@jbrowse/plugin-alignments 3.7.0 → 4.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (669) hide show
  1. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +1 -1
  2. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +9 -9
  3. package/esm/AlignmentsFeatureDetail/BreakpointSplitViewChoiceDialog.d.ts +1 -0
  4. package/esm/AlignmentsFeatureDetail/BreakpointSplitViewChoiceDialog.js +1 -0
  5. package/esm/AlignmentsFeatureDetail/Flags.js +1 -1
  6. package/esm/AlignmentsFeatureDetail/Formatter.js +2 -2
  7. package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts +2 -2
  8. package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js +7 -18
  9. package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts +1 -1
  10. package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js +19 -37
  11. package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts +1 -1
  12. package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js +1 -1
  13. package/esm/AlignmentsFeatureDetail/PairLink.d.ts +1 -1
  14. package/esm/AlignmentsFeatureDetail/PairLink.js +1 -1
  15. package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts +1 -1
  16. package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js +2 -2
  17. package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts +1 -1
  18. package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js +5 -4
  19. package/esm/AlignmentsFeatureDetail/configSchema.d.ts +1 -1
  20. package/esm/AlignmentsFeatureDetail/getSAFeatures.d.ts +1 -1
  21. package/esm/AlignmentsFeatureDetail/getSAFeatures.js +18 -17
  22. package/esm/AlignmentsFeatureDetail/index.js +3 -3
  23. package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +6 -7
  24. package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.js +3 -6
  25. package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts +37 -37
  26. package/esm/AlignmentsFeatureDetail/stateModelFactory.js +1 -1
  27. package/esm/AlignmentsFeatureDetail/util.d.ts +1 -1
  28. package/esm/AlignmentsFeatureDetail/util.js +1 -2
  29. package/esm/AlignmentsTrack/configSchemaF.d.ts +16 -11
  30. package/esm/AlignmentsTrack/index.js +14 -2
  31. package/esm/BamAdapter/BamAdapter.d.ts +15 -26
  32. package/esm/BamAdapter/BamAdapter.js +84 -124
  33. package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +17 -10
  34. package/esm/BamAdapter/BamSlightlyLazyFeature.js +162 -45
  35. package/esm/BamAdapter/configSchema.d.ts +5 -10
  36. package/esm/BamAdapter/configSchema.js +2 -7
  37. package/esm/BamAdapter/forEachMismatchNumeric.d.ts +2 -0
  38. package/esm/BamAdapter/forEachMismatchNumeric.js +207 -0
  39. package/esm/BamAdapter/index.js +2 -2
  40. package/esm/CramAdapter/CramAdapter.d.ts +10 -32
  41. package/esm/CramAdapter/CramAdapter.js +92 -143
  42. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +6 -2
  43. package/esm/CramAdapter/CramSlightlyLazyFeature.js +140 -19
  44. package/esm/CramAdapter/CramTestAdapters.d.ts +3 -2
  45. package/esm/CramAdapter/CramTestAdapters.js +8 -3
  46. package/esm/CramAdapter/configSchema.d.ts +2 -7
  47. package/esm/CramAdapter/configSchema.js +1 -6
  48. package/esm/CramAdapter/const.d.ts +12 -0
  49. package/esm/CramAdapter/const.js +12 -0
  50. package/esm/CramAdapter/index.js +2 -2
  51. package/esm/CramAdapter/readFeaturesToNumericCIGAR.d.ts +4 -0
  52. package/esm/CramAdapter/readFeaturesToNumericCIGAR.js +112 -0
  53. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +5 -9
  54. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js +13 -15
  55. package/esm/HtsgetBamAdapter/configSchema.d.ts +2 -7
  56. package/esm/HtsgetBamAdapter/configSchema.js +0 -5
  57. package/esm/HtsgetBamAdapter/index.js +2 -2
  58. package/esm/LinearAlignmentsDisplay/alignmentsModel.d.ts +9 -9
  59. package/esm/LinearAlignmentsDisplay/alignmentsModel.js +2 -2
  60. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +1 -1
  61. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +13 -7
  62. package/esm/LinearAlignmentsDisplay/configSchema.d.ts +3 -3
  63. package/esm/LinearAlignmentsDisplay/index.js +4 -4
  64. package/esm/LinearAlignmentsDisplay/model.d.ts +173 -48
  65. package/esm/LinearAlignmentsDisplay/model.js +60 -62
  66. package/esm/LinearAlignmentsDisplay/renderSvg.d.ts +14 -0
  67. package/esm/LinearAlignmentsDisplay/renderSvg.js +12 -0
  68. package/esm/LinearAlignmentsDisplay/util.js +2 -2
  69. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +1247 -137
  70. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +120 -89
  71. package/esm/LinearPileupDisplay/components/ColorByTagDialog.js +1 -1
  72. package/esm/LinearPileupDisplay/components/GroupByDialog.d.ts +1 -1
  73. package/esm/LinearPileupDisplay/components/GroupByDialog.js +4 -4
  74. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +1 -1
  75. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +2 -3
  76. package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.js +1 -1
  77. package/esm/LinearPileupDisplay/components/SortByTagDialog.js +1 -1
  78. package/esm/LinearPileupDisplay/configSchema.d.ts +8 -8
  79. package/esm/LinearPileupDisplay/configSchema.js +2 -2
  80. package/esm/LinearPileupDisplay/doAfterAttach.d.ts +4 -3
  81. package/esm/LinearPileupDisplay/doAfterAttach.js +17 -26
  82. package/esm/LinearPileupDisplay/index.d.ts +3 -3
  83. package/esm/LinearPileupDisplay/index.js +6 -5
  84. package/esm/LinearPileupDisplay/model.d.ts +1289 -169
  85. package/esm/LinearPileupDisplay/model.js +71 -154
  86. package/esm/LinearPileupDisplay/sharedDoAfterAttach.d.ts +10 -0
  87. package/esm/LinearPileupDisplay/sharedDoAfterAttach.js +28 -0
  88. package/esm/LinearReadArcsDisplay/afterAttachRPC.d.ts +2 -0
  89. package/esm/LinearReadArcsDisplay/afterAttachRPC.js +21 -0
  90. package/{dist/shared → esm/LinearReadArcsDisplay}/chainToSimpleFeature.d.ts +1 -1
  91. package/esm/{shared → LinearReadArcsDisplay}/chainToSimpleFeature.js +2 -2
  92. package/esm/LinearReadArcsDisplay/components/{ReactComponent.d.ts → LinearReadArcsReactComponent.d.ts} +1 -1
  93. package/esm/LinearReadArcsDisplay/components/{ReactComponent.js → LinearReadArcsReactComponent.js} +4 -4
  94. package/esm/LinearReadArcsDisplay/configSchema.d.ts +5 -5
  95. package/esm/LinearReadArcsDisplay/configSchema.js +1 -1
  96. package/esm/LinearReadArcsDisplay/index.js +4 -3
  97. package/esm/LinearReadArcsDisplay/model.d.ts +221 -58
  98. package/esm/LinearReadArcsDisplay/model.js +73 -56
  99. package/esm/LinearReadArcsDisplay/renderSvg.d.ts +3 -0
  100. package/esm/LinearReadArcsDisplay/renderSvg.js +39 -0
  101. package/esm/LinearReadCloudDisplay/afterAttachRPC.d.ts +2 -0
  102. package/esm/LinearReadCloudDisplay/afterAttachRPC.js +56 -0
  103. package/esm/LinearReadCloudDisplay/components/CloudYScaleBar.d.ts +8 -0
  104. package/esm/LinearReadCloudDisplay/components/CloudYScaleBar.js +27 -0
  105. package/{dist/LinearReadCloudDisplay/components/ReactComponent.d.ts → esm/LinearReadCloudDisplay/components/LinearReadCloudReactComponent.d.ts} +1 -1
  106. package/esm/LinearReadCloudDisplay/components/LinearReadCloudReactComponent.js +252 -0
  107. package/esm/LinearReadCloudDisplay/components/SetFeatureHeightDialog.js +1 -1
  108. package/esm/LinearReadCloudDisplay/configSchema.d.ts +21 -5
  109. package/esm/LinearReadCloudDisplay/configSchema.js +17 -1
  110. package/esm/LinearReadCloudDisplay/index.js +8 -4
  111. package/esm/LinearReadCloudDisplay/model.d.ts +320 -58
  112. package/esm/LinearReadCloudDisplay/model.js +205 -62
  113. package/esm/LinearReadCloudDisplay/renderSvg.d.ts +3 -0
  114. package/esm/LinearReadCloudDisplay/renderSvg.js +47 -0
  115. package/esm/LinearSNPCoverageDisplay/components/ArcTooltipContents.d.ts +4 -0
  116. package/esm/LinearSNPCoverageDisplay/components/ArcTooltipContents.js +6 -0
  117. package/esm/LinearSNPCoverageDisplay/components/FilterArcsByScoreDialog.d.ts +7 -0
  118. package/esm/LinearSNPCoverageDisplay/components/FilterArcsByScoreDialog.js +16 -0
  119. package/esm/LinearSNPCoverageDisplay/components/SNPCoverageDisplayComponent.d.ts +5 -0
  120. package/esm/LinearSNPCoverageDisplay/components/SNPCoverageDisplayComponent.js +9 -0
  121. package/esm/LinearSNPCoverageDisplay/components/SashimiArcs.d.ts +10 -0
  122. package/esm/LinearSNPCoverageDisplay/components/SashimiArcs.js +169 -0
  123. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +9 -3
  124. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +31 -7
  125. package/esm/LinearSNPCoverageDisplay/components/TooltipContents.d.ts +13 -9
  126. package/esm/LinearSNPCoverageDisplay/components/TooltipContents.js +86 -59
  127. package/esm/LinearSNPCoverageDisplay/components/arcUtils.d.ts +18 -0
  128. package/esm/LinearSNPCoverageDisplay/components/arcUtils.js +42 -0
  129. package/esm/LinearSNPCoverageDisplay/components/renderSvg.d.ts +10 -0
  130. package/esm/LinearSNPCoverageDisplay/components/renderSvg.js +32 -0
  131. package/esm/LinearSNPCoverageDisplay/configSchema.d.ts +7 -7
  132. package/esm/LinearSNPCoverageDisplay/configSchema.js +2 -2
  133. package/esm/LinearSNPCoverageDisplay/index.js +5 -4
  134. package/esm/LinearSNPCoverageDisplay/model.d.ts +302 -59
  135. package/esm/LinearSNPCoverageDisplay/model.js +154 -69
  136. package/esm/MismatchParser/cigarToMismatches.d.ts +1 -1
  137. package/esm/MismatchParser/cigarToMismatches.js +6 -9
  138. package/esm/MismatchParser/cigarToMismatches2.d.ts +2 -0
  139. package/{dist/MismatchParser/cigarToMismatches.js → esm/MismatchParser/cigarToMismatches2.js} +23 -28
  140. package/esm/MismatchParser/getNextRefPos.d.ts +1 -1
  141. package/esm/MismatchParser/getNextRefPos.js +13 -11
  142. package/esm/MismatchParser/index.d.ts +6 -3
  143. package/esm/MismatchParser/index.js +49 -11
  144. package/esm/MismatchParser/mdToMismatches.d.ts +1 -1
  145. package/esm/MismatchParser/mdToMismatches.js +87 -53
  146. package/esm/MismatchParser/mdToMismatches2.d.ts +2 -0
  147. package/esm/MismatchParser/mdToMismatches2.js +96 -0
  148. package/esm/ModificationParser/detectSimplexModifications.d.ts +1 -1
  149. package/esm/ModificationParser/getMethBins.d.ts +1 -1
  150. package/esm/ModificationParser/getMethBins.js +5 -5
  151. package/esm/ModificationParser/getModPositions.js +1 -1
  152. package/esm/ModificationParser/getModProbabilities.js +1 -1
  153. package/esm/ModificationParser/getModTypes.js +1 -1
  154. package/esm/PileupRPC/base.js +1 -2
  155. package/esm/PileupRPC/index.js +1 -2
  156. package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +1 -1
  157. package/esm/PileupRPC/methods/GetGlobalValueForTag.js +3 -6
  158. package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +2 -2
  159. package/esm/PileupRPC/methods/GetVisibleModifications.js +5 -8
  160. package/esm/PileupRPC/rpcMethods.d.ts +2 -3
  161. package/esm/PileupRPC/rpcMethods.js +2 -3
  162. package/esm/PileupRenderer/PileupLayoutSession.d.ts +9 -9
  163. package/esm/PileupRenderer/PileupLayoutSession.js +18 -5
  164. package/esm/PileupRenderer/PileupRenderer.d.ts +5 -47
  165. package/esm/PileupRenderer/PileupRenderer.js +25 -67
  166. package/esm/PileupRenderer/colorBy.js +2 -2
  167. package/esm/PileupRenderer/components/PileupRendering.d.ts +5 -5
  168. package/esm/PileupRenderer/components/PileupRendering.js +150 -116
  169. package/esm/PileupRenderer/components/PileupTooltip.d.ts +10 -0
  170. package/esm/PileupRenderer/components/PileupTooltip.js +12 -0
  171. package/esm/PileupRenderer/components/util.d.ts +7 -0
  172. package/esm/PileupRenderer/components/util.js +17 -0
  173. package/esm/PileupRenderer/configSchema.d.ts +14 -4
  174. package/esm/PileupRenderer/configSchema.js +11 -1
  175. package/esm/PileupRenderer/index.js +4 -4
  176. package/esm/PileupRenderer/layoutFeature.d.ts +4 -12
  177. package/esm/PileupRenderer/layoutFeature.js +13 -18
  178. package/esm/PileupRenderer/layoutFeatures.d.ts +2 -2
  179. package/esm/PileupRenderer/layoutFeatures.js +21 -16
  180. package/esm/PileupRenderer/makeImageData.d.ts +20 -17
  181. package/esm/PileupRenderer/makeImageData.js +66 -12
  182. package/esm/PileupRenderer/renderers/cigarUtil.d.ts +18 -0
  183. package/esm/PileupRenderer/renderers/cigarUtil.js +23 -0
  184. package/esm/PileupRenderer/renderers/getAlignmentShapeColor.js +2 -2
  185. package/esm/PileupRenderer/renderers/renderAlignment.d.ts +2 -2
  186. package/esm/PileupRenderer/renderers/renderAlignment.js +28 -32
  187. package/esm/PileupRenderer/renderers/renderAlignmentShape.d.ts +6 -3
  188. package/esm/PileupRenderer/renderers/renderAlignmentShape.js +113 -65
  189. package/esm/PileupRenderer/renderers/renderMethylation.d.ts +8 -6
  190. package/esm/PileupRenderer/renderers/renderMethylation.js +67 -27
  191. package/esm/PileupRenderer/renderers/renderMismatchesCallback.d.ts +32 -0
  192. package/esm/PileupRenderer/renderers/renderMismatchesCallback.js +304 -0
  193. package/esm/PileupRenderer/renderers/renderModifications.d.ts +11 -6
  194. package/esm/PileupRenderer/renderers/renderModifications.js +59 -41
  195. package/esm/PileupRenderer/renderers/renderPerBaseLettering.d.ts +2 -2
  196. package/esm/PileupRenderer/renderers/renderPerBaseLettering.js +38 -18
  197. package/esm/PileupRenderer/renderers/renderPerBaseQuality.d.ts +3 -4
  198. package/esm/PileupRenderer/renderers/renderPerBaseQuality.js +32 -16
  199. package/esm/PileupRenderer/renderers/renderSoftClipping.d.ts +2 -2
  200. package/esm/PileupRenderer/renderers/renderSoftClipping.js +45 -26
  201. package/esm/PileupRenderer/sortUtil.d.ts +2 -2
  202. package/esm/PileupRenderer/sortUtil.js +34 -22
  203. package/esm/PileupRenderer/types.d.ts +32 -7
  204. package/esm/PileupRenderer/types.js +71 -1
  205. package/esm/PileupRenderer/util.d.ts +1 -22
  206. package/esm/PileupRenderer/util.js +12 -38
  207. package/esm/RenderLinearReadArcsDisplayRPC/RenderLinearReadArcsDisplay.d.ts +34 -0
  208. package/esm/RenderLinearReadArcsDisplayRPC/RenderLinearReadArcsDisplay.js +49 -0
  209. package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.d.ts +24 -0
  210. package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.js +156 -0
  211. package/esm/RenderLinearReadArcsDisplayRPC/executeRenderLinearReadArcsDisplay.d.ts +6 -0
  212. package/esm/RenderLinearReadArcsDisplayRPC/executeRenderLinearReadArcsDisplay.js +105 -0
  213. package/{dist/GuessAlignmentsTypes → esm/RenderLinearReadArcsDisplayRPC}/index.d.ts +1 -1
  214. package/esm/RenderLinearReadArcsDisplayRPC/index.js +4 -0
  215. package/esm/RenderLinearReadCloudDisplayRPC/RenderLinearReadCloudDisplay.d.ts +43 -0
  216. package/esm/RenderLinearReadCloudDisplayRPC/RenderLinearReadCloudDisplay.js +49 -0
  217. package/esm/RenderLinearReadCloudDisplayRPC/drawChainsUtil.d.ts +82 -0
  218. package/esm/RenderLinearReadCloudDisplayRPC/drawChainsUtil.js +164 -0
  219. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.d.ts +17 -0
  220. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.js +53 -0
  221. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCommon.d.ts +72 -0
  222. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCommon.js +277 -0
  223. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsStack.d.ts +5 -0
  224. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsStack.js +16 -0
  225. package/esm/RenderLinearReadCloudDisplayRPC/drawLongReadChains.d.ts +27 -0
  226. package/esm/RenderLinearReadCloudDisplayRPC/drawLongReadChains.js +101 -0
  227. package/esm/RenderLinearReadCloudDisplayRPC/drawPairChains.d.ts +27 -0
  228. package/esm/RenderLinearReadCloudDisplayRPC/drawPairChains.js +95 -0
  229. package/esm/RenderLinearReadCloudDisplayRPC/executeRenderLinearReadCloudDisplay.d.ts +6 -0
  230. package/esm/RenderLinearReadCloudDisplayRPC/executeRenderLinearReadCloudDisplay.js +142 -0
  231. package/esm/RenderLinearReadCloudDisplayRPC/index.d.ts +2 -0
  232. package/esm/RenderLinearReadCloudDisplayRPC/index.js +4 -0
  233. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +18 -3
  234. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +205 -37
  235. package/esm/SNPCoverageAdapter/configSchema.d.ts +6 -2
  236. package/esm/SNPCoverageAdapter/configSchema.js +4 -0
  237. package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.d.ts +26 -0
  238. package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.js +438 -0
  239. package/esm/SNPCoverageAdapter/index.js +2 -2
  240. package/esm/SNPCoverageAdapter/processDepthPrefixSum.d.ts +10 -0
  241. package/esm/SNPCoverageAdapter/processDepthPrefixSum.js +55 -0
  242. package/esm/SNPCoverageAdapter/processModifications.d.ts +1 -1
  243. package/esm/SNPCoverageAdapter/processModifications.js +26 -38
  244. package/esm/SNPCoverageAdapter/processReferenceCpGs.d.ts +2 -3
  245. package/esm/SNPCoverageAdapter/processReferenceCpGs.js +46 -44
  246. package/esm/SNPCoverageAdapter/util.d.ts +9 -5
  247. package/esm/SNPCoverageAdapter/util.js +48 -28
  248. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +14 -4
  249. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +29 -8
  250. package/esm/SNPCoverageRenderer/WiggleRendering.d.ts +14 -0
  251. package/esm/SNPCoverageRenderer/WiggleRendering.js +33 -0
  252. package/esm/SNPCoverageRenderer/calculateModificationCounts.d.ts +20 -0
  253. package/esm/SNPCoverageRenderer/calculateModificationCounts.js +22 -0
  254. package/esm/SNPCoverageRenderer/components/SNPCoverageRendering.d.ts +18 -0
  255. package/esm/SNPCoverageRenderer/components/SNPCoverageRendering.js +114 -0
  256. package/esm/SNPCoverageRenderer/configSchema.d.ts +2 -2
  257. package/esm/SNPCoverageRenderer/index.js +4 -4
  258. package/esm/SNPCoverageRenderer/makeImage.d.ts +2 -2
  259. package/esm/SNPCoverageRenderer/makeImage.js +372 -200
  260. package/esm/SNPCoverageRenderer/types.d.ts +54 -5
  261. package/esm/SNPCoverageRenderer/types.js +103 -1
  262. package/esm/SVGErrorBox.d.ts +5 -0
  263. package/esm/SVGErrorBox.js +4 -0
  264. package/esm/index.d.ts +3 -3
  265. package/esm/index.js +23 -21
  266. package/esm/saveTrackFormats/sam.d.ts +6 -0
  267. package/esm/saveTrackFormats/sam.js +42 -0
  268. package/esm/shared/LinearReadArcsDisplaySettingsMixin.d.ts +14 -0
  269. package/esm/shared/LinearReadArcsDisplaySettingsMixin.js +33 -0
  270. package/esm/shared/LinearReadDisplayBaseMixin.d.ts +20 -11
  271. package/esm/shared/LinearReadDisplayBaseMixin.js +5 -21
  272. package/esm/shared/LinearReadDisplayWithLayoutMixin.d.ts +8 -3
  273. package/esm/shared/LinearReadDisplayWithLayoutMixin.js +9 -1
  274. package/esm/shared/LinearReadDisplayWithPairFiltersMixin.d.ts +6 -6
  275. package/esm/shared/LinearReadDisplayWithPairFiltersMixin.js +1 -1
  276. package/esm/shared/SharedModificationsMixin.d.ts +12 -0
  277. package/esm/shared/SharedModificationsMixin.js +40 -0
  278. package/esm/shared/afterAttach.d.ts +1 -1
  279. package/esm/shared/afterAttach.js +1 -5
  280. package/esm/shared/arcUtils.d.ts +20 -0
  281. package/esm/shared/arcUtils.js +73 -0
  282. package/esm/shared/canvasUtils.d.ts +1 -1
  283. package/esm/shared/canvasUtils.js +9 -14
  284. package/esm/shared/color.d.ts +21 -15
  285. package/esm/shared/color.js +41 -21
  286. package/esm/shared/components/FilterByTagDialog.d.ts +1 -1
  287. package/esm/shared/components/FilterByTagDialog.js +4 -5
  288. package/esm/shared/components/SetFeatureHeightDialog.js +1 -1
  289. package/esm/shared/components/SetMaxHeightDialog.js +3 -3
  290. package/esm/{LinearPileupDisplay → shared}/components/SetModificationThresholdDialog.d.ts +1 -1
  291. package/esm/{LinearPileupDisplay → shared}/components/SetModificationThresholdDialog.js +1 -1
  292. package/esm/shared/createRPCRenderingSetup.d.ts +37 -0
  293. package/esm/shared/createRPCRenderingSetup.js +82 -0
  294. package/esm/shared/decodeSeq.d.ts +2 -0
  295. package/esm/shared/decodeSeq.js +26 -0
  296. package/esm/shared/flatbushType.d.ts +16 -3
  297. package/esm/shared/forEachMismatchTypes.d.ts +18 -0
  298. package/esm/shared/forEachMismatchTypes.js +24 -0
  299. package/esm/shared/getMaximumModificationAtEachPosition.d.ts +1 -1
  300. package/esm/shared/getMaximumModificationAtEachPosition.js +6 -7
  301. package/esm/shared/getUniqueModifications.d.ts +5 -3
  302. package/esm/shared/getUniqueModifications.js +3 -2
  303. package/esm/shared/getUniqueTags.d.ts +2 -2
  304. package/esm/shared/getUniqueTags.js +2 -1
  305. package/{dist/PileupRPC/util.d.ts → esm/shared/insertSizeStats.d.ts} +2 -2
  306. package/esm/shared/insertSizeStats.js +23 -0
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  642. package/esm/LinearReadCloudDisplay/drawFeatsAbstract.js +0 -10
  643. package/esm/LinearReadCloudDisplay/drawFeatsCloud.d.ts +0 -2
  644. package/esm/LinearReadCloudDisplay/drawFeatsCloud.js +0 -21
  645. package/esm/LinearReadCloudDisplay/drawFeatsCommon.d.ts +0 -23
  646. package/esm/LinearReadCloudDisplay/drawFeatsCommon.js +0 -187
  647. package/esm/LinearReadCloudDisplay/drawFeatsStack.d.ts +0 -2
  648. package/esm/LinearReadCloudDisplay/drawFeatsStack.js +0 -30
  649. package/esm/PileupRPC/methods/GetReducedFeatures.d.ts +0 -37
  650. package/esm/PileupRPC/methods/GetReducedFeatures.js +0 -48
  651. package/esm/PileupRPC/util.d.ts +0 -8
  652. package/esm/PileupRPC/util.js +0 -14
  653. package/esm/PileupRenderer/renderers/renderMismatches.d.ts +0 -21
  654. package/esm/PileupRenderer/renderers/renderMismatches.js +0 -145
  655. package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +0 -13
  656. package/esm/SNPCoverageAdapter/generateCoverageBins.js +0 -84
  657. package/esm/SNPCoverageAdapter/processDepth.d.ts +0 -8
  658. package/esm/SNPCoverageAdapter/processDepth.js +0 -35
  659. package/esm/SNPCoverageAdapter/processMismatches.d.ts +0 -9
  660. package/esm/SNPCoverageAdapter/processMismatches.js +0 -55
  661. package/esm/shared/chainToSimpleFeature.d.ts +0 -3
  662. package/esm/shared/components/BaseDisplayComponent.d.ts +0 -16
  663. package/esm/shared/components/BaseDisplayComponent.js +0 -42
  664. package/esm/shared/drawLongReadChains.d.ts +0 -24
  665. package/esm/shared/drawLongReadChains.js +0 -101
  666. package/esm/shared/drawPairChains.d.ts +0 -24
  667. package/esm/shared/drawPairChains.js +0 -91
  668. package/esm/shared/fetchChains.d.ts +0 -28
  669. package/esm/shared/fetchChains.js +0 -19
@@ -1,515 +0,0 @@
1
- import type { ModificationType, ModificationTypeWithColor, SortedBy } from '../shared/types';
2
- import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
3
- import type { Instance } from 'mobx-state-tree';
4
- declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
5
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
6
- type: import("mobx-state-tree").ISimpleType<string>;
7
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
8
- } & {
9
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
10
- } & {
11
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
12
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
- } & {
14
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
15
- key: import("mobx-state-tree").ISimpleType<string>;
16
- region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
17
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
18
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
19
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
20
- }, {
21
- stopToken: string | undefined;
22
- filled: boolean;
23
- reactElement: React.ReactElement | undefined;
24
- features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
25
- layout: any;
26
- status: string;
27
- error: unknown;
28
- message: string | undefined;
29
- maxHeightReached: boolean;
30
- ReactComponent: ({ model, }: {
31
- model: {
32
- error?: unknown;
33
- reload: () => void;
34
- message: React.ReactNode;
35
- filled?: boolean;
36
- status?: string;
37
- reactElement?: React.ReactElement;
38
- };
39
- }) => import("react/jsx-runtime").JSX.Element | undefined;
40
- renderProps: any;
41
- } & {
42
- doReload(): void;
43
- afterAttach(): void;
44
- setStatus(message: string): void;
45
- setLoading(newStopToken: string): void;
46
- setMessage(messageText: string): void;
47
- setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
48
- setError(error: unknown): void;
49
- reload(): void;
50
- beforeDestroy(): void;
51
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
52
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
53
- maxFeatureScreenDensity: {
54
- type: string;
55
- description: string;
56
- defaultValue: number;
57
- };
58
- fetchSizeLimit: {
59
- type: string;
60
- defaultValue: number;
61
- description: string;
62
- };
63
- height: {
64
- type: string;
65
- defaultValue: number;
66
- description: string;
67
- };
68
- mouseover: {
69
- type: string;
70
- description: string;
71
- defaultValue: string;
72
- contextVariable: string[];
73
- };
74
- jexlFilters: {
75
- type: string;
76
- description: string;
77
- defaultValue: never[];
78
- };
79
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
80
- } & {
81
- configuration: AnyConfigurationSchemaType;
82
- featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
83
- noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
84
- fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
85
- trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
86
- colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
87
- filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
88
- jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
89
- hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
90
- } & {
91
- type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
92
- configuration: AnyConfigurationSchemaType;
93
- showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
94
- mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
95
- sortedBy: import("mobx-state-tree").IType<SortedBy | undefined, SortedBy | undefined, SortedBy | undefined>;
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 | import("@jbrowse/core/util").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: import("@jbrowse/core/util").Feature): void;
201
- } & {
202
- readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
203
- readonly featureUnderMouse: import("@jbrowse/core/util").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: import("@jbrowse/core/util").Feature): void;
224
- navToFeature(feature: import("@jbrowse/core/util").Feature): void;
225
- clearFeatureSelection(): void;
226
- setFeatureIdUnderMouse(feature?: string): void;
227
- setContextMenuFeature(feature?: import("@jbrowse/core/util").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
- colorTagMap: import("mobx").ObservableMap<string, string>;
240
- featureUnderMouseVolatile: undefined | import("@jbrowse/core/util").Feature;
241
- tagsReady: boolean;
242
- } & {
243
- readonly colorBy: any;
244
- readonly filterBy: any;
245
- } & {
246
- readonly autorunReady: boolean;
247
- readonly hideSmallIndels: boolean | undefined;
248
- } & {
249
- setTagsReady(flag: boolean): void;
250
- setMaxHeight(n?: number): void;
251
- setFeatureHeight(n?: number): void;
252
- setNoSpacing(flag?: boolean): void;
253
- setColorScheme(colorScheme: import("../shared/types").ColorBy): void;
254
- updateColorTagMap(uniqueTag: string[]): void;
255
- setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
256
- selectFeature(feature: import("@jbrowse/core/util").Feature): void;
257
- setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
258
- setFilterBy(filter: import("../shared/types").FilterBy): void;
259
- setJexlFilters(filters: string[]): void;
260
- setHideSmallIndels(arg: boolean): void;
261
- } & {
262
- copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
263
- readonly rendererConfig: {
264
- [x: string]: any;
265
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
266
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
267
- [x: string]: any;
268
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
269
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
270
- [x: string]: any;
271
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
272
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
273
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
274
- } & {
275
- readonly maxHeight: any;
276
- readonly featureHeightSetting: any;
277
- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
278
- renderReady(): boolean;
279
- readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
280
- } & {
281
- readonly rendererTypeName: string;
282
- contextMenuItems(): {
283
- label: string;
284
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
285
- muiName: string;
286
- };
287
- onClick: () => void;
288
- }[];
289
- readonly DisplayBlurb: ({ model, }: {
290
- model: {
291
- sortedBy?: SortedBy;
292
- };
293
- }) => import("react/jsx-runtime").JSX.Element | null;
294
- renderPropsPre(): any;
295
- colorSchemeSubMenuItems(): {
296
- label: string;
297
- onClick: () => void;
298
- }[];
299
- 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 | {
300
- label: string;
301
- priority: number;
302
- type: string;
303
- checked: boolean | undefined;
304
- onClick: () => void;
305
- icon?: undefined;
306
- } | {
307
- label: string;
308
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
309
- muiName: string;
310
- };
311
- onClick: () => void;
312
- priority?: undefined;
313
- type?: undefined;
314
- checked?: undefined;
315
- })[];
316
- } & {
317
- renderProps(): any;
318
- } & {
319
- afterAttach(): void;
320
- } & {
321
- sortReady: boolean;
322
- currSortBpPerPx: number;
323
- visibleModifications: import("mobx").ObservableMap<string, ModificationTypeWithColor>;
324
- simplexModifications: Set<string>;
325
- modificationsReady: boolean;
326
- } & {
327
- setCurrSortBpPerPx(n: number): void;
328
- updateVisibleModifications(uniqueModifications: ModificationType[]): void;
329
- setSimplexModifications(simplex: string[]): void;
330
- setModificationsReady(flag: boolean): void;
331
- setSortReady(flag: boolean): void;
332
- clearSelected(): void;
333
- toggleSoftClipping(): void;
334
- toggleMismatchAlpha(): void;
335
- setSortedBy(type: string, tag?: string): void;
336
- setFeatureHeight(n?: number): void;
337
- } & {
338
- reload(): void;
339
- } & {
340
- readonly visibleModificationTypes: string[];
341
- readonly modificationThreshold: any;
342
- readonly rendererConfig: {
343
- [x: string]: any;
344
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
345
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
346
- [x: string]: any;
347
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
348
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
349
- [x: string]: any;
350
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
351
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
352
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
353
- } & {
354
- readonly mismatchAlphaSetting: any;
355
- renderReady(): boolean;
356
- } & {
357
- renderPropsPre(): any;
358
- renderProps(): any;
359
- trackMenuItems(): readonly [...import("@jbrowse/core/ui").MenuItem[], {
360
- readonly label: "Sort by...";
361
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
362
- muiName: string;
363
- };
364
- readonly disabled: boolean;
365
- readonly subMenu: readonly [...{
366
- label: string;
367
- onClick: () => void;
368
- }[], {
369
- readonly label: "Sort by tag...";
370
- readonly onClick: () => void;
371
- }, {
372
- readonly label: "Clear sort";
373
- readonly onClick: () => void;
374
- }];
375
- }, {
376
- readonly label: "Color by...";
377
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
378
- muiName: string;
379
- };
380
- readonly subMenu: readonly [{
381
- readonly label: "Pair orientation";
382
- readonly onClick: () => void;
383
- }, {
384
- readonly label: "Modifications";
385
- readonly type: "subMenu";
386
- readonly subMenu: ({
387
- label: string;
388
- onClick: () => void;
389
- type?: undefined;
390
- } | {
391
- type: string;
392
- label?: undefined;
393
- onClick?: undefined;
394
- })[];
395
- }, {
396
- readonly label: "Insert size";
397
- readonly onClick: () => void;
398
- }, ...{
399
- label: string;
400
- onClick: () => void;
401
- }[]];
402
- }, {
403
- readonly label: "Group by...";
404
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
405
- muiName: string;
406
- };
407
- readonly onClick: () => void;
408
- }, {
409
- readonly label: "Show soft clipping";
410
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
411
- muiName: string;
412
- };
413
- readonly type: "checkbox";
414
- readonly checked: boolean;
415
- readonly onClick: () => void;
416
- }, {
417
- readonly label: "Fade mismatches by quality";
418
- readonly type: "checkbox";
419
- readonly checked: any;
420
- readonly onClick: () => void;
421
- }];
422
- } & {
423
- afterAttach(): void;
424
- }, {
425
- type: string;
426
- } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
427
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
428
- type: import("mobx-state-tree").ISimpleType<string>;
429
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
430
- } & {
431
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
432
- } & {
433
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
434
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
435
- } & {
436
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
437
- key: import("mobx-state-tree").ISimpleType<string>;
438
- region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
439
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
440
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
441
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
442
- }, {
443
- stopToken: string | undefined;
444
- filled: boolean;
445
- reactElement: React.ReactElement | undefined;
446
- features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
447
- layout: any;
448
- status: string;
449
- error: unknown;
450
- message: string | undefined;
451
- maxHeightReached: boolean;
452
- ReactComponent: ({ model, }: {
453
- model: {
454
- error?: unknown;
455
- reload: () => void;
456
- message: React.ReactNode;
457
- filled?: boolean;
458
- status?: string;
459
- reactElement?: React.ReactElement;
460
- };
461
- }) => import("react/jsx-runtime").JSX.Element | undefined;
462
- renderProps: any;
463
- } & {
464
- doReload(): void;
465
- afterAttach(): void;
466
- setStatus(message: string): void;
467
- setLoading(newStopToken: string): void;
468
- setMessage(messageText: string): void;
469
- setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
470
- setError(error: unknown): void;
471
- reload(): void;
472
- beforeDestroy(): void;
473
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
474
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
475
- maxFeatureScreenDensity: {
476
- type: string;
477
- description: string;
478
- defaultValue: number;
479
- };
480
- fetchSizeLimit: {
481
- type: string;
482
- defaultValue: number;
483
- description: string;
484
- };
485
- height: {
486
- type: string;
487
- defaultValue: number;
488
- description: string;
489
- };
490
- mouseover: {
491
- type: string;
492
- description: string;
493
- defaultValue: string;
494
- contextVariable: string[];
495
- };
496
- jexlFilters: {
497
- type: string;
498
- description: string;
499
- defaultValue: never[];
500
- };
501
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
502
- } & {
503
- configuration: AnyConfigurationSchemaType;
504
- featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
505
- noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
506
- fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
507
- trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
508
- colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
509
- filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
510
- jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
511
- hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
512
- }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
513
- export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
514
- export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
515
- export default stateModelFactory;