@jbrowse/plugin-alignments 3.6.5 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (640) 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 +41 -41
  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 +93 -144
  42. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +6 -2
  43. package/esm/CramAdapter/CramSlightlyLazyFeature.js +140 -18
  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 +19 -9
  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 +1249 -124
  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 +8 -8
  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 +5 -3
  81. package/esm/LinearPileupDisplay/doAfterAttach.js +17 -25
  82. package/esm/LinearPileupDisplay/index.d.ts +3 -3
  83. package/esm/LinearPileupDisplay/index.js +6 -5
  84. package/esm/LinearPileupDisplay/model.d.ts +1293 -155
  85. package/esm/LinearPileupDisplay/model.js +74 -122
  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/esm/LinearReadArcsDisplay/chainToSimpleFeature.d.ts +3 -0
  91. package/esm/LinearReadArcsDisplay/chainToSimpleFeature.js +40 -0
  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 +5 -4
  97. package/esm/LinearReadArcsDisplay/model.d.ts +225 -69
  98. package/esm/LinearReadArcsDisplay/model.js +60 -121
  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 +24 -0
  108. package/esm/LinearReadCloudDisplay/configSchema.d.ts +28 -5
  109. package/esm/LinearReadCloudDisplay/configSchema.js +21 -0
  110. package/esm/LinearReadCloudDisplay/index.js +9 -5
  111. package/esm/LinearReadCloudDisplay/model.d.ts +343 -61
  112. package/esm/LinearReadCloudDisplay/model.js +237 -76
  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 -6
  126. package/esm/LinearSNPCoverageDisplay/components/TooltipContents.js +191 -35
  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 +162 -66
  136. package/esm/MismatchParser/cigarToMismatches.d.ts +1 -1
  137. package/esm/MismatchParser/cigarToMismatches.js +6 -8
  138. package/esm/MismatchParser/cigarToMismatches2.d.ts +2 -0
  139. package/{dist/MismatchParser/cigarToMismatches.js → esm/MismatchParser/cigarToMismatches2.js} +23 -27
  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 +4 -0
  149. package/esm/ModificationParser/detectSimplexModifications.js +17 -0
  150. package/esm/ModificationParser/getMethBins.d.ts +1 -1
  151. package/esm/ModificationParser/getMethBins.js +5 -5
  152. package/esm/ModificationParser/getModPositions.d.ts +1 -1
  153. package/esm/ModificationParser/getModPositions.js +14 -17
  154. package/esm/ModificationParser/getModProbabilities.js +1 -1
  155. package/esm/ModificationParser/getModTypes.js +1 -1
  156. package/esm/PileupRPC/base.js +1 -2
  157. package/esm/PileupRPC/index.js +1 -2
  158. package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +1 -1
  159. package/esm/PileupRPC/methods/GetGlobalValueForTag.js +3 -6
  160. package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +6 -3
  161. package/esm/PileupRPC/methods/GetVisibleModifications.js +20 -10
  162. package/esm/PileupRPC/rpcMethods.d.ts +2 -3
  163. package/esm/PileupRPC/rpcMethods.js +2 -3
  164. package/esm/PileupRenderer/PileupLayoutSession.d.ts +9 -9
  165. package/esm/PileupRenderer/PileupLayoutSession.js +18 -5
  166. package/esm/PileupRenderer/PileupRenderer.d.ts +5 -42
  167. package/esm/PileupRenderer/PileupRenderer.js +25 -70
  168. package/esm/PileupRenderer/colorBy.js +2 -2
  169. package/esm/PileupRenderer/components/PileupRendering.d.ts +9 -16
  170. package/esm/PileupRenderer/components/PileupRendering.js +152 -105
  171. package/esm/PileupRenderer/components/PileupTooltip.d.ts +10 -0
  172. package/esm/PileupRenderer/components/PileupTooltip.js +12 -0
  173. package/esm/PileupRenderer/components/util.d.ts +7 -0
  174. package/esm/PileupRenderer/components/util.js +17 -0
  175. package/esm/PileupRenderer/configSchema.d.ts +14 -4
  176. package/esm/PileupRenderer/configSchema.js +11 -1
  177. package/esm/PileupRenderer/index.js +4 -4
  178. package/esm/PileupRenderer/layoutFeature.d.ts +4 -12
  179. package/esm/PileupRenderer/layoutFeature.js +13 -18
  180. package/esm/PileupRenderer/layoutFeatures.d.ts +2 -2
  181. package/esm/PileupRenderer/layoutFeatures.js +21 -16
  182. package/esm/PileupRenderer/makeImageData.d.ts +20 -14
  183. package/esm/PileupRenderer/makeImageData.js +96 -14
  184. package/esm/PileupRenderer/renderers/cigarUtil.d.ts +18 -0
  185. package/esm/PileupRenderer/renderers/cigarUtil.js +23 -0
  186. package/esm/PileupRenderer/{getAlignmentShapeColor.js → renderers/getAlignmentShapeColor.js} +2 -2
  187. package/esm/PileupRenderer/{renderAlignment.d.ts → renderers/renderAlignment.d.ts} +6 -3
  188. package/esm/PileupRenderer/{renderAlignment.js → renderers/renderAlignment.js} +31 -26
  189. package/esm/PileupRenderer/renderers/renderAlignmentShape.d.ts +10 -0
  190. package/esm/PileupRenderer/renderers/renderAlignmentShape.js +165 -0
  191. package/esm/PileupRenderer/{renderMethylation.d.ts → renderers/renderMethylation.d.ts} +8 -6
  192. package/esm/PileupRenderer/renderers/renderMethylation.js +97 -0
  193. package/esm/PileupRenderer/renderers/renderMismatchesCallback.d.ts +32 -0
  194. package/esm/PileupRenderer/renderers/renderMismatchesCallback.js +304 -0
  195. package/esm/PileupRenderer/renderers/renderModifications.d.ts +20 -0
  196. package/esm/PileupRenderer/renderers/renderModifications.js +99 -0
  197. package/{dist/PileupRenderer → esm/PileupRenderer/renderers}/renderPerBaseLettering.d.ts +2 -2
  198. package/esm/PileupRenderer/renderers/renderPerBaseLettering.js +59 -0
  199. package/{dist/PileupRenderer → esm/PileupRenderer/renderers}/renderPerBaseQuality.d.ts +3 -4
  200. package/esm/PileupRenderer/renderers/renderPerBaseQuality.js +48 -0
  201. package/{dist/PileupRenderer → esm/PileupRenderer/renderers}/renderSoftClipping.d.ts +2 -2
  202. package/esm/PileupRenderer/renderers/renderSoftClipping.js +75 -0
  203. package/esm/PileupRenderer/sortUtil.d.ts +2 -2
  204. package/esm/PileupRenderer/sortUtil.js +34 -22
  205. package/esm/PileupRenderer/types.d.ts +32 -1
  206. package/esm/PileupRenderer/types.js +71 -1
  207. package/esm/PileupRenderer/util.d.ts +1 -22
  208. package/esm/PileupRenderer/util.js +12 -38
  209. package/esm/RenderLinearReadArcsDisplayRPC/RenderLinearReadArcsDisplay.d.ts +34 -0
  210. package/esm/RenderLinearReadArcsDisplayRPC/RenderLinearReadArcsDisplay.js +49 -0
  211. package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.d.ts +24 -0
  212. package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.js +156 -0
  213. package/esm/RenderLinearReadArcsDisplayRPC/executeRenderLinearReadArcsDisplay.d.ts +6 -0
  214. package/esm/RenderLinearReadArcsDisplayRPC/executeRenderLinearReadArcsDisplay.js +105 -0
  215. package/{dist/GuessAlignmentsTypes → esm/RenderLinearReadArcsDisplayRPC}/index.d.ts +1 -1
  216. package/esm/RenderLinearReadArcsDisplayRPC/index.js +4 -0
  217. package/esm/RenderLinearReadCloudDisplayRPC/RenderLinearReadCloudDisplay.d.ts +43 -0
  218. package/esm/RenderLinearReadCloudDisplayRPC/RenderLinearReadCloudDisplay.js +49 -0
  219. package/esm/RenderLinearReadCloudDisplayRPC/drawChainsUtil.d.ts +82 -0
  220. package/esm/RenderLinearReadCloudDisplayRPC/drawChainsUtil.js +164 -0
  221. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.d.ts +17 -0
  222. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.js +53 -0
  223. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCommon.d.ts +72 -0
  224. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCommon.js +277 -0
  225. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsStack.d.ts +5 -0
  226. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsStack.js +16 -0
  227. package/esm/RenderLinearReadCloudDisplayRPC/drawLongReadChains.d.ts +27 -0
  228. package/esm/RenderLinearReadCloudDisplayRPC/drawLongReadChains.js +101 -0
  229. package/esm/RenderLinearReadCloudDisplayRPC/drawPairChains.d.ts +27 -0
  230. package/esm/RenderLinearReadCloudDisplayRPC/drawPairChains.js +95 -0
  231. package/esm/RenderLinearReadCloudDisplayRPC/executeRenderLinearReadCloudDisplay.d.ts +6 -0
  232. package/esm/RenderLinearReadCloudDisplayRPC/executeRenderLinearReadCloudDisplay.js +142 -0
  233. package/esm/RenderLinearReadCloudDisplayRPC/index.d.ts +2 -0
  234. package/esm/RenderLinearReadCloudDisplayRPC/index.js +4 -0
  235. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +18 -3
  236. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +205 -37
  237. package/esm/SNPCoverageAdapter/configSchema.d.ts +6 -2
  238. package/esm/SNPCoverageAdapter/configSchema.js +4 -0
  239. package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.d.ts +26 -0
  240. package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.js +438 -0
  241. package/esm/SNPCoverageAdapter/index.js +2 -2
  242. package/esm/SNPCoverageAdapter/processDepthPrefixSum.d.ts +10 -0
  243. package/esm/SNPCoverageAdapter/processDepthPrefixSum.js +55 -0
  244. package/esm/SNPCoverageAdapter/processModifications.d.ts +1 -1
  245. package/esm/SNPCoverageAdapter/processModifications.js +34 -36
  246. package/esm/SNPCoverageAdapter/processReferenceCpGs.d.ts +2 -3
  247. package/esm/SNPCoverageAdapter/processReferenceCpGs.js +46 -44
  248. package/esm/SNPCoverageAdapter/util.d.ts +9 -5
  249. package/esm/SNPCoverageAdapter/util.js +48 -28
  250. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +14 -4
  251. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +29 -8
  252. package/esm/SNPCoverageRenderer/WiggleRendering.d.ts +14 -0
  253. package/esm/SNPCoverageRenderer/WiggleRendering.js +33 -0
  254. package/esm/SNPCoverageRenderer/calculateModificationCounts.d.ts +20 -0
  255. package/esm/SNPCoverageRenderer/calculateModificationCounts.js +22 -0
  256. package/esm/SNPCoverageRenderer/components/SNPCoverageRendering.d.ts +18 -0
  257. package/esm/SNPCoverageRenderer/components/SNPCoverageRendering.js +114 -0
  258. package/esm/SNPCoverageRenderer/configSchema.d.ts +2 -2
  259. package/esm/SNPCoverageRenderer/index.js +4 -4
  260. package/esm/SNPCoverageRenderer/makeImage.d.ts +2 -2
  261. package/esm/SNPCoverageRenderer/makeImage.js +384 -201
  262. package/esm/SNPCoverageRenderer/types.d.ts +55 -5
  263. package/esm/SNPCoverageRenderer/types.js +103 -1
  264. package/esm/SVGErrorBox.d.ts +5 -0
  265. package/esm/SVGErrorBox.js +4 -0
  266. package/esm/index.d.ts +3 -3
  267. package/esm/index.js +23 -21
  268. package/esm/saveTrackFormats/sam.d.ts +6 -0
  269. package/esm/saveTrackFormats/sam.js +42 -0
  270. package/esm/shared/LinearReadArcsDisplaySettingsMixin.d.ts +14 -0
  271. package/esm/shared/LinearReadArcsDisplaySettingsMixin.js +33 -0
  272. package/esm/shared/LinearReadDisplayBaseMixin.d.ts +33 -0
  273. package/esm/shared/LinearReadDisplayBaseMixin.js +31 -0
  274. package/esm/shared/LinearReadDisplayWithLayoutMixin.d.ts +16 -0
  275. package/esm/shared/LinearReadDisplayWithLayoutMixin.js +29 -0
  276. package/esm/shared/LinearReadDisplayWithPairFiltersMixin.d.ts +11 -0
  277. package/esm/shared/LinearReadDisplayWithPairFiltersMixin.js +24 -0
  278. package/esm/shared/SharedModificationsMixin.d.ts +12 -0
  279. package/esm/shared/SharedModificationsMixin.js +40 -0
  280. package/esm/shared/afterAttach.d.ts +1 -1
  281. package/esm/shared/afterAttach.js +4 -7
  282. package/esm/shared/arcUtils.d.ts +20 -0
  283. package/esm/shared/arcUtils.js +73 -0
  284. package/{dist/LinearReadCloudDisplay/util.d.ts → esm/shared/canvasUtils.d.ts} +1 -1
  285. package/esm/{LinearReadCloudDisplay/util.js → shared/canvasUtils.js} +9 -14
  286. package/esm/shared/chevron.d.ts +1 -0
  287. package/esm/shared/chevron.js +24 -0
  288. package/esm/shared/color.d.ts +54 -11
  289. package/esm/shared/color.js +121 -25
  290. package/esm/shared/components/FilterByTagDialog.d.ts +1 -1
  291. package/esm/shared/components/FilterByTagDialog.js +4 -5
  292. package/esm/shared/components/SetFeatureHeightDialog.d.ts +10 -0
  293. package/esm/shared/components/SetFeatureHeightDialog.js +24 -0
  294. package/esm/{LinearPileupDisplay → shared}/components/SetMaxHeightDialog.js +3 -3
  295. package/esm/shared/components/SetModificationThresholdDialog.d.ts +10 -0
  296. package/esm/shared/components/SetModificationThresholdDialog.js +37 -0
  297. package/esm/shared/createRPCRenderingSetup.d.ts +37 -0
  298. package/esm/shared/createRPCRenderingSetup.js +82 -0
  299. package/esm/shared/decodeSeq.d.ts +2 -0
  300. package/esm/shared/decodeSeq.js +26 -0
  301. package/esm/shared/flatbushType.d.ts +25 -0
  302. package/esm/shared/flatbushType.js +1 -0
  303. package/esm/shared/forEachMismatchTypes.d.ts +18 -0
  304. package/esm/shared/forEachMismatchTypes.js +24 -0
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  638. /package/{dist/LinearPileupDisplay → esm/LinearReadCloudDisplay}/components/SetFeatureHeightDialog.d.ts +0 -0
  639. /package/{dist/PileupRenderer → esm/PileupRenderer/renderers}/getAlignmentShapeColor.d.ts +0 -0
  640. /package/{dist/LinearPileupDisplay → esm/shared}/components/SetMaxHeightDialog.d.ts +0 -0
@@ -1,497 +0,0 @@
1
- import type { ModificationType, ModificationTypeWithColor, SortedBy } from '../shared/types';
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- import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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- import type { Instance } from 'mobx-state-tree';
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- declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
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- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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- type: import("mobx-state-tree").ISimpleType<string>;
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- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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- } & {
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- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- } & {
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- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- } & {
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- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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- key: import("mobx-state-tree").ISimpleType<string>;
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- region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
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- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
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- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- }, {
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- stopToken: string | undefined;
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- filled: boolean;
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- reactElement: React.ReactElement | undefined;
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- features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
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- layout: any;
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- status: string;
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- error: unknown;
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- message: string | undefined;
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- maxHeightReached: boolean;
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- ReactComponent: ({ model, }: {
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- model: {
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- error?: unknown;
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- reload: () => void;
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- message: React.ReactNode;
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- filled?: boolean;
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- status?: string;
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- reactElement?: React.ReactElement;
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- };
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- }) => import("react/jsx-runtime").JSX.Element | undefined;
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- renderProps: any;
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- } & {
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- doReload(): void;
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- afterAttach(): void;
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- setStatus(message: string): void;
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- setLoading(newStopToken: string): void;
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- setMessage(messageText: string): void;
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- setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
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- setError(error: unknown): void;
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- reload(): void;
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- beforeDestroy(): void;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- maxFeatureScreenDensity: {
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- type: string;
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- description: string;
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- defaultValue: number;
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- };
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- fetchSizeLimit: {
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- type: string;
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- defaultValue: number;
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- description: string;
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- };
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- height: {
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- type: string;
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- defaultValue: number;
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- description: string;
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- };
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- mouseover: {
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- type: string;
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- description: string;
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- defaultValue: string;
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- contextVariable: string[];
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- };
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- jexlFilters: {
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- type: string;
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- description: string;
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- defaultValue: never[];
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- };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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- } & {
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- configuration: AnyConfigurationSchemaType;
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- featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
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- filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
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- jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
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- hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- } & {
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- type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
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- configuration: AnyConfigurationSchemaType;
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- showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- sortedBy: import("mobx-state-tree").IType<SortedBy | undefined, SortedBy | undefined, SortedBy | undefined>;
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- }, {
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- rendererTypeName: string;
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- error: unknown;
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- message: string | undefined;
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- } & {
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- readonly RenderingComponent: React.FC<{
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- model: {
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- id: string;
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- type: string;
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- rpcDriverName: string | undefined;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- rendererTypeName: string;
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- error: unknown;
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- message: string | undefined;
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- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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- type: import("mobx-state-tree").ISimpleType<string>;
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- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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- }, {
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- rendererTypeName: string;
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- error: unknown;
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- message: string | undefined;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: () => void;
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- blockState?: Record<string, any>;
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- }>;
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- readonly DisplayBlurb: React.FC<{
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- model: {
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- id: string;
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- type: string;
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- rpcDriverName: string | undefined;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- rendererTypeName: string;
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- error: unknown;
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- message: string | undefined;
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- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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- type: import("mobx-state-tree").ISimpleType<string>;
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- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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- }, {
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- rendererTypeName: string;
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- error: unknown;
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- message: string | undefined;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- }> | null;
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- readonly adapterConfig: any;
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- readonly parentTrack: any;
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- renderProps(): any;
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- readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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- readonly DisplayMessageComponent: undefined | React.FC<any>;
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- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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- readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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- regionCannotBeRendered(): null;
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- } & {
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- setMessage(arg?: string): void;
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- setError(error?: unknown): void;
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- setRpcDriverName(rpcDriverName: string): void;
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- reload(): void;
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- } & {
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- scrollTop: number;
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- } & {
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- readonly height: number;
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- } & {
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- setScrollTop(scrollTop: number): void;
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- setHeight(displayHeight: number): number;
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- resizeHeight(distance: number): number;
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- } & {
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- featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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- featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
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- currStatsBpPerPx: number;
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- } & {
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- readonly currentBytesRequested: number;
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- readonly currentFeatureScreenDensity: number;
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- readonly maxFeatureScreenDensity: any;
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- readonly featureDensityStatsReady: boolean;
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- readonly maxAllowableBytes: number;
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- } & {
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- afterAttach(): void;
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- } & {
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- setCurrStatsBpPerPx(n: number): void;
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- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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- getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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- setFeatureDensityStatsP(arg: any): void;
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- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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- clearFeatureDensityStats(): void;
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- } & {
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- readonly regionTooLarge: boolean;
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- readonly regionTooLargeReason: string;
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- } & {
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- readonly statsReadyAndRegionNotTooLarge: boolean;
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- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
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- } & {
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- featureIdUnderMouse: undefined | string;
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- contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
191
- } & {
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- readonly DisplayMessageComponent: undefined | React.FC<any>;
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- readonly blockType: "staticBlocks" | "dynamicBlocks";
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- readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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- } & {
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- readonly renderDelay: number;
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- readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
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- readonly selectedFeatureId: string | undefined;
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- copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
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- } & {
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- readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
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- getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
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- getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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- searchFeatureByID(id: string): [number, number, number, number] | undefined;
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- } & {
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- addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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- deleteBlock(key: string): void;
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- selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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- navToFeature(feature: import("@jbrowse/core/util").Feature): void;
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- clearFeatureSelection(): void;
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- setFeatureIdUnderMouse(feature?: string): void;
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- setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
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- } & {
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- reload(): Promise<void>;
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- } & {
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- trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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- contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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- renderProps(): any;
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- } & {
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- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
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- afterAttach(): void;
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- } & {
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- colorTagMap: import("mobx").ObservableMap<string, string>;
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- featureUnderMouseVolatile: undefined | import("@jbrowse/core/util").Feature;
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- tagsReady: boolean;
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- } & {
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- readonly colorBy: any;
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- readonly filterBy: any;
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- } & {
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- readonly autorunReady: boolean;
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- readonly hideSmallIndels: boolean | undefined;
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- } & {
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- setTagsReady(flag: boolean): void;
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- setMaxHeight(n?: number): void;
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- setFeatureHeight(n?: number): void;
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- setNoSpacing(flag?: boolean): void;
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- setColorScheme(colorScheme: import("../shared/types").ColorBy): void;
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- updateColorTagMap(uniqueTag: string[]): void;
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- setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
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- selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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- setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
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- setFilterBy(filter: import("../shared/types").FilterBy): void;
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- setJexlFilters(filters: string[]): void;
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- setHideSmallIndels(arg: boolean): void;
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- } & {
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- copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
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- readonly rendererConfig: {
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- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
257
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
258
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
259
- } & {
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- readonly maxHeight: any;
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- readonly featureHeightSetting: any;
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- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
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- renderReady(): boolean;
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- readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
265
- } & {
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- readonly rendererTypeName: string;
267
- contextMenuItems(): {
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- label: string;
269
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
270
- muiName: string;
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- };
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- onClick: () => void;
273
- }[];
274
- readonly DisplayBlurb: ({ model, }: {
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- model: {
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- sortedBy?: SortedBy;
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- };
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- }) => import("react/jsx-runtime").JSX.Element | null;
279
- renderPropsPre(): any;
280
- colorSchemeSubMenuItems(): {
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- label: string;
282
- onClick: () => void;
283
- }[];
284
- 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 | {
285
- label: string;
286
- priority: number;
287
- type: string;
288
- checked: boolean | undefined;
289
- onClick: () => void;
290
- icon?: undefined;
291
- } | {
292
- label: string;
293
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
294
- muiName: string;
295
- };
296
- onClick: () => void;
297
- priority?: undefined;
298
- type?: undefined;
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- checked?: undefined;
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- })[];
301
- } & {
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- renderProps(): any;
303
- } & {
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- afterAttach(): void;
305
- } & {
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- sortReady: boolean;
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- currSortBpPerPx: number;
308
- visibleModifications: import("mobx").ObservableMap<string, ModificationTypeWithColor>;
309
- modificationsReady: boolean;
310
- } & {
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- setCurrSortBpPerPx(n: number): void;
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- updateVisibleModifications(uniqueModifications: ModificationType[]): void;
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- setModificationsReady(flag: boolean): void;
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- setSortReady(flag: boolean): void;
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- clearSelected(): void;
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- toggleSoftClipping(): void;
317
- toggleMismatchAlpha(): void;
318
- setSortedBy(type: string, tag?: string): void;
319
- setFeatureHeight(n?: number): void;
320
- } & {
321
- reload(): void;
322
- } & {
323
- readonly visibleModificationTypes: string[];
324
- readonly rendererConfig: {
325
- [x: string]: any;
326
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
327
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
328
- [x: string]: any;
329
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
330
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
331
- [x: string]: any;
332
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
333
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
334
- } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
335
- } & {
336
- readonly mismatchAlphaSetting: any;
337
- renderReady(): boolean;
338
- } & {
339
- renderPropsPre(): any;
340
- renderProps(): any;
341
- trackMenuItems(): readonly [...import("@jbrowse/core/ui").MenuItem[], {
342
- readonly label: "Sort by...";
343
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
344
- muiName: string;
345
- };
346
- readonly disabled: boolean;
347
- readonly subMenu: readonly [...{
348
- label: string;
349
- onClick: () => void;
350
- }[], {
351
- readonly label: "Sort by tag...";
352
- readonly onClick: () => void;
353
- }, {
354
- readonly label: "Clear sort";
355
- readonly onClick: () => void;
356
- }];
357
- }, {
358
- readonly label: "Color by...";
359
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
360
- muiName: string;
361
- };
362
- readonly subMenu: readonly [{
363
- readonly label: "Pair orientation";
364
- readonly onClick: () => void;
365
- }, {
366
- readonly label: "Modifications";
367
- readonly type: "subMenu";
368
- readonly subMenu: ({
369
- label: string;
370
- onClick: () => void;
371
- type?: undefined;
372
- } | {
373
- type: string;
374
- label?: undefined;
375
- onClick?: undefined;
376
- })[];
377
- }, {
378
- readonly label: "Insert size";
379
- readonly onClick: () => void;
380
- }, ...{
381
- label: string;
382
- onClick: () => void;
383
- }[]];
384
- }, {
385
- readonly label: "Group by...";
386
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
387
- muiName: string;
388
- };
389
- readonly onClick: () => void;
390
- }, {
391
- readonly label: "Show soft clipping";
392
- readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
393
- muiName: string;
394
- };
395
- readonly type: "checkbox";
396
- readonly checked: boolean;
397
- readonly onClick: () => void;
398
- }, {
399
- readonly label: "Fade mismatches by quality";
400
- readonly type: "checkbox";
401
- readonly checked: any;
402
- readonly onClick: () => void;
403
- }];
404
- } & {
405
- afterAttach(): void;
406
- }, {
407
- type: string;
408
- } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
409
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
410
- type: import("mobx-state-tree").ISimpleType<string>;
411
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
412
- } & {
413
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
414
- } & {
415
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
416
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
417
- } & {
418
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
419
- key: import("mobx-state-tree").ISimpleType<string>;
420
- region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
421
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
422
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
423
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
424
- }, {
425
- stopToken: string | undefined;
426
- filled: boolean;
427
- reactElement: React.ReactElement | undefined;
428
- features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
429
- layout: any;
430
- status: string;
431
- error: unknown;
432
- message: string | undefined;
433
- maxHeightReached: boolean;
434
- ReactComponent: ({ model, }: {
435
- model: {
436
- error?: unknown;
437
- reload: () => void;
438
- message: React.ReactNode;
439
- filled?: boolean;
440
- status?: string;
441
- reactElement?: React.ReactElement;
442
- };
443
- }) => import("react/jsx-runtime").JSX.Element | undefined;
444
- renderProps: any;
445
- } & {
446
- doReload(): void;
447
- afterAttach(): void;
448
- setStatus(message: string): void;
449
- setLoading(newStopToken: string): void;
450
- setMessage(messageText: string): void;
451
- setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
452
- setError(error: unknown): void;
453
- reload(): void;
454
- beforeDestroy(): void;
455
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
456
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
457
- maxFeatureScreenDensity: {
458
- type: string;
459
- description: string;
460
- defaultValue: number;
461
- };
462
- fetchSizeLimit: {
463
- type: string;
464
- defaultValue: number;
465
- description: string;
466
- };
467
- height: {
468
- type: string;
469
- defaultValue: number;
470
- description: string;
471
- };
472
- mouseover: {
473
- type: string;
474
- description: string;
475
- defaultValue: string;
476
- contextVariable: string[];
477
- };
478
- jexlFilters: {
479
- type: string;
480
- description: string;
481
- defaultValue: never[];
482
- };
483
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
484
- } & {
485
- configuration: AnyConfigurationSchemaType;
486
- featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
487
- noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
488
- fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
489
- trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
490
- colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
491
- filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
492
- jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
493
- hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
494
- }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
495
- export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
496
- export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
497
- export default stateModelFactory;