplay_1.default)(pluginManager);
39
- (0, MultiLinearVariantDisplay_1.default)(pluginManager);
40
- (0, MultiLinearVariantRenderer_1.default)(pluginManager);
41
- (0, MultiLinearVariantMatrixRenderer_1.default)(pluginManager);
42
- (0, StructuralVariantChordRenderer_1.default)(pluginManager);
43
- (0, ChordVariantDisplay_1.default)(pluginManager);
44
- pluginManager.addRpcMethod(() => new MultiVariantGetSources_1.MultiVariantGetSources(pluginManager));
45
- pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix_1.MultiVariantGetGenotypeMatrix(pluginManager));
46
- pluginManager.addRpcMethod(() => new MultiVariantClusterGenotypeMatrix_1.MultiVariantClusterGenotypeMatrix(pluginManager));
47
- pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures_1.MultiVariantGetSimplifiedFeatures(pluginManager));
48
- }
49
- }
50
- exports.default = VariantsPlugin;
51
- var VcfFeature_1 = require("./VcfFeature");
52
- Object.defineProperty(exports, "VcfFeature", { enumerable: true, get: function () { return __importDefault(VcfFeature_1).default; } });
@@ -1,413 +0,0 @@
1
- import type { SampleInfo, Source } from './types';
2
- import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
3
- import type { Feature } from '@jbrowse/core/util';
4
- import type { Instance } from 'mobx-state-tree';
5
- export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
6
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
7
- type: import("mobx-state-tree").ISimpleType<string>;
8
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
9
- } & {
10
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
11
- } & {
12
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
14
- } & {
15
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
16
- key: import("mobx-state-tree").ISimpleType<string>;
17
- region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
18
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
19
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
20
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
21
- }, {
22
- stopToken: string | undefined;
23
- filled: boolean;
24
- reactElement: React.ReactElement | undefined;
25
- features: Map<string, Feature> | undefined;
26
- layout: any;
27
- status: string;
28
- error: unknown;
29
- message: string | undefined;
30
- maxHeightReached: boolean;
31
- ReactComponent: ({ model, }: {
32
- model: {
33
- error?: unknown;
34
- reload: () => void;
35
- message: React.ReactNode;
36
- filled?: boolean;
37
- status?: string;
38
- reactElement?: React.ReactElement;
39
- };
40
- }) => import("react/jsx-runtime").JSX.Element | undefined;
41
- renderProps: any;
42
- } & {
43
- doReload(): void;
44
- afterAttach(): void;
45
- setStatus(message: string): void;
46
- setLoading(newStopToken: string): void;
47
- setMessage(messageText: string): void;
48
- setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
49
- setError(error: unknown): void;
50
- reload(): void;
51
- beforeDestroy(): void;
52
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
53
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
54
- maxFeatureScreenDensity: {
55
- type: string;
56
- description: string;
57
- defaultValue: number;
58
- };
59
- fetchSizeLimit: {
60
- type: string;
61
- defaultValue: number;
62
- description: string;
63
- };
64
- height: {
65
- type: string;
66
- defaultValue: number;
67
- description: string;
68
- };
69
- mouseover: {
70
- type: string;
71
- description: string;
72
- defaultValue: string;
73
- contextVariable: string[];
74
- };
75
- jexlFilters: {
76
- type: string;
77
- description: string;
78
- defaultValue: never[];
79
- };
80
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
81
- } & {
82
- type: import("mobx-state-tree").ISimpleType<"LinearBareDisplay">;
83
- configuration: AnyConfigurationSchemaType;
84
- } & {
85
- type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
86
- layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
87
- configuration: AnyConfigurationSchemaType;
88
- minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
89
- showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
90
- renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
91
- rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
92
- autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
93
- lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
94
- jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
95
- referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
96
- }, {
97
- rendererTypeName: string;
98
- error: unknown;
99
- message: string | undefined;
100
- } & {
101
- readonly RenderingComponent: React.FC<{
102
- model: {
103
- id: string;
104
- type: string;
105
- rpcDriverName: string | undefined;
106
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
107
- rendererTypeName: string;
108
- error: unknown;
109
- message: string | undefined;
110
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
111
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
112
- type: import("mobx-state-tree").ISimpleType<string>;
113
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
114
- }, {
115
- rendererTypeName: string;
116
- error: unknown;
117
- message: string | undefined;
118
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
119
- onHorizontalScroll?: () => void;
120
- blockState?: Record<string, any>;
121
- }>;
122
- readonly DisplayBlurb: React.FC<{
123
- model: {
124
- id: string;
125
- type: string;
126
- rpcDriverName: string | undefined;
127
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
128
- rendererTypeName: string;
129
- error: unknown;
130
- message: string | undefined;
131
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
132
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
133
- type: import("mobx-state-tree").ISimpleType<string>;
134
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
135
- }, {
136
- rendererTypeName: string;
137
- error: unknown;
138
- message: string | undefined;
139
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
140
- }> | null;
141
- readonly adapterConfig: any;
142
- readonly parentTrack: any;
143
- renderProps(): any;
144
- readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
145
- readonly DisplayMessageComponent: undefined | React.FC<any>;
146
- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
147
- readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
148
- regionCannotBeRendered(): null;
149
- } & {
150
- setMessage(arg?: string): void;
151
- setError(error?: unknown): void;
152
- setRpcDriverName(rpcDriverName: string): void;
153
- reload(): void;
154
- } & {
155
- scrollTop: number;
156
- } & {
157
- readonly height: number;
158
- } & {
159
- setScrollTop(scrollTop: number): void;
160
- setHeight(displayHeight: number): number;
161
- resizeHeight(distance: number): number;
162
- } & {
163
- featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
164
- featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
165
- currStatsBpPerPx: number;
166
- } & {
167
- readonly currentBytesRequested: number;
168
- readonly currentFeatureScreenDensity: number;
169
- readonly maxFeatureScreenDensity: any;
170
- readonly featureDensityStatsReady: boolean;
171
- readonly maxAllowableBytes: number;
172
- } & {
173
- afterAttach(): void;
174
- } & {
175
- setCurrStatsBpPerPx(n: number): void;
176
- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
177
- getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
178
- setFeatureDensityStatsP(arg: any): void;
179
- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
180
- clearFeatureDensityStats(): void;
181
- } & {
182
- readonly regionTooLarge: boolean;
183
- readonly regionTooLargeReason: string;
184
- } & {
185
- readonly statsReadyAndRegionNotTooLarge: boolean;
186
- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
187
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
188
- } & {
189
- mouseoverExtraInformation: string | undefined;
190
- featureIdUnderMouse: undefined | string;
191
- contextMenuFeature: undefined | Feature;
192
- } & {
193
- readonly DisplayMessageComponent: undefined | React.FC<any>;
194
- readonly blockType: "staticBlocks" | "dynamicBlocks";
195
- readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
196
- } & {
197
- readonly renderDelay: number;
198
- readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
199
- readonly selectedFeatureId: string | undefined;
200
- copyInfoToClipboard(feature: Feature): void;
201
- } & {
202
- readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
203
- readonly featureUnderMouse: Feature | undefined;
204
- readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
205
- label?: string;
206
- description?: string;
207
- refName: string;
208
- }]>;
209
- getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
210
- getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
211
- label?: string;
212
- description?: string;
213
- refName: string;
214
- }]) | undefined;
215
- searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
216
- label?: string;
217
- description?: string;
218
- refName: string;
219
- }]) | undefined;
220
- } & {
221
- addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
222
- deleteBlock(key: string): void;
223
- selectFeature(feature: Feature): void;
224
- navToFeature(feature: Feature): void;
225
- clearFeatureSelection(): void;
226
- setFeatureIdUnderMouse(feature?: string): void;
227
- setContextMenuFeature(feature?: Feature): void;
228
- setMouseoverExtraInformation(extra?: string): void;
229
- } & {
230
- reload(): Promise<void>;
231
- } & {
232
- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
233
- contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
234
- renderProps(): any;
235
- } & {
236
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
237
- afterAttach(): void;
238
- } & {
239
- readonly rendererConfig: {
240
- [x: string]: any;
241
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
242
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
243
- [x: string]: any;
244
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
245
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
246
- [x: string]: any;
247
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
248
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
249
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
250
- readonly rendererTypeName: any;
251
- } & {
252
- renderProps(): any;
253
- } & {
254
- sourcesLoadingStopToken: string | undefined;
255
- simplifiedFeaturesStopToken: string | undefined;
256
- featureUnderMouseVolatile: Feature | undefined;
257
- sourcesVolatile: Source[] | undefined;
258
- featuresVolatile: Feature[] | undefined;
259
- hasPhased: boolean;
260
- sampleInfo: undefined | Record<string, SampleInfo>;
261
- hoveredGenotype: {
262
- genotype: string;
263
- name: string;
264
- } | undefined;
265
- } & {
266
- setJexlFilters(f?: string[]): void;
267
- setRowHeight(arg: number): void;
268
- setHoveredGenotype(arg?: {
269
- genotype: string;
270
- name: string;
271
- }): void;
272
- setFeatures(f: Feature[]): void;
273
- setLayout(layout: Source[]): void;
274
- clearLayout(): void;
275
- setSourcesLoading(str: string): void;
276
- setSimplifiedFeaturesLoading(str: string): void;
277
- setSources(sources: Source[]): void;
278
- setMafFilter(arg: number): void;
279
- setShowSidebarLabels(arg: boolean): void;
280
- setPhasedMode(arg: string): void;
281
- setAutoHeight(arg: boolean): void;
282
- setHasPhased(arg: boolean): void;
283
- setSampleInfo(arg: Record<string, SampleInfo>): void;
284
- setReferenceDrawingMode(arg: string): void;
285
- } & {
286
- readonly activeFilters: any;
287
- readonly preSources: Source[] | undefined;
288
- readonly sourcesWithoutLayout: {
289
- label: string;
290
- id: string;
291
- baseUri?: string;
292
- name: string;
293
- color?: string;
294
- group?: string;
295
- HP?: number;
296
- }[] | undefined;
297
- readonly sources: {
298
- label: string;
299
- id: string;
300
- baseUri?: string;
301
- name: string;
302
- color?: string;
303
- group?: string;
304
- HP?: number;
305
- }[] | undefined;
306
- } & {
307
- readonly sourceMap: {
308
- [k: string]: {
309
- label: string;
310
- id: string;
311
- baseUri?: string;
312
- name: string;
313
- color?: string;
314
- group?: string;
315
- HP?: number;
316
- };
317
- } | undefined;
318
- readonly rowHeight: number;
319
- adapterProps(): any;
320
- trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
321
- label: string;
322
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
323
- muiName: string;
324
- };
325
- type: string;
326
- checked: boolean;
327
- onClick: () => void;
328
- subMenu?: undefined;
329
- } | {
330
- label: string;
331
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
332
- muiName: string;
333
- };
334
- subMenu: ({
335
- label: string;
336
- disabled: boolean;
337
- onClick: () => void;
338
- type?: undefined;
339
- checked?: undefined;
340
- } | {
341
- label: string;
342
- type: string;
343
- checked: boolean;
344
- onClick: () => void;
345
- disabled?: undefined;
346
- })[];
347
- type?: undefined;
348
- checked?: undefined;
349
- onClick?: undefined;
350
- } | {
351
- label: string;
352
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
353
- muiName: string;
354
- };
355
- subMenu: ({
356
- label: string;
357
- type: string;
358
- checked: boolean;
359
- onClick: () => void;
360
- disabled?: undefined;
361
- } | {
362
- label: string;
363
- disabled: boolean;
364
- checked: boolean;
365
- type: string;
366
- onClick: () => void;
367
- })[];
368
- type?: undefined;
369
- checked?: undefined;
370
- onClick?: undefined;
371
- } | {
372
- label: string;
373
- type: string;
374
- subMenu: {
375
- label: string;
376
- type: string;
377
- checked: boolean;
378
- onClick: () => void;
379
- }[];
380
- icon?: undefined;
381
- checked?: undefined;
382
- onClick?: undefined;
383
- } | {
384
- label: string;
385
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
386
- muiName: string;
387
- };
388
- subMenu: {
389
- label: string;
390
- onClick: () => void;
391
- }[];
392
- type?: undefined;
393
- checked?: undefined;
394
- onClick?: undefined;
395
- } | {
396
- label: string;
397
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
398
- muiName: string;
399
- };
400
- onClick: () => void;
401
- type?: undefined;
402
- checked?: undefined;
403
- subMenu?: undefined;
404
- })[];
405
- } & {
406
- readonly canDisplayLabels: boolean;
407
- readonly totalHeight: number;
408
- readonly featuresReady: boolean;
409
- } & {
410
- renderProps(): any;
411
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
412
- export type MultiVariantBaseStateModel = ReturnType<typeof MultiVariantBaseModelF>;
413
- export type MultiVariantBaseModel = Instance<MultiVariantBaseStateModel>;