@jbrowse/plugin-alignments 2.2.2 → 2.3.0

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 (308) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +1 -1
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  3. package/dist/AlignmentsTrack/index.js +1 -0
  4. package/dist/AlignmentsTrack/index.js.map +1 -1
  5. package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -4
  6. package/dist/BamAdapter/BamSlightlyLazyFeature.js +11 -18
  7. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  8. package/dist/BamAdapter/index.js +1 -0
  9. package/dist/BamAdapter/index.js.map +1 -1
  10. package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +5 -7
  11. package/dist/CramAdapter/CramSlightlyLazyFeature.js +6 -8
  12. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  13. package/dist/CramAdapter/index.js +1 -0
  14. package/dist/CramAdapter/index.js.map +1 -1
  15. package/dist/GuessAlignmentsTypes/index.d.ts +3 -0
  16. package/dist/GuessAlignmentsTypes/index.js +56 -0
  17. package/dist/GuessAlignmentsTypes/index.js.map +1 -0
  18. package/dist/HtsgetBamAdapter/index.js +11 -11
  19. package/dist/HtsgetBamAdapter/index.js.map +1 -1
  20. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -13
  21. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  22. package/dist/LinearAlignmentsDisplay/index.js +1 -0
  23. package/dist/LinearAlignmentsDisplay/index.js.map +1 -1
  24. package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +6 -3
  25. package/dist/LinearAlignmentsDisplay/models/configSchema.js +2 -3
  26. package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
  27. package/dist/LinearAlignmentsDisplay/models/model.d.ts +22 -36
  28. package/dist/LinearAlignmentsDisplay/models/model.js +166 -151
  29. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  30. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +2 -2
  31. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -4
  32. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  33. package/dist/LinearPileupDisplay/configSchema.d.ts +0 -3
  34. package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
  35. package/dist/LinearPileupDisplay/index.js +2 -0
  36. package/dist/LinearPileupDisplay/index.js.map +1 -1
  37. package/dist/LinearPileupDisplay/model.d.ts +19 -16
  38. package/dist/LinearPileupDisplay/model.js +28 -13
  39. package/dist/LinearPileupDisplay/model.js.map +1 -1
  40. package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts +6 -0
  41. package/dist/LinearReadArcsDisplay/components/ReactComponent.js +49 -0
  42. package/dist/LinearReadArcsDisplay/components/ReactComponent.js.map +1 -0
  43. package/dist/LinearReadArcsDisplay/configSchema.d.ts +6 -0
  44. package/dist/LinearReadArcsDisplay/configSchema.js +52 -0
  45. package/dist/LinearReadArcsDisplay/configSchema.js.map +1 -0
  46. package/dist/LinearReadArcsDisplay/drawFeats.d.ts +14 -0
  47. package/dist/LinearReadArcsDisplay/drawFeats.js +162 -0
  48. package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -0
  49. package/dist/LinearReadArcsDisplay/index.d.ts +2 -0
  50. package/dist/LinearReadArcsDisplay/index.js +27 -0
  51. package/dist/LinearReadArcsDisplay/index.js.map +1 -0
  52. package/dist/LinearReadArcsDisplay/model.d.ts +342 -0
  53. package/dist/LinearReadArcsDisplay/model.js +327 -0
  54. package/dist/LinearReadArcsDisplay/model.js.map +1 -0
  55. package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts +6 -0
  56. package/dist/LinearReadCloudDisplay/components/ReactComponent.js +49 -0
  57. package/dist/LinearReadCloudDisplay/components/ReactComponent.js.map +1 -0
  58. package/dist/LinearReadCloudDisplay/configSchema.d.ts +6 -0
  59. package/dist/LinearReadCloudDisplay/configSchema.js +51 -0
  60. package/dist/LinearReadCloudDisplay/configSchema.js.map +1 -0
  61. package/dist/LinearReadCloudDisplay/drawFeats.d.ts +10 -0
  62. package/dist/LinearReadCloudDisplay/drawFeats.js +159 -0
  63. package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -0
  64. package/dist/LinearReadCloudDisplay/index.d.ts +2 -0
  65. package/dist/LinearReadCloudDisplay/index.js +27 -0
  66. package/dist/LinearReadCloudDisplay/index.js.map +1 -0
  67. package/dist/LinearReadCloudDisplay/model.d.ts +320 -0
  68. package/dist/LinearReadCloudDisplay/model.js +252 -0
  69. package/dist/LinearReadCloudDisplay/model.js.map +1 -0
  70. package/dist/LinearSNPCoverageDisplay/index.js +1 -0
  71. package/dist/LinearSNPCoverageDisplay/index.js.map +1 -1
  72. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +19 -20
  73. package/dist/LinearSNPCoverageDisplay/models/model.js +1 -6
  74. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  75. package/dist/{BamAdapter/MismatchParser.d.ts → MismatchParser/index.d.ts} +23 -0
  76. package/dist/{BamAdapter/MismatchParser.js → MismatchParser/index.js} +116 -3
  77. package/dist/MismatchParser/index.js.map +1 -0
  78. package/dist/PileupRPC/base.d.ts +8 -0
  79. package/dist/PileupRPC/base.js +22 -0
  80. package/dist/PileupRPC/base.js.map +1 -0
  81. package/dist/PileupRPC/index.d.ts +3 -0
  82. package/dist/PileupRPC/index.js +9 -0
  83. package/dist/PileupRPC/index.js.map +1 -0
  84. package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts +14 -0
  85. package/dist/PileupRPC/methods/GetGlobalValueForTag.js +29 -0
  86. package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -0
  87. package/dist/PileupRPC/methods/GetReducedFeatures.d.ts +25 -0
  88. package/dist/PileupRPC/methods/GetReducedFeatures.js +61 -0
  89. package/dist/PileupRPC/methods/GetReducedFeatures.js.map +1 -0
  90. package/dist/PileupRPC/methods/GetVisibleModifications.d.ts +14 -0
  91. package/dist/PileupRPC/methods/GetVisibleModifications.js +32 -0
  92. package/dist/PileupRPC/methods/GetVisibleModifications.js.map +1 -0
  93. package/dist/PileupRPC/rpcMethods.d.ts +4 -34
  94. package/dist/PileupRPC/rpcMethods.js +7 -77
  95. package/dist/PileupRPC/rpcMethods.js.map +1 -1
  96. package/dist/PileupRPC/util.d.ts +8 -0
  97. package/dist/PileupRPC/util.js +20 -0
  98. package/dist/PileupRPC/util.js.map +1 -0
  99. package/dist/PileupRenderer/PileupRenderer.d.ts +1 -1
  100. package/dist/PileupRenderer/PileupRenderer.js +5 -5
  101. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  102. package/dist/PileupRenderer/index.js +1 -0
  103. package/dist/PileupRenderer/index.js.map +1 -1
  104. package/dist/PileupRenderer/sortUtil.d.ts +1 -1
  105. package/dist/PileupRenderer/sortUtil.js +2 -2
  106. package/dist/PileupRenderer/sortUtil.js.map +1 -1
  107. package/dist/SNPCoverageAdapter/generateCoverageBins.js +1 -1
  108. package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
  109. package/dist/SNPCoverageAdapter/index.js +1 -3
  110. package/dist/SNPCoverageAdapter/index.js.map +1 -1
  111. package/dist/index.d.ts +2 -2
  112. package/dist/index.js +12 -58
  113. package/dist/index.js.map +1 -1
  114. package/dist/{LinearPileupDisplay/components → shared}/FilterByTag.d.ts +0 -0
  115. package/dist/{LinearPileupDisplay/components → shared}/FilterByTag.js +3 -9
  116. package/dist/shared/FilterByTag.js.map +1 -0
  117. package/dist/shared/color.d.ts +17 -0
  118. package/dist/shared/color.js +43 -0
  119. package/dist/shared/color.js.map +1 -0
  120. package/dist/shared/fetchChains.d.ts +27 -0
  121. package/dist/shared/fetchChains.js +30 -0
  122. package/dist/shared/fetchChains.js.map +1 -0
  123. package/dist/shared/index.d.ts +36 -0
  124. package/dist/{shared.js → shared/index.js} +12 -2
  125. package/dist/shared/index.js.map +1 -0
  126. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +1 -1
  127. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  128. package/esm/AlignmentsTrack/index.js +1 -0
  129. package/esm/AlignmentsTrack/index.js.map +1 -1
  130. package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -4
  131. package/esm/BamAdapter/BamSlightlyLazyFeature.js +11 -18
  132. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  133. package/esm/BamAdapter/index.js +1 -0
  134. package/esm/BamAdapter/index.js.map +1 -1
  135. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +5 -7
  136. package/esm/CramAdapter/CramSlightlyLazyFeature.js +6 -8
  137. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  138. package/esm/CramAdapter/index.js +1 -0
  139. package/esm/CramAdapter/index.js.map +1 -1
  140. package/esm/GuessAlignmentsTypes/index.d.ts +3 -0
  141. package/esm/GuessAlignmentsTypes/index.js +54 -0
  142. package/esm/GuessAlignmentsTypes/index.js.map +1 -0
  143. package/esm/HtsgetBamAdapter/index.js +11 -11
  144. package/esm/HtsgetBamAdapter/index.js.map +1 -1
  145. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -13
  146. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  147. package/esm/LinearAlignmentsDisplay/index.js +1 -0
  148. package/esm/LinearAlignmentsDisplay/index.js.map +1 -1
  149. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +6 -3
  150. package/esm/LinearAlignmentsDisplay/models/configSchema.js +2 -4
  151. package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
  152. package/esm/LinearAlignmentsDisplay/models/model.d.ts +22 -36
  153. package/esm/LinearAlignmentsDisplay/models/model.js +167 -152
  154. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  155. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +2 -2
  156. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +2 -4
  157. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  158. package/esm/LinearPileupDisplay/configSchema.d.ts +0 -3
  159. package/esm/LinearPileupDisplay/configSchema.js.map +1 -1
  160. package/esm/LinearPileupDisplay/index.js +2 -0
  161. package/esm/LinearPileupDisplay/index.js.map +1 -1
  162. package/esm/LinearPileupDisplay/model.d.ts +19 -16
  163. package/esm/LinearPileupDisplay/model.js +29 -14
  164. package/esm/LinearPileupDisplay/model.js.map +1 -1
  165. package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts +6 -0
  166. package/esm/LinearReadArcsDisplay/components/ReactComponent.js +44 -0
  167. package/esm/LinearReadArcsDisplay/components/ReactComponent.js.map +1 -0
  168. package/esm/LinearReadArcsDisplay/configSchema.d.ts +6 -0
  169. package/esm/LinearReadArcsDisplay/configSchema.js +50 -0
  170. package/esm/LinearReadArcsDisplay/configSchema.js.map +1 -0
  171. package/esm/LinearReadArcsDisplay/drawFeats.d.ts +14 -0
  172. package/esm/LinearReadArcsDisplay/drawFeats.js +157 -0
  173. package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -0
  174. package/esm/LinearReadArcsDisplay/index.d.ts +2 -0
  175. package/esm/LinearReadArcsDisplay/index.js +21 -0
  176. package/esm/LinearReadArcsDisplay/index.js.map +1 -0
  177. package/esm/LinearReadArcsDisplay/model.d.ts +342 -0
  178. package/esm/LinearReadArcsDisplay/model.js +299 -0
  179. package/esm/LinearReadArcsDisplay/model.js.map +1 -0
  180. package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts +6 -0
  181. package/esm/LinearReadCloudDisplay/components/ReactComponent.js +44 -0
  182. package/esm/LinearReadCloudDisplay/components/ReactComponent.js.map +1 -0
  183. package/esm/LinearReadCloudDisplay/configSchema.d.ts +6 -0
  184. package/esm/LinearReadCloudDisplay/configSchema.js +49 -0
  185. package/esm/LinearReadCloudDisplay/configSchema.js.map +1 -0
  186. package/esm/LinearReadCloudDisplay/drawFeats.d.ts +10 -0
  187. package/esm/LinearReadCloudDisplay/drawFeats.js +156 -0
  188. package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -0
  189. package/esm/LinearReadCloudDisplay/index.d.ts +2 -0
  190. package/esm/LinearReadCloudDisplay/index.js +21 -0
  191. package/esm/LinearReadCloudDisplay/index.js.map +1 -0
  192. package/esm/LinearReadCloudDisplay/model.d.ts +320 -0
  193. package/esm/LinearReadCloudDisplay/model.js +224 -0
  194. package/esm/LinearReadCloudDisplay/model.js.map +1 -0
  195. package/esm/LinearSNPCoverageDisplay/index.js +1 -0
  196. package/esm/LinearSNPCoverageDisplay/index.js.map +1 -1
  197. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +19 -20
  198. package/esm/LinearSNPCoverageDisplay/models/model.js +2 -7
  199. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  200. package/esm/{BamAdapter/MismatchParser.d.ts → MismatchParser/index.d.ts} +23 -0
  201. package/esm/{BamAdapter/MismatchParser.js → MismatchParser/index.js} +107 -2
  202. package/esm/MismatchParser/index.js.map +1 -0
  203. package/esm/PileupRPC/base.d.ts +8 -0
  204. package/esm/PileupRPC/base.js +16 -0
  205. package/esm/PileupRPC/base.js.map +1 -0
  206. package/esm/PileupRPC/index.d.ts +3 -0
  207. package/esm/PileupRPC/index.js +7 -0
  208. package/esm/PileupRPC/index.js.map +1 -0
  209. package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +14 -0
  210. package/esm/PileupRPC/methods/GetGlobalValueForTag.js +23 -0
  211. package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -0
  212. package/esm/PileupRPC/methods/GetReducedFeatures.d.ts +25 -0
  213. package/esm/PileupRPC/methods/GetReducedFeatures.js +55 -0
  214. package/esm/PileupRPC/methods/GetReducedFeatures.js.map +1 -0
  215. package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +14 -0
  216. package/esm/PileupRPC/methods/GetVisibleModifications.js +26 -0
  217. package/esm/PileupRPC/methods/GetVisibleModifications.js.map +1 -0
  218. package/esm/PileupRPC/rpcMethods.d.ts +4 -34
  219. package/esm/PileupRPC/rpcMethods.js +4 -74
  220. package/esm/PileupRPC/rpcMethods.js.map +1 -1
  221. package/esm/PileupRPC/util.d.ts +8 -0
  222. package/esm/PileupRPC/util.js +15 -0
  223. package/esm/PileupRPC/util.js.map +1 -0
  224. package/esm/PileupRenderer/PileupRenderer.d.ts +1 -1
  225. package/esm/PileupRenderer/PileupRenderer.js +5 -5
  226. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  227. package/esm/PileupRenderer/index.js +1 -0
  228. package/esm/PileupRenderer/index.js.map +1 -1
  229. package/esm/PileupRenderer/sortUtil.d.ts +1 -1
  230. package/esm/PileupRenderer/sortUtil.js +1 -1
  231. package/esm/PileupRenderer/sortUtil.js.map +1 -1
  232. package/esm/SNPCoverageAdapter/generateCoverageBins.js +1 -1
  233. package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
  234. package/esm/SNPCoverageAdapter/index.js +1 -3
  235. package/esm/SNPCoverageAdapter/index.js.map +1 -1
  236. package/esm/index.d.ts +2 -2
  237. package/esm/index.js +10 -56
  238. package/esm/index.js.map +1 -1
  239. package/esm/{LinearPileupDisplay/components → shared}/FilterByTag.d.ts +0 -0
  240. package/esm/{LinearPileupDisplay/components → shared}/FilterByTag.js +3 -9
  241. package/esm/shared/FilterByTag.js.map +1 -0
  242. package/esm/shared/color.d.ts +17 -0
  243. package/esm/shared/color.js +37 -0
  244. package/esm/shared/color.js.map +1 -0
  245. package/esm/shared/fetchChains.d.ts +27 -0
  246. package/esm/shared/fetchChains.js +26 -0
  247. package/esm/shared/fetchChains.js.map +1 -0
  248. package/esm/shared/index.d.ts +36 -0
  249. package/esm/{shared.js → shared/index.js} +11 -1
  250. package/esm/shared/index.js.map +1 -0
  251. package/package.json +4 -4
  252. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +1 -1
  253. package/src/AlignmentsTrack/index.ts +1 -0
  254. package/src/BamAdapter/BamSlightlyLazyFeature.ts +13 -19
  255. package/src/BamAdapter/index.ts +1 -0
  256. package/src/CramAdapter/CramSlightlyLazyFeature.ts +13 -15
  257. package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +0 -10
  258. package/src/CramAdapter/index.ts +1 -0
  259. package/src/GuessAlignmentsTypes/index.ts +79 -0
  260. package/src/HtsgetBamAdapter/index.ts +11 -15
  261. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +21 -29
  262. package/src/LinearAlignmentsDisplay/index.ts +1 -0
  263. package/src/LinearAlignmentsDisplay/models/configSchema.ts +2 -6
  264. package/src/LinearAlignmentsDisplay/models/model.tsx +238 -199
  265. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +4 -6
  266. package/src/LinearPileupDisplay/configSchema.ts +1 -3
  267. package/src/LinearPileupDisplay/index.ts +2 -0
  268. package/src/LinearPileupDisplay/model.ts +36 -23
  269. package/src/LinearReadArcsDisplay/components/ReactComponent.tsx +86 -0
  270. package/src/LinearReadArcsDisplay/configSchema.ts +58 -0
  271. package/src/LinearReadArcsDisplay/declare.d.ts +1 -0
  272. package/src/LinearReadArcsDisplay/drawFeats.ts +199 -0
  273. package/src/LinearReadArcsDisplay/index.ts +23 -0
  274. package/src/LinearReadArcsDisplay/model.tsx +370 -0
  275. package/src/LinearReadCloudDisplay/components/ReactComponent.tsx +86 -0
  276. package/src/LinearReadCloudDisplay/configSchema.ts +57 -0
  277. package/src/LinearReadCloudDisplay/drawFeats.ts +201 -0
  278. package/src/LinearReadCloudDisplay/index.ts +23 -0
  279. package/src/LinearReadCloudDisplay/model.tsx +289 -0
  280. package/src/LinearSNPCoverageDisplay/index.ts +1 -0
  281. package/src/LinearSNPCoverageDisplay/models/model.ts +3 -13
  282. package/src/{BamAdapter/MismatchParser.test.ts → MismatchParser/index.test.ts} +1 -1
  283. package/src/{BamAdapter/MismatchParser.ts → MismatchParser/index.ts} +129 -2
  284. package/src/PileupRPC/base.ts +24 -0
  285. package/src/PileupRPC/index.ts +12 -0
  286. package/src/PileupRPC/methods/GetGlobalValueForTag.ts +41 -0
  287. package/src/PileupRPC/methods/GetReducedFeatures.ts +76 -0
  288. package/src/PileupRPC/methods/GetVisibleModifications.ts +45 -0
  289. package/src/PileupRPC/rpcMethods.ts +8 -113
  290. package/src/PileupRPC/util.ts +19 -0
  291. package/src/PileupRenderer/PileupRenderer.ts +5 -8
  292. package/src/PileupRenderer/index.ts +1 -0
  293. package/src/PileupRenderer/sortUtil.ts +2 -3
  294. package/src/SNPCoverageAdapter/generateCoverageBins.ts +1 -1
  295. package/src/SNPCoverageAdapter/index.ts +1 -3
  296. package/src/index.ts +12 -93
  297. package/src/{LinearPileupDisplay/components → shared}/FilterByTag.tsx +3 -9
  298. package/src/shared/color.ts +47 -0
  299. package/src/shared/fetchChains.ts +63 -0
  300. package/src/{shared.ts → shared/index.ts} +17 -4
  301. package/dist/BamAdapter/MismatchParser.js.map +0 -1
  302. package/dist/LinearPileupDisplay/components/FilterByTag.js.map +0 -1
  303. package/dist/shared.d.ts +0 -25
  304. package/dist/shared.js.map +0 -1
  305. package/esm/BamAdapter/MismatchParser.js.map +0 -1
  306. package/esm/LinearPileupDisplay/components/FilterByTag.js.map +0 -1
  307. package/esm/shared.d.ts +0 -25
  308. package/esm/shared.js.map +0 -1
@@ -4,25 +4,58 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const react_1 = __importDefault(require("react"));
7
- const configuration_1 = require("@jbrowse/core/configuration");
8
- const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
9
7
  const mobx_1 = require("mobx");
10
8
  const mobx_state_tree_1 = require("mobx-state-tree");
11
- const util_1 = require("@jbrowse/core/util");
12
9
  const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
10
+ // jbrowse
11
+ const configuration_1 = require("@jbrowse/core/configuration");
12
+ const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
13
13
  const minDisplayHeight = 20;
14
- /**
15
- * #stateModel LinearAlignmentsDisplay
16
- * extends `BaseDisplay`
17
- */
18
- function stateModelFactory(pluginManager, configSchema) {
19
- return mobx_state_tree_1.types
20
- .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
14
+ function getLowerPanelDisplays(pluginManager) {
15
+ return (pluginManager
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+ .getDisplayElements()
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+ // @ts-ignore
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+ .filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
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+ // @ts-ignore
20
+ .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
21
+ }
22
+ function deepSnap(x1, x2) {
23
+ return (0, fast_deep_equal_1.default)(x1 ? (0, mobx_state_tree_1.getSnapshot)(x1) : undefined, x2 ? (0, mobx_state_tree_1.getSnapshot)(x2) : undefined);
24
+ }
25
+ function preCheck(self) {
26
+ const { PileupDisplay, SNPCoverageDisplay } = self;
27
+ return (PileupDisplay ||
28
+ (0, mobx_state_tree_1.isAlive)(PileupDisplay) ||
29
+ SNPCoverageDisplay ||
30
+ (0, mobx_state_tree_1.isAlive)(SNPCoverageDisplay));
31
+ }
32
+ function propagateColorBy(self) {
33
+ const { PileupDisplay, SNPCoverageDisplay } = self;
34
+ if (!preCheck(self) || !PileupDisplay.colorBy) {
35
+ return;
36
+ }
37
+ if (!deepSnap(PileupDisplay.colorBy, SNPCoverageDisplay.colorBy)) {
38
+ SNPCoverageDisplay.setColorBy((0, mobx_state_tree_1.getSnapshot)(PileupDisplay.colorBy));
39
+ }
40
+ }
41
+ function propagateFilterBy(self) {
42
+ const { PileupDisplay, SNPCoverageDisplay } = self;
43
+ if (!preCheck(self) || !PileupDisplay.filterBy) {
44
+ return;
45
+ }
46
+ if (!deepSnap(PileupDisplay.filterBy, SNPCoverageDisplay.filterBy)) {
47
+ SNPCoverageDisplay.setFilterBy((0, mobx_state_tree_1.getSnapshot)(PileupDisplay.filterBy));
48
+ }
49
+ }
50
+ function AlignmentsModel(pluginManager, configSchema) {
51
+ const lowerPanelDisplays = getLowerPanelDisplays(pluginManager).map(f => f.stateModel);
52
+ return mobx_state_tree_1.types.model({
21
53
  /**
22
54
  * #property
23
55
  * refers to LinearPileupDisplay sub-display model
24
56
  */
25
- PileupDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
57
+ // @ts-ignore
58
+ PileupDisplay: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(...lowerPanelDisplays)),
26
59
  /**
27
60
  * #property
28
61
  * refers to LinearSNPCoverageDisplay sub-display model
@@ -47,16 +80,20 @@ function stateModelFactory(pluginManager, configSchema) {
47
80
  /**
48
81
  * #property
49
82
  */
50
- showCoverage: true,
51
- /**
52
- * #property
53
- */
54
- showPileup: true,
83
+ userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
55
84
  /**
56
85
  * #property
57
86
  */
58
- userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
59
- }))
87
+ lowerPanelType: 'LinearPileupDisplay',
88
+ });
89
+ }
90
+ /**
91
+ * #stateModel LinearAlignmentsDisplay
92
+ * extends `BaseDisplay`
93
+ */
94
+ function stateModelFactory(pluginManager, configSchema) {
95
+ return mobx_state_tree_1.types
96
+ .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, AlignmentsModel(pluginManager, configSchema))
60
97
  .volatile(() => ({
61
98
  scrollTop: 0,
62
99
  }))
@@ -64,120 +101,70 @@ function stateModelFactory(pluginManager, configSchema) {
64
101
  /**
65
102
  * #action
66
103
  */
67
- toggleCoverage() {
68
- self.showCoverage = !self.showCoverage;
104
+ setScrollTop(scrollTop) {
105
+ self.scrollTop = scrollTop;
69
106
  },
70
107
  /**
71
108
  * #action
72
109
  */
73
- togglePileup() {
74
- self.showPileup = !self.showPileup;
110
+ setSNPCoverageHeight(n) {
111
+ self.snpCovHeight = n;
75
112
  },
113
+ }))
114
+ .views(self => ({
76
115
  /**
77
- * #action
116
+ * #getter
78
117
  */
79
- setScrollTop(scrollTop) {
80
- self.scrollTop = scrollTop;
118
+ get pileupConf() {
119
+ const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
120
+ return {
121
+ ...conf,
122
+ type: self.lowerPanelType,
123
+ displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
124
+ };
81
125
  },
82
126
  /**
83
- * #action
127
+ * #method
84
128
  */
85
- setSNPCoverageHeight(n) {
86
- self.snpCovHeight = n;
129
+ getFeatureByID(blockKey, id) {
130
+ return self.PileupDisplay.getFeatureByID(blockKey, id);
131
+ },
132
+ /**
133
+ * #method
134
+ */
135
+ searchFeatureByID(id) {
136
+ return self.PileupDisplay.searchFeatureByID(id);
137
+ },
138
+ /**
139
+ * #getter
140
+ */
141
+ get features() {
142
+ return self.PileupDisplay.features;
143
+ },
144
+ /**
145
+ * #getter
146
+ */
147
+ get DisplayBlurb() {
148
+ var _a;
149
+ return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
150
+ },
151
+ /**
152
+ * #getter
153
+ */
154
+ get sortedBy() {
155
+ return self.PileupDisplay.sortedBy;
156
+ },
157
+ /**
158
+ * #getter
159
+ */
160
+ get coverageConf() {
161
+ const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
162
+ return {
163
+ ...conf,
164
+ displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
165
+ };
87
166
  },
88
167
  }))
89
- .views(self => {
90
- const { trackMenuItems: superTrackMenuItems } = self;
91
- return {
92
- /**
93
- * #getter
94
- */
95
- get pileupDisplayConfig() {
96
- const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
97
- const track = (0, util_1.getContainingTrack)(self);
98
- return {
99
- ...conf,
100
- type: 'LinearPileupDisplay',
101
- name: `${(0, configuration_1.getConf)(track, 'name')} pileup`,
102
- displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
103
- };
104
- },
105
- /**
106
- * #method
107
- */
108
- getFeatureByID(blockKey, id) {
109
- return self.PileupDisplay.getFeatureByID(blockKey, id);
110
- },
111
- /**
112
- * #method
113
- */
114
- searchFeatureByID(id) {
115
- return self.PileupDisplay.searchFeatureByID(id);
116
- },
117
- /**
118
- * #getter
119
- */
120
- get features() {
121
- return self.PileupDisplay.features;
122
- },
123
- /**
124
- * #getter
125
- */
126
- get DisplayBlurb() {
127
- var _a;
128
- return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
129
- },
130
- /**
131
- * #getter
132
- */
133
- get sortedBy() {
134
- return self.PileupDisplay.sortedBy;
135
- },
136
- /**
137
- * #getter
138
- */
139
- get sortedByPosition() {
140
- return self.PileupDisplay.sortedByPosition;
141
- },
142
- /**
143
- * #getter
144
- */
145
- get sortedByRefName() {
146
- return self.PileupDisplay.sortedByRefName;
147
- },
148
- /**
149
- * #getter
150
- */
151
- get snpCoverageDisplayConfig() {
152
- const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
153
- const track = (0, util_1.getContainingTrack)(self);
154
- return {
155
- ...conf,
156
- type: 'LinearSNPCoverageDisplay',
157
- name: `${(0, configuration_1.getConf)(track, 'name')} snp coverage`,
158
- displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
159
- };
160
- },
161
- /**
162
- * #method
163
- */
164
- trackMenuItems() {
165
- return [
166
- ...superTrackMenuItems(),
167
- {
168
- type: 'subMenu',
169
- label: 'Pileup settings',
170
- subMenu: self.PileupDisplay.trackMenuItems(),
171
- },
172
- {
173
- type: 'subMenu',
174
- label: 'SNPCoverage settings',
175
- subMenu: self.SNPCoverageDisplay.trackMenuItems(),
176
- },
177
- ];
178
- },
179
- };
180
- })
181
168
  .actions(self => ({
182
169
  /**
183
170
  * #action
@@ -201,22 +188,23 @@ function stateModelFactory(pluginManager, configSchema) {
201
188
  */
202
189
  setPileupDisplay(configuration) {
203
190
  self.PileupDisplay = {
204
- type: 'LinearPileupDisplay',
191
+ type: configuration.type || 'LinearPileupDisplay',
205
192
  configuration,
206
193
  };
207
194
  },
208
195
  /**
209
196
  * #action
210
197
  */
211
- setHeight(displayHeight) {
212
- if (displayHeight > minDisplayHeight) {
213
- self.height = displayHeight;
214
- }
215
- else {
216
- self.height = minDisplayHeight;
217
- }
198
+ setHeight(n) {
199
+ self.height = Math.max(n, minDisplayHeight);
218
200
  return self.height;
219
201
  },
202
+ /**
203
+ * #action
204
+ */
205
+ setLowerPanelType(type) {
206
+ self.lowerPanelType = type;
207
+ },
220
208
  /**
221
209
  * #action
222
210
  */
@@ -229,36 +217,29 @@ function stateModelFactory(pluginManager, configSchema) {
229
217
  .actions(self => ({
230
218
  afterAttach() {
231
219
  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
232
- if (!self.SNPCoverageDisplay) {
233
- self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig);
220
+ const { SNPCoverageDisplay, PileupDisplay, coverageConf, pileupConf, } = self;
221
+ if (!SNPCoverageDisplay) {
222
+ self.setSNPCoverageDisplay(coverageConf);
234
223
  }
235
- else if (!(0, fast_deep_equal_1.default)(self.snpCoverageDisplayConfig, (0, mobx_state_tree_1.getSnapshot)(self.SNPCoverageDisplay.configuration))) {
236
- self.SNPCoverageDisplay.setHeight(self.snpCovHeight);
237
- self.SNPCoverageDisplay.setConfig(self.snpCoverageDisplayConfig);
224
+ else if (!(0, fast_deep_equal_1.default)(coverageConf, (0, mobx_state_tree_1.getSnapshot)(SNPCoverageDisplay.configuration))) {
225
+ SNPCoverageDisplay.setHeight(self.snpCovHeight);
226
+ SNPCoverageDisplay.setConfig(self.coverageConf);
238
227
  }
239
- if (!self.PileupDisplay) {
240
- self.setPileupDisplay(self.pileupDisplayConfig);
228
+ if (!PileupDisplay || self.lowerPanelType !== PileupDisplay.type) {
229
+ self.setPileupDisplay(pileupConf);
241
230
  }
242
- else if (!(0, fast_deep_equal_1.default)(self.pileupDisplayConfig, (0, mobx_state_tree_1.getSnapshot)(self.PileupDisplay.configuration))) {
243
- self.PileupDisplay.setConfig(self.pileupDisplayConfig);
244
- }
245
- // propagate the filterBy setting from pileupdisplay to snpcoverage
246
- // note: the snpcoverage display is not able to control filterBy
247
- // itself
248
- if (self.PileupDisplay.filterBy &&
249
- !(0, fast_deep_equal_1.default)((0, mobx_state_tree_1.getSnapshot)(self.PileupDisplay.filterBy), (0, mobx_state_tree_1.getSnapshot)(self.SNPCoverageDisplay.filterBy))) {
250
- self.SNPCoverageDisplay.setFilterBy((0, mobx_state_tree_1.getSnapshot)(self.PileupDisplay.filterBy));
251
- }
252
- if (self.PileupDisplay.colorBy &&
253
- !(0, fast_deep_equal_1.default)((0, mobx_state_tree_1.getSnapshot)(self.PileupDisplay.colorBy), self.SNPCoverageDisplay.colorBy
254
- ? (0, mobx_state_tree_1.getSnapshot)(self.SNPCoverageDisplay.colorBy)
255
- : {})) {
256
- self.SNPCoverageDisplay.setColorBy((0, mobx_state_tree_1.getSnapshot)(self.PileupDisplay.colorBy));
231
+ else if (!(0, fast_deep_equal_1.default)(pileupConf, (0, mobx_state_tree_1.getSnapshot)(PileupDisplay.configuration))) {
232
+ PileupDisplay.setConfig(self.pileupConf);
257
233
  }
234
+ propagateColorBy(self);
235
+ propagateFilterBy(self);
258
236
  }));
259
237
  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
260
238
  self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
261
239
  }));
240
+ (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
241
+ self.PileupDisplay.setHeight(self.height - self.SNPCoverageDisplay.height);
242
+ }));
262
243
  },
263
244
  /**
264
245
  * #action
@@ -273,7 +254,41 @@ function stateModelFactory(pluginManager, configSchema) {
273
254
  overrideHeight: pileupHeight,
274
255
  }))));
275
256
  },
276
- }));
257
+ }))
258
+ .views(self => {
259
+ const { trackMenuItems: superTrackMenuItems } = self;
260
+ return {
261
+ /**
262
+ * #method
263
+ */
264
+ trackMenuItems() {
265
+ const extra = getLowerPanelDisplays(pluginManager).map(d => ({
266
+ type: 'radio',
267
+ label: d.displayName,
268
+ checked: d.name === self.PileupDisplay.type,
269
+ onClick: () => self.setLowerPanelType(d.name),
270
+ }));
271
+ return [
272
+ ...superTrackMenuItems(),
273
+ {
274
+ type: 'subMenu',
275
+ label: 'Pileup settings',
276
+ subMenu: self.PileupDisplay.trackMenuItems(),
277
+ },
278
+ {
279
+ type: 'subMenu',
280
+ label: 'SNPCoverage settings',
281
+ subMenu: self.SNPCoverageDisplay.trackMenuItems(),
282
+ },
283
+ {
284
+ type: 'subMenu',
285
+ label: `Replace lower panel with...`,
286
+ subMenu: extra,
287
+ },
288
+ ];
289
+ },
290
+ };
291
+ });
277
292
  }
278
293
  exports.default = stateModelFactory;
279
294
  //# sourceMappingURL=model.js.map
@@ -1 +1 @@
1
- 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@@ -1,8 +1,8 @@
1
1
  /// <reference types="react" />
2
2
  declare function SetFeatureHeightDlg(props: {
3
3
  model: {
4
- setFeatureHeight: Function;
5
- setNoSpacing: Function;
4
+ setFeatureHeight: (arg?: number) => void;
5
+ setNoSpacing: (arg?: boolean) => void;
6
6
  featureHeightSetting: number;
7
7
  noSpacing?: boolean;
8
8
  };
@@ -33,12 +33,10 @@ function SetFeatureHeightDlg(props) {
33
33
  const [height, setHeight] = (0, react_1.useState)(`${featureHeightSetting}`);
34
34
  const [noSpacing, setNoSpacing] = (0, react_1.useState)(noSpacingSetting);
35
35
  const ok = height !== '' && !Number.isNaN(+height);
36
- return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: 'Set feature height' },
36
+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set feature height" },
37
37
  react_1.default.createElement(material_1.DialogContent, null,
38
38
  react_1.default.createElement(material_1.Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."),
39
- react_1.default.createElement(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => {
40
- setHeight(event.target.value);
41
- } }),
39
+ react_1.default.createElement(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => setHeight(event.target.value) }),
42
40
  react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: !!noSpacing, onChange: () => setNoSpacing(val => !val) }), label: "Remove spacing between features in y-direction?" }),
43
41
  react_1.default.createElement(material_1.DialogActions, null,
44
42
  react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !ok, onClick: () => {
@@ -1 +1 @@
1
- {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AAEzC,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,oBAAoB;QAC5D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}
1
+ {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AAEzC,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,oBAAoB;QAC3D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAChD;YACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}
@@ -1,6 +1,3 @@
1
- import { Instance } from 'mobx-state-tree';
2
1
  import PluginManager from '@jbrowse/core/PluginManager';
3
2
  declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
- export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>;
5
- export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
6
3
  export default configSchemaF;
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAiD;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAID,kBAAe,aAAa,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAuC;AAGvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,kBAAe,aAAa,CAAA"}
@@ -15,8 +15,10 @@ function register(pluginManager) {
15
15
  const configSchema = (0, configSchema_1.default)(pluginManager);
16
16
  return new DisplayType_1.default({
17
17
  name: 'LinearPileupDisplay',
18
+ displayName: 'Pileup display',
18
19
  configSchema,
19
20
  stateModel: (0, model_1.default)(configSchema),
21
+ subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
20
22
  trackType: 'AlignmentsTrack',
21
23
  viewType: 'LinearGenomeView',
22
24
  ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;AAsBvB,iDAtBlB,sBAAmB,CAsBqC;AArB/D,oDAAkC;AAoBhB,+CApBX,eAAY,CAoBmC;AAnBtD,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;AAwBvB,iDAxBlB,sBAAmB,CAwBqC;AAvB/D,oDAAkC;AAsBhB,+CAtBX,eAAY,CAsBmC;AArBtD,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAdD,2BAcC"}
@@ -1,14 +1,13 @@
1
1
  /// <reference types="react" />
2
2
  import { Instance } from 'mobx-state-tree';
3
- import { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
+ import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
4
4
  import { Feature } from '@jbrowse/core/util';
5
5
  import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
6
- import { LinearPileupDisplayConfigModel } from './configSchema';
7
6
  /**
8
7
  * #stateModel LinearPileupDisplay
9
8
  * extends `BaseLinearDisplay`
10
9
  */
11
- declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): import("mobx-state-tree").IModelType<{
10
+ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
12
11
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
13
12
  type: import("mobx-state-tree").ISimpleType<string>;
14
13
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -35,9 +34,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
35
34
  */
36
35
  filled: boolean;
37
36
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
38
- features: Map<string, Feature> | undefined; /**
39
- * #property
40
- */
37
+ features: Map<string, Feature> | undefined;
41
38
  layout: any;
42
39
  status: string;
43
40
  error: unknown;
@@ -48,9 +45,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
48
45
  }) => any;
49
46
  renderProps: any;
50
47
  } & {
51
- doReload(): void; /**
52
- * #property
53
- */
48
+ doReload(): void;
54
49
  afterAttach(): void;
55
50
  setStatus(message: string): void;
56
51
  setLoading(abortController: AbortController): void;
@@ -152,10 +147,10 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
152
147
  reload(): void;
153
148
  } & {
154
149
  currBpPerPx: number;
150
+ scrollTop: number;
155
151
  message: string;
156
152
  featureIdUnderMouse: string | undefined;
157
153
  contextMenuFeature: Feature | undefined;
158
- scrollTop: number;
159
154
  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
160
155
  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
161
156
  } & {
@@ -244,11 +239,11 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
244
239
  /**
245
240
  * #action
246
241
  */
247
- setFeatureHeight(n: number): void;
242
+ setFeatureHeight(n?: number): void;
248
243
  /**
249
244
  * #action
250
245
  */
251
- setNoSpacing(flag: boolean): void;
246
+ setNoSpacing(flag?: boolean): void;
252
247
  /**
253
248
  * #action
254
249
  */
@@ -325,7 +320,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
325
320
  [x: string]: any;
326
321
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
327
322
  setSubschema(slotName: string, data: unknown): any;
328
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
323
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
329
324
  /**
330
325
  * #getter
331
326
  */
@@ -346,11 +341,17 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
346
341
  /**
347
342
  * #method
348
343
  */
349
- contextMenuItems(): {
344
+ contextMenuItems(): ({
345
+ label: string;
346
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
347
+ muiName: string;
348
+ };
349
+ onClick: () => void;
350
+ } | {
350
351
  label: string;
351
352
  icon: typeof ContentCopyIcon;
352
353
  onClick: () => void;
353
- }[];
354
+ })[];
354
355
  /**
355
356
  * #getter
356
357
  */
@@ -419,7 +420,9 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
419
420
  })[];
420
421
  }, import("mobx-state-tree")._NotCustomized, {
421
422
  type: string;
422
- height: number;
423
+ height: number; /**
424
+ * #action
425
+ */
423
426
  id: string;
424
427
  rpcDriverName: string | undefined;
425
428
  userBpPerPxLimit: number | undefined;