@jbrowse/plugin-alignments 2.17.0 → 3.0.0

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Files changed (471) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +2 -3
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +25 -24
  3. package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js +0 -1
  4. package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js +0 -1
  5. package/dist/AlignmentsFeatureDetail/Flags.d.ts +1 -2
  6. package/dist/AlignmentsFeatureDetail/Flags.js +8 -10
  7. package/dist/AlignmentsFeatureDetail/Formatter.d.ts +1 -2
  8. package/dist/AlignmentsFeatureDetail/Formatter.js +11 -39
  9. package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts +4 -7
  10. package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js +46 -54
  11. package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts +4 -7
  12. package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js +58 -61
  13. package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts +3 -4
  14. package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js +4 -5
  15. package/dist/AlignmentsFeatureDetail/PairLink.d.ts +2 -3
  16. package/dist/AlignmentsFeatureDetail/PairLink.js +3 -7
  17. package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts +3 -4
  18. package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js +6 -9
  19. package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts +2 -3
  20. package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js +21 -31
  21. package/dist/AlignmentsFeatureDetail/getSAFeatures.d.ts +2 -2
  22. package/dist/AlignmentsFeatureDetail/getSAFeatures.js +0 -4
  23. package/dist/AlignmentsFeatureDetail/index.d.ts +1 -1
  24. package/dist/AlignmentsFeatureDetail/index.js +17 -7
  25. package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +2 -2
  26. package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts +2 -2
  27. package/dist/AlignmentsFeatureDetail/stateModelFactory.js +1 -1
  28. package/dist/AlignmentsFeatureDetail/tagInfo.js +1 -1
  29. package/dist/AlignmentsFeatureDetail/util.d.ts +1 -1
  30. package/dist/AlignmentsTrack/configSchemaF.d.ts +1 -1
  31. package/dist/AlignmentsTrack/configSchemaF.js +1 -8
  32. package/dist/AlignmentsTrack/index.d.ts +1 -1
  33. package/dist/AlignmentsTrack/index.js +0 -3
  34. package/dist/BamAdapter/BamAdapter.d.ts +6 -5
  35. package/dist/BamAdapter/BamAdapter.js +21 -39
  36. package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -3
  37. package/dist/BamAdapter/BamSlightlyLazyFeature.js +0 -3
  38. package/dist/BamAdapter/configSchema.d.ts +0 -17
  39. package/dist/BamAdapter/configSchema.js +1 -22
  40. package/dist/BamAdapter/index.d.ts +1 -1
  41. package/dist/BamAdapter/index.js +17 -7
  42. package/dist/CramAdapter/CramAdapter.d.ts +6 -9
  43. package/dist/CramAdapter/CramAdapter.js +25 -43
  44. package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +3 -3
  45. package/dist/CramAdapter/CramSlightlyLazyFeature.js +0 -17
  46. package/dist/CramAdapter/CramTestAdapters.d.ts +3 -3
  47. package/dist/CramAdapter/CramTestAdapters.js +6 -6
  48. package/dist/CramAdapter/configSchema.d.ts +0 -14
  49. package/dist/CramAdapter/configSchema.js +1 -19
  50. package/dist/CramAdapter/index.d.ts +1 -1
  51. package/dist/CramAdapter/index.js +17 -8
  52. package/dist/CramAdapter/util.d.ts +2 -2
  53. package/dist/CramAdapter/util.js +1 -24
  54. package/dist/GuessAlignmentsTypes/index.d.ts +1 -1
  55. package/dist/GuessAlignmentsTypes/index.js +19 -34
  56. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +2 -2
  57. package/dist/HtsgetBamAdapter/configSchema.d.ts +0 -9
  58. package/dist/HtsgetBamAdapter/configSchema.js +1 -14
  59. package/dist/HtsgetBamAdapter/index.d.ts +1 -1
  60. package/dist/HtsgetBamAdapter/index.js +18 -8
  61. package/dist/LinearAlignmentsDisplay/alignmentsModel.d.ts +2 -5
  62. package/dist/LinearAlignmentsDisplay/alignmentsModel.js +1 -31
  63. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +2 -3
  64. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -18
  65. package/dist/LinearAlignmentsDisplay/configSchema.d.ts +2 -16
  66. package/dist/LinearAlignmentsDisplay/configSchema.js +3 -20
  67. package/dist/LinearAlignmentsDisplay/index.d.ts +1 -1
  68. package/dist/LinearAlignmentsDisplay/index.js +1 -2
  69. package/dist/LinearAlignmentsDisplay/model.d.ts +7 -77
  70. package/dist/LinearAlignmentsDisplay/model.js +10 -85
  71. package/dist/LinearAlignmentsDisplay/util.d.ts +1 -1
  72. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +52 -164
  73. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +71 -145
  74. package/dist/LinearPileupDisplay/components/ColorByTagDialog.d.ts +1 -2
  75. package/dist/LinearPileupDisplay/components/ColorByTagDialog.js +12 -41
  76. package/dist/LinearPileupDisplay/components/GroupByDialog.d.ts +3 -4
  77. package/dist/LinearPileupDisplay/components/GroupByDialog.js +106 -92
  78. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +3 -8
  79. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +3 -7
  80. package/dist/LinearPileupDisplay/components/SetFeatureHeightDialog.d.ts +1 -2
  81. package/dist/LinearPileupDisplay/components/SetFeatureHeightDialog.js +15 -44
  82. package/dist/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts +1 -2
  83. package/dist/LinearPileupDisplay/components/SetMaxHeightDialog.js +12 -40
  84. package/dist/LinearPileupDisplay/components/SortByTagDialog.d.ts +1 -2
  85. package/dist/LinearPileupDisplay/components/SortByTagDialog.js +17 -46
  86. package/dist/LinearPileupDisplay/configSchema.d.ts +13 -16
  87. package/dist/LinearPileupDisplay/configSchema.js +12 -30
  88. package/dist/LinearPileupDisplay/index.d.ts +1 -1
  89. package/dist/LinearPileupDisplay/index.js +2 -2
  90. package/dist/LinearPileupDisplay/model.d.ts +123 -111
  91. package/dist/LinearPileupDisplay/model.js +29 -109
  92. package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts +2 -3
  93. package/dist/LinearReadArcsDisplay/components/ReactComponent.js +6 -33
  94. package/dist/LinearReadArcsDisplay/configSchema.d.ts +12 -20
  95. package/dist/LinearReadArcsDisplay/configSchema.js +8 -31
  96. package/dist/LinearReadArcsDisplay/drawFeats.d.ts +1 -1
  97. package/dist/LinearReadArcsDisplay/drawFeats.js +1 -9
  98. package/dist/LinearReadArcsDisplay/index.d.ts +1 -1
  99. package/dist/LinearReadArcsDisplay/index.js +18 -9
  100. package/dist/LinearReadArcsDisplay/model.d.ts +16 -94
  101. package/dist/LinearReadArcsDisplay/model.js +34 -111
  102. package/dist/LinearReadArcsDisplay/util.d.ts +1 -1
  103. package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts +2 -3
  104. package/dist/LinearReadCloudDisplay/components/ReactComponent.js +6 -33
  105. package/dist/LinearReadCloudDisplay/configSchema.d.ts +5 -17
  106. package/dist/LinearReadCloudDisplay/configSchema.js +3 -28
  107. package/dist/LinearReadCloudDisplay/drawFeats.d.ts +1 -1
  108. package/dist/LinearReadCloudDisplay/drawFeats.js +2 -2
  109. package/dist/LinearReadCloudDisplay/drawLongReadChains.d.ts +4 -4
  110. package/dist/LinearReadCloudDisplay/drawLongReadChains.js +1 -4
  111. package/dist/LinearReadCloudDisplay/drawPairChains.d.ts +4 -4
  112. package/dist/LinearReadCloudDisplay/drawPairChains.js +0 -3
  113. package/dist/LinearReadCloudDisplay/index.d.ts +1 -1
  114. package/dist/LinearReadCloudDisplay/index.js +18 -9
  115. package/dist/LinearReadCloudDisplay/model.d.ts +14 -56
  116. package/dist/LinearReadCloudDisplay/model.js +34 -75
  117. package/dist/LinearReadCloudDisplay/util.js +0 -1
  118. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +2 -3
  119. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +16 -55
  120. package/dist/LinearSNPCoverageDisplay/configSchema.d.ts +17 -22
  121. package/dist/LinearSNPCoverageDisplay/configSchema.js +16 -32
  122. package/dist/LinearSNPCoverageDisplay/index.d.ts +1 -1
  123. package/dist/LinearSNPCoverageDisplay/index.js +1 -2
  124. package/dist/LinearSNPCoverageDisplay/model.d.ts +13 -54
  125. package/dist/LinearSNPCoverageDisplay/model.js +69 -159
  126. package/dist/MismatchParser/cigarToMismatches.d.ts +2 -3
  127. package/dist/MismatchParser/cigarToMismatches.js +4 -7
  128. package/dist/MismatchParser/getNextRefPos.js +0 -2
  129. package/dist/MismatchParser/index.d.ts +3 -4
  130. package/dist/MismatchParser/index.js +1 -9
  131. package/dist/MismatchParser/mdToMismatches.d.ts +2 -3
  132. package/dist/MismatchParser/mdToMismatches.js +0 -6
  133. package/dist/ModificationParser/index.d.ts +1 -1
  134. package/dist/ModificationParser/index.js +1 -18
  135. package/dist/PileupRPC/base.d.ts +2 -2
  136. package/dist/PileupRPC/base.js +0 -1
  137. package/dist/PileupRPC/index.d.ts +1 -1
  138. package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts +2 -3
  139. package/dist/PileupRPC/methods/GetGlobalValueForTag.js +1 -2
  140. package/dist/PileupRPC/methods/GetReducedFeatures.d.ts +2 -3
  141. package/dist/PileupRPC/methods/GetReducedFeatures.js +3 -5
  142. package/dist/PileupRPC/methods/GetVisibleModifications.d.ts +3 -4
  143. package/dist/PileupRPC/methods/GetVisibleModifications.js +1 -1
  144. package/dist/PileupRPC/util.d.ts +1 -1
  145. package/dist/PileupRenderer/PileupLayoutSession.d.ts +5 -5
  146. package/dist/PileupRenderer/PileupLayoutSession.js +2 -5
  147. package/dist/PileupRenderer/PileupRenderer.d.ts +14 -24
  148. package/dist/PileupRenderer/PileupRenderer.js +28 -23
  149. package/dist/PileupRenderer/colorBy.d.ts +2 -2
  150. package/dist/PileupRenderer/colorBy.js +0 -6
  151. package/dist/PileupRenderer/components/PileupRendering.d.ts +2 -3
  152. package/dist/PileupRenderer/components/PileupRendering.js +15 -43
  153. package/dist/PileupRenderer/configSchema.d.ts +5 -31
  154. package/dist/PileupRenderer/configSchema.js +6 -35
  155. package/dist/PileupRenderer/getAlignmentShapeColor.d.ts +2 -2
  156. package/dist/PileupRenderer/getAlignmentShapeColor.js +1 -6
  157. package/dist/PileupRenderer/index.d.ts +1 -1
  158. package/dist/PileupRenderer/index.js +1 -1
  159. package/dist/PileupRenderer/layoutFeature.d.ts +2 -2
  160. package/dist/PileupRenderer/layoutFeature.js +0 -1
  161. package/dist/PileupRenderer/layoutFeatures.d.ts +5 -2
  162. package/dist/PileupRenderer/layoutFeatures.js +6 -4
  163. package/dist/PileupRenderer/makeImageData.d.ts +3 -4
  164. package/dist/PileupRenderer/makeImageData.js +10 -2
  165. package/dist/PileupRenderer/renderAlignment.d.ts +3 -3
  166. package/dist/PileupRenderer/renderAlignment.js +3 -5
  167. package/dist/PileupRenderer/renderAlignmentShape.d.ts +3 -3
  168. package/dist/PileupRenderer/renderAlignmentShape.js +1 -1
  169. package/dist/PileupRenderer/renderMethylation.d.ts +4 -4
  170. package/dist/PileupRenderer/renderMethylation.js +0 -4
  171. package/dist/PileupRenderer/renderMismatches.d.ts +5 -4
  172. package/dist/PileupRenderer/renderMismatches.js +19 -25
  173. package/dist/PileupRenderer/renderModifications.d.ts +3 -3
  174. package/dist/PileupRenderer/renderModifications.js +1 -3
  175. package/dist/PileupRenderer/renderPerBaseLettering.d.ts +2 -2
  176. package/dist/PileupRenderer/renderPerBaseLettering.js +0 -1
  177. package/dist/PileupRenderer/renderPerBaseQuality.d.ts +2 -2
  178. package/dist/PileupRenderer/renderPerBaseQuality.js +2 -2
  179. package/dist/PileupRenderer/renderSoftClipping.d.ts +5 -5
  180. package/dist/PileupRenderer/renderSoftClipping.js +0 -4
  181. package/dist/PileupRenderer/sortUtil.d.ts +2 -2
  182. package/dist/PileupRenderer/sortUtil.js +1 -4
  183. package/dist/PileupRenderer/types.d.ts +26 -0
  184. package/dist/PileupRenderer/types.js +2 -0
  185. package/dist/PileupRenderer/util.d.ts +2 -2
  186. package/dist/PileupRenderer/util.js +1 -3
  187. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +4 -3
  188. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -6
  189. package/dist/SNPCoverageAdapter/configSchema.d.ts +0 -4
  190. package/dist/SNPCoverageAdapter/configSchema.js +1 -8
  191. package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +4 -8
  192. package/dist/SNPCoverageAdapter/generateCoverageBins.js +25 -247
  193. package/dist/SNPCoverageAdapter/index.d.ts +1 -1
  194. package/dist/SNPCoverageAdapter/index.js +17 -7
  195. package/dist/SNPCoverageAdapter/processDepth.d.ts +8 -0
  196. package/dist/SNPCoverageAdapter/processDepth.js +38 -0
  197. package/dist/SNPCoverageAdapter/processMismatches.d.ts +9 -0
  198. package/dist/SNPCoverageAdapter/processMismatches.js +58 -0
  199. package/dist/SNPCoverageAdapter/processModifications.d.ts +10 -0
  200. package/dist/SNPCoverageAdapter/processModifications.js +49 -0
  201. package/dist/SNPCoverageAdapter/processReferenceCpGs.d.ts +9 -0
  202. package/dist/SNPCoverageAdapter/processReferenceCpGs.js +63 -0
  203. package/dist/SNPCoverageAdapter/util.d.ts +10 -0
  204. package/dist/SNPCoverageAdapter/util.js +41 -0
  205. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -18
  206. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +35 -288
  207. package/dist/SNPCoverageRenderer/configSchema.d.ts +3 -18
  208. package/dist/SNPCoverageRenderer/configSchema.js +4 -22
  209. package/dist/SNPCoverageRenderer/index.d.ts +1 -1
  210. package/dist/SNPCoverageRenderer/index.js +2 -2
  211. package/dist/SNPCoverageRenderer/makeImage.d.ts +2 -0
  212. package/dist/SNPCoverageRenderer/makeImage.js +270 -0
  213. package/dist/SNPCoverageRenderer/types.d.ts +19 -0
  214. package/dist/SNPCoverageRenderer/types.js +2 -0
  215. package/dist/index.d.ts +2 -2
  216. package/dist/index.js +29 -19
  217. package/dist/shared/afterAttach.d.ts +1 -1
  218. package/dist/shared/afterAttach.js +0 -2
  219. package/dist/shared/color.d.ts +1 -1
  220. package/dist/shared/color.js +0 -8
  221. package/dist/shared/components/BaseDisplayComponent.d.ts +3 -4
  222. package/dist/shared/components/BaseDisplayComponent.js +13 -19
  223. package/dist/shared/components/FilterByTagDialog.d.ts +2 -3
  224. package/dist/shared/components/FilterByTagDialog.js +44 -94
  225. package/dist/shared/fetchChains.d.ts +2 -2
  226. package/dist/shared/fetchChains.js +1 -2
  227. package/dist/shared/getMaximumModificationAtEachPosition.d.ts +1 -1
  228. package/dist/shared/getMaximumModificationAtEachPosition.js +1 -2
  229. package/dist/shared/getUniqueModifications.d.ts +5 -5
  230. package/dist/shared/getUniqueTags.d.ts +4 -4
  231. package/dist/shared/renderSvgUtil.d.ts +1 -2
  232. package/dist/shared/renderSvgUtil.js +20 -19
  233. package/dist/shared/util.d.ts +11 -1
  234. package/dist/shared/util.js +27 -1
  235. package/dist/util.d.ts +4 -4
  236. package/dist/util.js +3 -9
  237. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +2 -3
  238. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +8 -17
  239. package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js +0 -1
  240. package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js +0 -1
  241. package/esm/AlignmentsFeatureDetail/Flags.d.ts +1 -2
  242. package/esm/AlignmentsFeatureDetail/Flags.js +8 -10
  243. package/esm/AlignmentsFeatureDetail/Formatter.d.ts +1 -2
  244. package/esm/AlignmentsFeatureDetail/Formatter.js +11 -16
  245. package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts +4 -7
  246. package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js +30 -48
  247. package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts +4 -7
  248. package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js +41 -54
  249. package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts +3 -4
  250. package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js +4 -5
  251. package/esm/AlignmentsFeatureDetail/PairLink.d.ts +2 -3
  252. package/esm/AlignmentsFeatureDetail/PairLink.js +3 -4
  253. package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts +3 -4
  254. package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js +6 -9
  255. package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts +2 -3
  256. package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js +22 -29
  257. package/esm/AlignmentsFeatureDetail/getSAFeatures.d.ts +2 -2
  258. package/esm/AlignmentsFeatureDetail/getSAFeatures.js +0 -4
  259. package/esm/AlignmentsFeatureDetail/index.d.ts +1 -1
  260. package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +2 -2
  261. package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts +2 -2
  262. package/esm/AlignmentsFeatureDetail/stateModelFactory.js +1 -1
  263. package/esm/AlignmentsFeatureDetail/tagInfo.js +1 -1
  264. package/esm/AlignmentsFeatureDetail/util.d.ts +1 -1
  265. package/esm/AlignmentsTrack/configSchemaF.d.ts +1 -1
  266. package/esm/AlignmentsTrack/configSchemaF.js +1 -8
  267. package/esm/AlignmentsTrack/index.d.ts +1 -1
  268. package/esm/AlignmentsTrack/index.js +0 -3
  269. package/esm/BamAdapter/BamAdapter.d.ts +6 -5
  270. package/esm/BamAdapter/BamAdapter.js +19 -37
  271. package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -3
  272. package/esm/BamAdapter/BamSlightlyLazyFeature.js +0 -3
  273. package/esm/BamAdapter/configSchema.d.ts +0 -17
  274. package/esm/BamAdapter/configSchema.js +1 -22
  275. package/esm/BamAdapter/index.d.ts +1 -1
  276. package/esm/CramAdapter/CramAdapter.d.ts +6 -9
  277. package/esm/CramAdapter/CramAdapter.js +24 -42
  278. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +3 -3
  279. package/esm/CramAdapter/CramSlightlyLazyFeature.js +0 -17
  280. package/esm/CramAdapter/CramTestAdapters.d.ts +3 -3
  281. package/esm/CramAdapter/CramTestAdapters.js +6 -6
  282. package/esm/CramAdapter/configSchema.d.ts +0 -14
  283. package/esm/CramAdapter/configSchema.js +1 -19
  284. package/esm/CramAdapter/index.d.ts +1 -1
  285. package/esm/CramAdapter/index.js +0 -1
  286. package/esm/CramAdapter/util.d.ts +2 -2
  287. package/esm/CramAdapter/util.js +1 -24
  288. package/esm/GuessAlignmentsTypes/index.d.ts +1 -1
  289. package/esm/GuessAlignmentsTypes/index.js +20 -35
  290. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +2 -2
  291. package/esm/HtsgetBamAdapter/configSchema.d.ts +0 -9
  292. package/esm/HtsgetBamAdapter/configSchema.js +1 -14
  293. package/esm/HtsgetBamAdapter/index.d.ts +1 -1
  294. package/esm/HtsgetBamAdapter/index.js +1 -1
  295. package/esm/LinearAlignmentsDisplay/alignmentsModel.d.ts +2 -5
  296. package/esm/LinearAlignmentsDisplay/alignmentsModel.js +1 -31
  297. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +2 -3
  298. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -15
  299. package/esm/LinearAlignmentsDisplay/configSchema.d.ts +2 -16
  300. package/esm/LinearAlignmentsDisplay/configSchema.js +3 -20
  301. package/esm/LinearAlignmentsDisplay/index.d.ts +1 -1
  302. package/esm/LinearAlignmentsDisplay/index.js +1 -2
  303. package/esm/LinearAlignmentsDisplay/model.d.ts +7 -77
  304. package/esm/LinearAlignmentsDisplay/model.js +11 -86
  305. package/esm/LinearAlignmentsDisplay/util.d.ts +1 -1
  306. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +52 -164
  307. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +56 -140
  308. package/esm/LinearPileupDisplay/components/ColorByTagDialog.d.ts +1 -2
  309. package/esm/LinearPileupDisplay/components/ColorByTagDialog.js +12 -18
  310. package/esm/LinearPileupDisplay/components/GroupByDialog.d.ts +3 -4
  311. package/esm/LinearPileupDisplay/components/GroupByDialog.js +106 -69
  312. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +3 -8
  313. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +3 -4
  314. package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.d.ts +1 -2
  315. package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.js +15 -21
  316. package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts +1 -2
  317. package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.js +12 -17
  318. package/esm/LinearPileupDisplay/components/SortByTagDialog.d.ts +1 -2
  319. package/esm/LinearPileupDisplay/components/SortByTagDialog.js +17 -23
  320. package/esm/LinearPileupDisplay/configSchema.d.ts +13 -16
  321. package/esm/LinearPileupDisplay/configSchema.js +12 -30
  322. package/esm/LinearPileupDisplay/index.d.ts +1 -1
  323. package/esm/LinearPileupDisplay/index.js +2 -2
  324. package/esm/LinearPileupDisplay/model.d.ts +123 -111
  325. package/esm/LinearPileupDisplay/model.js +13 -103
  326. package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts +2 -3
  327. package/esm/LinearReadArcsDisplay/components/ReactComponent.js +6 -10
  328. package/esm/LinearReadArcsDisplay/configSchema.d.ts +12 -20
  329. package/esm/LinearReadArcsDisplay/configSchema.js +8 -31
  330. package/esm/LinearReadArcsDisplay/drawFeats.d.ts +1 -1
  331. package/esm/LinearReadArcsDisplay/drawFeats.js +1 -9
  332. package/esm/LinearReadArcsDisplay/index.d.ts +1 -1
  333. package/esm/LinearReadArcsDisplay/index.js +1 -2
  334. package/esm/LinearReadArcsDisplay/model.d.ts +16 -94
  335. package/esm/LinearReadArcsDisplay/model.js +18 -105
  336. package/esm/LinearReadArcsDisplay/util.d.ts +1 -1
  337. package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts +2 -3
  338. package/esm/LinearReadCloudDisplay/components/ReactComponent.js +6 -10
  339. package/esm/LinearReadCloudDisplay/configSchema.d.ts +5 -17
  340. package/esm/LinearReadCloudDisplay/configSchema.js +3 -28
  341. package/esm/LinearReadCloudDisplay/drawFeats.d.ts +1 -1
  342. package/esm/LinearReadCloudDisplay/drawFeats.js +2 -2
  343. package/esm/LinearReadCloudDisplay/drawLongReadChains.d.ts +4 -4
  344. package/esm/LinearReadCloudDisplay/drawLongReadChains.js +1 -4
  345. package/esm/LinearReadCloudDisplay/drawPairChains.d.ts +4 -4
  346. package/esm/LinearReadCloudDisplay/drawPairChains.js +0 -3
  347. package/esm/LinearReadCloudDisplay/index.d.ts +1 -1
  348. package/esm/LinearReadCloudDisplay/index.js +1 -2
  349. package/esm/LinearReadCloudDisplay/model.d.ts +14 -56
  350. package/esm/LinearReadCloudDisplay/model.js +17 -68
  351. package/esm/LinearReadCloudDisplay/util.js +0 -1
  352. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +2 -3
  353. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +16 -52
  354. package/esm/LinearSNPCoverageDisplay/configSchema.d.ts +17 -22
  355. package/esm/LinearSNPCoverageDisplay/configSchema.js +16 -32
  356. package/esm/LinearSNPCoverageDisplay/index.d.ts +1 -1
  357. package/esm/LinearSNPCoverageDisplay/index.js +1 -2
  358. package/esm/LinearSNPCoverageDisplay/model.d.ts +13 -54
  359. package/esm/LinearSNPCoverageDisplay/model.js +53 -153
  360. package/esm/MismatchParser/cigarToMismatches.d.ts +2 -3
  361. package/esm/MismatchParser/cigarToMismatches.js +4 -7
  362. package/esm/MismatchParser/getNextRefPos.js +0 -2
  363. package/esm/MismatchParser/index.d.ts +3 -4
  364. package/esm/MismatchParser/index.js +1 -9
  365. package/esm/MismatchParser/mdToMismatches.d.ts +2 -3
  366. package/esm/MismatchParser/mdToMismatches.js +0 -6
  367. package/esm/ModificationParser/index.d.ts +1 -1
  368. package/esm/ModificationParser/index.js +1 -18
  369. package/esm/PileupRPC/base.d.ts +2 -2
  370. package/esm/PileupRPC/base.js +0 -1
  371. package/esm/PileupRPC/index.d.ts +1 -1
  372. package/esm/PileupRPC/index.js +1 -1
  373. package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +2 -3
  374. package/esm/PileupRPC/methods/GetGlobalValueForTag.js +1 -2
  375. package/esm/PileupRPC/methods/GetReducedFeatures.d.ts +2 -3
  376. package/esm/PileupRPC/methods/GetReducedFeatures.js +3 -5
  377. package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +3 -4
  378. package/esm/PileupRPC/methods/GetVisibleModifications.js +1 -1
  379. package/esm/PileupRPC/util.d.ts +1 -1
  380. package/esm/PileupRenderer/PileupLayoutSession.d.ts +5 -5
  381. package/esm/PileupRenderer/PileupLayoutSession.js +2 -5
  382. package/esm/PileupRenderer/PileupRenderer.d.ts +14 -24
  383. package/esm/PileupRenderer/PileupRenderer.js +12 -17
  384. package/esm/PileupRenderer/colorBy.d.ts +2 -2
  385. package/esm/PileupRenderer/colorBy.js +1 -7
  386. package/esm/PileupRenderer/components/PileupRendering.d.ts +2 -3
  387. package/esm/PileupRenderer/components/PileupRendering.js +15 -20
  388. package/esm/PileupRenderer/configSchema.d.ts +5 -31
  389. package/esm/PileupRenderer/configSchema.js +6 -35
  390. package/esm/PileupRenderer/getAlignmentShapeColor.d.ts +2 -2
  391. package/esm/PileupRenderer/getAlignmentShapeColor.js +2 -7
  392. package/esm/PileupRenderer/index.d.ts +1 -1
  393. package/esm/PileupRenderer/index.js +1 -1
  394. package/esm/PileupRenderer/layoutFeature.d.ts +2 -2
  395. package/esm/PileupRenderer/layoutFeature.js +0 -1
  396. package/esm/PileupRenderer/layoutFeatures.d.ts +5 -2
  397. package/esm/PileupRenderer/layoutFeatures.js +7 -5
  398. package/esm/PileupRenderer/makeImageData.d.ts +3 -4
  399. package/esm/PileupRenderer/makeImageData.js +10 -2
  400. package/esm/PileupRenderer/renderAlignment.d.ts +3 -3
  401. package/esm/PileupRenderer/renderAlignment.js +3 -5
  402. package/esm/PileupRenderer/renderAlignmentShape.d.ts +3 -3
  403. package/esm/PileupRenderer/renderAlignmentShape.js +1 -1
  404. package/esm/PileupRenderer/renderMethylation.d.ts +4 -4
  405. package/esm/PileupRenderer/renderMethylation.js +0 -4
  406. package/esm/PileupRenderer/renderMismatches.d.ts +5 -4
  407. package/esm/PileupRenderer/renderMismatches.js +19 -25
  408. package/esm/PileupRenderer/renderModifications.d.ts +3 -3
  409. package/esm/PileupRenderer/renderModifications.js +1 -3
  410. package/esm/PileupRenderer/renderPerBaseLettering.d.ts +2 -2
  411. package/esm/PileupRenderer/renderPerBaseLettering.js +0 -1
  412. package/esm/PileupRenderer/renderPerBaseQuality.d.ts +2 -2
  413. package/esm/PileupRenderer/renderPerBaseQuality.js +2 -2
  414. package/esm/PileupRenderer/renderSoftClipping.d.ts +5 -5
  415. package/esm/PileupRenderer/renderSoftClipping.js +1 -5
  416. package/esm/PileupRenderer/sortUtil.d.ts +2 -2
  417. package/esm/PileupRenderer/sortUtil.js +1 -4
  418. package/esm/PileupRenderer/types.d.ts +26 -0
  419. package/esm/PileupRenderer/types.js +1 -0
  420. package/esm/PileupRenderer/util.d.ts +2 -2
  421. package/esm/PileupRenderer/util.js +1 -3
  422. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +4 -3
  423. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +5 -7
  424. package/esm/SNPCoverageAdapter/configSchema.d.ts +0 -4
  425. package/esm/SNPCoverageAdapter/configSchema.js +1 -8
  426. package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +4 -8
  427. package/esm/SNPCoverageAdapter/generateCoverageBins.js +24 -246
  428. package/esm/SNPCoverageAdapter/index.d.ts +1 -1
  429. package/esm/SNPCoverageAdapter/processDepth.d.ts +8 -0
  430. package/esm/SNPCoverageAdapter/processDepth.js +35 -0
  431. package/esm/SNPCoverageAdapter/processMismatches.d.ts +9 -0
  432. package/esm/SNPCoverageAdapter/processMismatches.js +55 -0
  433. package/esm/SNPCoverageAdapter/processModifications.d.ts +10 -0
  434. package/esm/SNPCoverageAdapter/processModifications.js +46 -0
  435. package/esm/SNPCoverageAdapter/processReferenceCpGs.d.ts +9 -0
  436. package/esm/SNPCoverageAdapter/processReferenceCpGs.js +60 -0
  437. package/esm/SNPCoverageAdapter/util.d.ts +10 -0
  438. package/esm/SNPCoverageAdapter/util.js +35 -0
  439. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -18
  440. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +3 -289
  441. package/esm/SNPCoverageRenderer/configSchema.d.ts +3 -18
  442. package/esm/SNPCoverageRenderer/configSchema.js +4 -22
  443. package/esm/SNPCoverageRenderer/index.d.ts +1 -1
  444. package/esm/SNPCoverageRenderer/index.js +2 -2
  445. package/esm/SNPCoverageRenderer/makeImage.d.ts +2 -0
  446. package/esm/SNPCoverageRenderer/makeImage.js +267 -0
  447. package/esm/SNPCoverageRenderer/types.d.ts +19 -0
  448. package/esm/SNPCoverageRenderer/types.js +1 -0
  449. package/esm/index.d.ts +2 -2
  450. package/esm/index.js +10 -10
  451. package/esm/shared/afterAttach.d.ts +1 -1
  452. package/esm/shared/afterAttach.js +0 -2
  453. package/esm/shared/color.d.ts +1 -1
  454. package/esm/shared/color.js +0 -8
  455. package/esm/shared/components/BaseDisplayComponent.d.ts +3 -4
  456. package/esm/shared/components/BaseDisplayComponent.js +13 -16
  457. package/esm/shared/components/FilterByTagDialog.d.ts +2 -3
  458. package/esm/shared/components/FilterByTagDialog.js +44 -71
  459. package/esm/shared/fetchChains.d.ts +2 -2
  460. package/esm/shared/fetchChains.js +1 -2
  461. package/esm/shared/getMaximumModificationAtEachPosition.d.ts +1 -1
  462. package/esm/shared/getMaximumModificationAtEachPosition.js +1 -2
  463. package/esm/shared/getUniqueModifications.d.ts +5 -5
  464. package/esm/shared/getUniqueTags.d.ts +4 -4
  465. package/esm/shared/renderSvgUtil.d.ts +1 -2
  466. package/esm/shared/renderSvgUtil.js +3 -9
  467. package/esm/shared/util.d.ts +11 -1
  468. package/esm/shared/util.js +24 -0
  469. package/esm/util.d.ts +4 -4
  470. package/esm/util.js +3 -9
  471. package/package.json +6 -7
@@ -1,11 +1,9 @@
1
- import React from 'react';
2
- import { autorun, when } from 'mobx';
3
- import { addDisposer, getSnapshot, isAlive, types, } from 'mobx-state-tree';
4
- import deepEqual from 'fast-deep-equal';
5
- // jbrowse
6
- import { getConf, } from '@jbrowse/core/configuration';
1
+ import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { getConf } from '@jbrowse/core/configuration';
7
3
  import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
8
- // locals
4
+ import deepEqual from 'fast-deep-equal';
5
+ import { autorun, when } from 'mobx';
6
+ import { addDisposer, getSnapshot, isAlive, types } from 'mobx-state-tree';
9
7
  import { LinearAlignmentsDisplayMixin } from './alignmentsModel';
10
8
  import { getLowerPanelDisplays } from './util';
11
9
  const minDisplayHeight = 20;
@@ -38,110 +36,65 @@ function propagateFilterBy(self) {
38
36
  });
39
37
  }
40
38
  }
41
- /**
42
- * #stateModel LinearAlignmentsDisplay
43
- * extends
44
- * - [BaseDisplay](../basedisplay)
45
- * - [LinearAlignmentsDisplayMixin](../linearalignmentsdisplaymixin)
46
- */
47
39
  function stateModelFactory(pluginManager, configSchema) {
48
40
  return types
49
41
  .compose('LinearAlignmentsDisplay', BaseDisplay, LinearAlignmentsDisplayMixin(pluginManager, configSchema))
50
42
  .volatile(() => ({
51
- /**
52
- * #volatile
53
- */
54
43
  scrollTop: 0,
55
44
  }))
56
45
  .actions(self => ({
57
- /**
58
- * #action
59
- */
60
46
  setScrollTop(scrollTop) {
61
47
  self.scrollTop = scrollTop;
62
48
  },
63
- /**
64
- * #action
65
- */
66
49
  setSNPCoverageHeight(n) {
67
50
  self.snpCovHeight = n;
68
51
  },
69
52
  }))
70
53
  .views(self => ({
71
- /**
72
- * #getter
73
- */
74
54
  get height() {
75
55
  var _a;
76
56
  return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : getConf(self, 'height');
77
57
  },
78
- /**
79
- * #getter
80
- */
81
58
  get featureIdUnderMouse() {
82
59
  return (self.PileupDisplay.featureIdUnderMouse ||
83
60
  self.SNPCoverageDisplay.featureIdUnderMouse);
84
61
  },
85
62
  }))
86
63
  .views(self => ({
87
- /**
88
- * #getter
89
- */
90
64
  get pileupConf() {
91
65
  const conf = getConf(self, 'pileupDisplay');
92
66
  return {
93
67
  ...conf,
94
68
  type: self.lowerPanelType,
95
- displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
69
+ displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`,
96
70
  };
97
71
  },
98
- /**
99
- * #method
100
- */
101
72
  getFeatureByID(blockKey, id) {
102
73
  return self.PileupDisplay.getFeatureByID(blockKey, id);
103
74
  },
104
- /**
105
- * #method
106
- */
107
75
  searchFeatureByID(id) {
108
76
  var _a, _b;
109
77
  return (_b = (_a = self.PileupDisplay).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, id);
110
78
  },
111
- /**
112
- * #getter
113
- */
114
79
  get features() {
115
80
  return self.PileupDisplay.features;
116
81
  },
117
- /**
118
- * #getteralignmentsdisplaymodel
119
- */
120
82
  get DisplayBlurb() {
121
83
  var _a;
122
84
  return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
123
85
  },
124
- /**
125
- * #getter
126
- */
127
86
  get sortedBy() {
128
87
  return self.PileupDisplay.sortedBy;
129
88
  },
130
- /**
131
- * #getter
132
- */
133
89
  get coverageConf() {
134
90
  const conf = getConf(self, 'snpCoverageDisplay');
135
91
  return {
136
92
  ...conf,
137
- displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
93
+ displayId: `${self.configuration.displayId}_snpcoverage_xyz`,
138
94
  };
139
95
  },
140
96
  }))
141
97
  .actions(self => ({
142
- /**
143
- * #action
144
- */
145
98
  setSNPCoverageDisplay(configuration) {
146
99
  self.SNPCoverageDisplay = {
147
100
  type: 'LinearSNPCoverageDisplay',
@@ -149,45 +102,27 @@ function stateModelFactory(pluginManager, configSchema) {
149
102
  height: self.snpCovHeight,
150
103
  };
151
104
  },
152
- /**
153
- * #action
154
- */
155
105
  setFeatureDensityStatsLimit(stats) {
156
106
  self.PileupDisplay.setFeatureDensityStatsLimit(stats);
157
107
  self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
158
108
  },
159
- /**
160
- * #action
161
- */
162
109
  setPileupDisplay(configuration) {
163
110
  self.PileupDisplay = {
164
111
  type: configuration.type || 'LinearPileupDisplay',
165
112
  configuration,
166
113
  };
167
114
  },
168
- /**
169
- * #action
170
- */
171
115
  setHeight(n) {
172
116
  self.heightPreConfig = Math.max(n, minDisplayHeight);
173
117
  return self.heightPreConfig;
174
118
  },
175
- /**
176
- * #action
177
- */
178
119
  setFilterBy(filter) {
179
120
  self.PileupDisplay.setFilterBy(filter);
180
121
  self.SNPCoverageDisplay.setFilterBy(filter);
181
122
  },
182
- /**
183
- * #action
184
- */
185
123
  setLowerPanelType(type) {
186
124
  self.lowerPanelType = type;
187
125
  },
188
- /**
189
- * #action
190
- */
191
126
  resizeHeight(distance) {
192
127
  const oldHeight = self.height;
193
128
  const newHeight = this.setHeight(self.height + distance);
@@ -221,27 +156,19 @@ function stateModelFactory(pluginManager, configSchema) {
221
156
  self.PileupDisplay.setHeight(self.height - self.SNPCoverageDisplay.height);
222
157
  }));
223
158
  },
224
- /**
225
- * #action
226
- */
227
159
  async renderSvg(opts) {
228
160
  const pileupHeight = self.height - self.SNPCoverageDisplay.height;
229
161
  await when(() => !self.PileupDisplay.renderProps().notReady &&
230
162
  !self.SNPCoverageDisplay.renderProps().notReady);
231
- return (React.createElement(React.Fragment, null,
232
- React.createElement("g", null, await self.SNPCoverageDisplay.renderSvg(opts)),
233
- React.createElement("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})` }, await self.PileupDisplay.renderSvg({
234
- ...opts,
235
- overrideHeight: pileupHeight,
236
- }))));
163
+ return (_jsxs(_Fragment, { children: [_jsx("g", { children: await self.SNPCoverageDisplay.renderSvg(opts) }), _jsx("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})`, children: await self.PileupDisplay.renderSvg({
164
+ ...opts,
165
+ overrideHeight: pileupHeight,
166
+ }) })] }));
237
167
  },
238
168
  }))
239
169
  .views(self => {
240
170
  const { trackMenuItems: superTrackMenuItems } = self;
241
171
  return {
242
- /**
243
- * #method
244
- */
245
172
  trackMenuItems() {
246
173
  if (!self.PileupDisplay) {
247
174
  return [];
@@ -276,11 +203,9 @@ function stateModelFactory(pluginManager, configSchema) {
276
203
  };
277
204
  })
278
205
  .preProcessSnapshot(snap => {
279
- // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
280
206
  if (!snap) {
281
207
  return snap;
282
208
  }
283
- // @ts-expect-error
284
209
  const { height, ...rest } = snap;
285
210
  return { heightPreConfig: height, ...rest };
286
211
  });
@@ -1,2 +1,2 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
1
+ import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  export declare function getLowerPanelDisplays(pluginManager: PluginManager): import("@jbrowse/core/pluggableElementTypes").DisplayType[];
@@ -1,13 +1,8 @@
1
- import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
2
1
  import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
3
- import { Feature } from '@jbrowse/core/util';
4
2
  import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
5
- import { ColorBy, FilterBy } from '../shared/types';
6
- /**
7
- * #stateModel SharedLinearPileupDisplayMixin
8
- * #category display
9
- * extends `BaseLinearDisplay`
10
- */
3
+ import type { ColorBy, FilterBy } from '../shared/types';
4
+ import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
5
+ import type { Feature } from '@jbrowse/core/util';
11
6
  export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
12
7
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
13
8
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -20,21 +15,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
20
15
  } & {
21
16
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
22
17
  key: import("mobx-state-tree").ISimpleType<string>;
23
- region: import("mobx-state-tree").IModelType<{
24
- refName: import("mobx-state-tree").ISimpleType<string>;
25
- start: import("mobx-state-tree").ISimpleType<number>;
26
- end: import("mobx-state-tree").ISimpleType<number>;
27
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
28
- } & {
29
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
30
- }, {
31
- setRefName(newRefName: string): void;
32
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
18
+ region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
33
19
  reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
34
20
  isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
35
21
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
36
22
  }, {
37
- renderInProgress: AbortController | undefined;
23
+ stopToken: string | undefined;
38
24
  filled: boolean;
39
25
  reactElement: React.ReactElement | undefined;
40
26
  features: Map<string, Feature> | undefined;
@@ -52,21 +38,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
52
38
  status?: string;
53
39
  reactElement?: React.ReactElement;
54
40
  };
55
- }) => import("react").JSX.Element | undefined;
41
+ }) => import("react/jsx-runtime").JSX.Element | undefined;
56
42
  renderProps: any;
57
43
  } & {
58
44
  doReload(): void;
59
45
  afterAttach(): void;
60
46
  setStatus(message: string): void;
61
- setLoading(abortController: AbortController): void;
47
+ setLoading(newStopToken: string): void;
62
48
  setMessage(messageText: string): void;
63
- setRendered(props: {
64
- reactElement: React.ReactElement;
65
- features: Map<string, Feature>;
66
- layout: any;
67
- maxHeightReached: boolean;
68
- renderProps: any;
69
- } | undefined): void;
49
+ setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
70
50
  setError(error: unknown): void;
71
51
  reload(): void;
72
52
  beforeDestroy(): void;
@@ -100,38 +80,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
100
80
  };
101
81
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
102
82
  } & {
103
- /**
104
- * #property
105
- */
106
83
  configuration: AnyConfigurationSchemaType;
107
- /**
108
- * #property
109
- */
110
84
  featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
111
- /**
112
- * #property
113
- */
114
85
  noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
115
- /**
116
- * #property
117
- */
118
86
  fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
119
- /**
120
- * #property
121
- */
122
87
  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
123
- /**
124
- * #property
125
- */
126
- colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
127
- /**
128
- * #property
129
- */
130
- filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
131
- /**
132
- * #property
133
- */
88
+ colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
89
+ filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
134
90
  jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
91
+ hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
135
92
  }, {
136
93
  rendererTypeName: string;
137
94
  error: unknown;
@@ -221,14 +178,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
221
178
  readonly regionTooLarge: boolean;
222
179
  readonly regionTooLargeReason: string;
223
180
  } & {
181
+ readonly statsReadyAndRegionNotTooLarge: boolean;
224
182
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
225
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
183
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
226
184
  } & {
227
185
  featureIdUnderMouse: undefined | string;
228
186
  contextMenuFeature: undefined | Feature;
229
187
  } & {
230
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
231
- readonly blockType: "dynamicBlocks" | "staticBlocks";
188
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
189
+ readonly blockType: "staticBlocks" | "dynamicBlocks";
232
190
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
233
191
  } & {
234
192
  readonly renderDelay: number;
@@ -255,68 +213,33 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
255
213
  contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
256
214
  renderProps(): any;
257
215
  } & {
258
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
216
+ renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
259
217
  afterAttach(): void;
260
218
  } & {
261
219
  colorTagMap: import("mobx").ObservableMap<string, string>;
262
220
  featureUnderMouseVolatile: undefined | Feature;
263
221
  tagsReady: boolean;
222
+ } & {
223
+ readonly colorBy: any;
224
+ readonly filterBy: any;
264
225
  } & {
265
226
  readonly autorunReady: boolean;
227
+ readonly hideSmallIndels: boolean | undefined;
266
228
  } & {
267
- /**
268
- * #action
269
- */
270
229
  setTagsReady(flag: boolean): void;
271
- /**
272
- * #action
273
- */
274
230
  setMaxHeight(n?: number): void;
275
- /**
276
- * #action
277
- */
278
231
  setFeatureHeight(n?: number): void;
279
- /**
280
- * #action
281
- */
282
232
  setNoSpacing(flag?: boolean): void;
283
- /**
284
- * #action
285
- */
286
233
  setColorScheme(colorScheme: ColorBy): void;
287
- /**
288
- * #action
289
- */
290
234
  updateColorTagMap(uniqueTag: string[]): void;
291
- /**
292
- * #action
293
- */
294
235
  setFeatureUnderMouse(feat?: Feature): void;
295
- /**
296
- * #action
297
- */
298
236
  selectFeature(feature: Feature): void;
299
- /**
300
- * #action
301
- * uses copy-to-clipboard and generates notification
302
- */
303
237
  copyFeatureToClipboard(feature: Feature): void;
304
- /**
305
- * #action
306
- */
307
238
  setConfig(conf: AnyConfigurationModel): void;
308
- /**
309
- * #action
310
- */
311
239
  setFilterBy(filter: FilterBy): void;
312
- /**
313
- * #action
314
- */
315
240
  setJexlFilters(filters: string[]): void;
241
+ setHideSmallIndels(arg: boolean): void;
316
242
  } & {
317
- /**
318
- * #getter
319
- */
320
243
  readonly rendererConfig: {
321
244
  [x: string]: any;
322
245
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -329,34 +252,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
329
252
  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
330
253
  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
331
254
  } & {
332
- /**
333
- * #getter
334
- */
335
255
  readonly maxHeight: any;
336
- /**
337
- * #getter
338
- */
339
256
  readonly featureHeightSetting: any;
340
- /**
341
- * #getter
342
- */
343
257
  readonly featureUnderMouse: Feature | undefined;
344
- /**
345
- * #getter
346
- */
347
258
  renderReady(): boolean;
348
- /**
349
- * #getter
350
- */
351
259
  readonly filters: SerializableFilterChain;
352
260
  } & {
353
- /**
354
- * #getter
355
- */
356
261
  readonly rendererTypeName: string;
357
- /**
358
- * #method
359
- */
360
262
  contextMenuItems(): ({
361
263
  label: string;
362
264
  icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -368,47 +270,38 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
368
270
  icon: typeof ContentCopyIcon;
369
271
  onClick: () => void;
370
272
  })[];
371
- /**
372
- * #getter
373
- */
374
273
  readonly DisplayBlurb: ({ model, }: {
375
274
  model: {
376
- sortedBy?: {
377
- pos: number;
378
- refName: number;
379
- type: string;
380
- tag?: string;
381
- };
275
+ sortedBy?: import("../shared/types").SortedBy;
382
276
  };
383
- }) => import("react").JSX.Element | null;
384
- /**
385
- * #method
386
- */
277
+ }) => import("react/jsx-runtime").JSX.Element | null;
387
278
  renderPropsPre(): any;
388
- /**
389
- * #method
390
- */
391
279
  colorSchemeSubMenuItems(): {
392
280
  label: string;
393
281
  onClick: () => void;
394
282
  }[];
395
- /**
396
- * #method
397
- */
398
283
  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 | {
284
+ label: string;
285
+ priority: number;
286
+ type: string;
287
+ checked: boolean | undefined;
288
+ onClick: () => void;
289
+ icon?: undefined;
290
+ } | {
399
291
  label: string;
400
292
  icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
401
293
  muiName: string;
402
294
  };
403
295
  onClick: () => void;
296
+ priority?: undefined;
297
+ type?: undefined;
298
+ checked?: undefined;
404
299
  })[];
405
300
  } & {
406
301
  renderProps(): any;
407
302
  } & {
408
303
  afterAttach(): void;
409
- }, {
410
- type: string;
411
- } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
304
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
412
305
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
413
306
  type: import("mobx-state-tree").ISimpleType<string>;
414
307
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -420,21 +313,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
420
313
  } & {
421
314
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
422
315
  key: import("mobx-state-tree").ISimpleType<string>;
423
- region: import("mobx-state-tree").IModelType<{
424
- refName: import("mobx-state-tree").ISimpleType<string>;
425
- start: import("mobx-state-tree").ISimpleType<number>;
426
- end: import("mobx-state-tree").ISimpleType<number>;
427
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
428
- } & {
429
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
430
- }, {
431
- setRefName(newRefName: string): void;
432
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
316
+ region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
433
317
  reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
434
318
  isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
435
319
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
436
320
  }, {
437
- renderInProgress: AbortController | undefined;
321
+ stopToken: string | undefined;
438
322
  filled: boolean;
439
323
  reactElement: React.ReactElement | undefined;
440
324
  features: Map<string, Feature> | undefined;
@@ -452,21 +336,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
452
336
  status?: string;
453
337
  reactElement?: React.ReactElement;
454
338
  };
455
- }) => import("react").JSX.Element | undefined;
339
+ }) => import("react/jsx-runtime").JSX.Element | undefined;
456
340
  renderProps: any;
457
341
  } & {
458
342
  doReload(): void;
459
343
  afterAttach(): void;
460
344
  setStatus(message: string): void;
461
- setLoading(abortController: AbortController): void;
345
+ setLoading(newStopToken: string): void;
462
346
  setMessage(messageText: string): void;
463
- setRendered(props: {
464
- reactElement: React.ReactElement;
465
- features: Map<string, Feature>;
466
- layout: any;
467
- maxHeightReached: boolean;
468
- renderProps: any;
469
- } | undefined): void;
347
+ setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
470
348
  setError(error: unknown): void;
471
349
  reload(): void;
472
350
  beforeDestroy(): void;
@@ -499,12 +377,22 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
499
377
  defaultValue: never[];
500
378
  };
501
379
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
502
- }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
503
- type: string;
380
+ } & {
381
+ configuration: AnyConfigurationSchemaType;
382
+ featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
383
+ noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
384
+ fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
385
+ trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
386
+ colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
387
+ filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
388
+ jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
389
+ hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
390
+ }>>, {
504
391
  id: string;
392
+ type: string;
505
393
  configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
506
- heightPreConfig: number | undefined;
507
394
  rpcDriverName: string | undefined;
395
+ heightPreConfig: number | undefined;
508
396
  userBpPerPxLimit: number | undefined;
509
397
  userByteSizeLimit: number | undefined;
510
398
  } & import("mobx-state-tree")._NotCustomized>;