react-msaview 6.5.0 → 8.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (414) hide show
  1. package/README.md +13 -11
  2. package/bundle/index.js +122 -112
  3. package/bundle/index.js.map +4 -4
  4. package/dist/colorSchemes.js +1 -2
  5. package/dist/colorSchemes.js.map +1 -1
  6. package/dist/columnStats.d.ts +28 -0
  7. package/dist/columnStats.js +34 -0
  8. package/dist/columnStats.js.map +1 -0
  9. package/dist/components/DragHandle.d.ts +3 -2
  10. package/dist/components/DragHandle.js +11 -5
  11. package/dist/components/DragHandle.js.map +1 -1
  12. package/dist/components/Loading.js +2 -2
  13. package/dist/components/Loading.js.map +1 -1
  14. package/dist/components/MSAView.js +17 -6
  15. package/dist/components/MSAView.js.map +1 -1
  16. package/dist/components/MSAViewer.d.ts +69 -4
  17. package/dist/components/MSAViewer.js +201 -8
  18. package/dist/components/MSAViewer.js.map +1 -1
  19. package/dist/components/PortalTooltip.d.ts +11 -0
  20. package/dist/components/PortalTooltip.js +29 -0
  21. package/dist/components/PortalTooltip.js.map +1 -0
  22. package/dist/components/ResizeHandles.d.ts +3 -3
  23. package/dist/components/ResizeHandles.js +13 -24
  24. package/dist/components/ResizeHandles.js.map +1 -1
  25. package/dist/components/SequenceTextArea.js +3 -3
  26. package/dist/components/SequenceTextArea.js.map +1 -1
  27. package/dist/components/Track.js +41 -22
  28. package/dist/components/Track.js.map +1 -1
  29. package/dist/components/dialogs/{InterProScanDialog.d.ts → AnnotationFileDialog.d.ts} +2 -2
  30. package/dist/components/dialogs/AnnotationFileDialog.js +92 -0
  31. package/dist/components/dialogs/AnnotationFileDialog.js.map +1 -0
  32. package/dist/components/dialogs/ExportSVGDialog.js +5 -3
  33. package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
  34. package/dist/components/dialogs/FeatureDialog.js +13 -9
  35. package/dist/components/dialogs/FeatureDialog.js.map +1 -1
  36. package/dist/components/dialogs/TrackInfoDialog.js +1 -1
  37. package/dist/components/dialogs/TrackInfoDialog.js.map +1 -1
  38. package/dist/components/header/GappynessSlider.js +6 -11
  39. package/dist/components/header/GappynessSlider.js.map +1 -1
  40. package/dist/components/header/Header.js +7 -0
  41. package/dist/components/header/Header.js.map +1 -1
  42. package/dist/components/header/HeaderStatusArea.js +0 -2
  43. package/dist/components/header/HeaderStatusArea.js.map +1 -1
  44. package/dist/components/header/LoadWarnings.d.ts +6 -0
  45. package/dist/components/header/LoadWarnings.js +35 -0
  46. package/dist/components/header/LoadWarnings.js.map +1 -0
  47. package/dist/components/header/MultiAlignmentSelector.js +0 -0
  48. package/dist/components/header/MultiAlignmentSelector.js.map +1 -1
  49. package/dist/components/header/ScrollZoomIcons.d.ts +6 -0
  50. package/dist/components/header/ScrollZoomIcons.js +35 -0
  51. package/dist/components/header/ScrollZoomIcons.js.map +1 -0
  52. package/dist/components/header/TreeSettingsMenu.js +7 -1
  53. package/dist/components/header/TreeSettingsMenu.js.map +1 -1
  54. package/dist/components/header/UnshareableDataWarning.d.ts +6 -0
  55. package/dist/components/header/UnshareableDataWarning.js +40 -0
  56. package/dist/components/header/UnshareableDataWarning.js.map +1 -0
  57. package/dist/components/header/ZoomControls.js +49 -6
  58. package/dist/components/header/ZoomControls.js.map +1 -1
  59. package/dist/components/header/getAnnotationsMenu.js +11 -14
  60. package/dist/components/header/getAnnotationsMenu.js.map +1 -1
  61. package/dist/components/header/settingsMenuItems.js +10 -7
  62. package/dist/components/header/settingsMenuItems.js.map +1 -1
  63. package/dist/components/import/ImportForm.js +1 -1
  64. package/dist/components/import/ImportForm.js.map +1 -1
  65. package/dist/components/import/ImportFormExamples.js +2 -6
  66. package/dist/components/import/ImportFormExamples.js.map +1 -1
  67. package/dist/components/import/util.js +2 -0
  68. package/dist/components/import/util.js.map +1 -1
  69. package/dist/components/minimap/Minimap.js +1 -2
  70. package/dist/components/minimap/Minimap.js.map +1 -1
  71. package/dist/components/msa/AnnotationLegend.js +27 -19
  72. package/dist/components/msa/AnnotationLegend.js.map +1 -1
  73. package/dist/components/msa/MSACanvas.js +1 -1
  74. package/dist/components/msa/MSACanvas.js.map +1 -1
  75. package/dist/components/msa/MSACanvasBlock.js +17 -20
  76. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  77. package/dist/components/msa/MSAMouseoverCanvas.js +2 -1
  78. package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -1
  79. package/dist/components/msa/domainBandCursor.d.ts +7 -11
  80. package/dist/components/msa/domainBandCursor.js +7 -11
  81. package/dist/components/msa/domainBandCursor.js.map +1 -1
  82. package/dist/components/msa/drawFeatureSpans.d.ts +53 -0
  83. package/dist/components/msa/drawFeatureSpans.js +78 -0
  84. package/dist/components/msa/drawFeatureSpans.js.map +1 -0
  85. package/dist/components/msa/legendRows.d.ts +8 -0
  86. package/dist/components/msa/legendRows.js +16 -0
  87. package/dist/components/msa/legendRows.js.map +1 -0
  88. package/dist/components/msa/msaRaster.d.ts +30 -27
  89. package/dist/components/msa/msaRaster.js +193 -90
  90. package/dist/components/msa/msaRaster.js.map +1 -1
  91. package/dist/components/msa/packDomainLanes.d.ts +20 -0
  92. package/dist/components/msa/packDomainLanes.js +33 -0
  93. package/dist/components/msa/packDomainLanes.js.map +1 -0
  94. package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts +3 -1
  95. package/dist/components/msa/renderBoxFeatureCanvasBlock.js +51 -87
  96. package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
  97. package/dist/components/msa/renderHighlights.d.ts +44 -4
  98. package/dist/components/msa/renderHighlights.js +99 -11
  99. package/dist/components/msa/renderHighlights.js.map +1 -1
  100. package/dist/components/msa/renderMSABlock.d.ts +1 -2
  101. package/dist/components/msa/renderMSABlock.js +28 -31
  102. package/dist/components/msa/renderMSABlock.js.map +1 -1
  103. package/dist/components/msa/renderMSAMouseover.js +9 -30
  104. package/dist/components/msa/renderMSAMouseover.js.map +1 -1
  105. package/dist/components/msa/tileColor.js +4 -7
  106. package/dist/components/msa/tileColor.js.map +1 -1
  107. package/dist/components/msa/useMsaBlockMouse.d.ts +5 -3
  108. package/dist/components/msa/useMsaBlockMouse.js +6 -6
  109. package/dist/components/msa/useMsaBlockMouse.js.map +1 -1
  110. package/dist/components/renderCtx.d.ts +1 -1
  111. package/dist/components/rowpanels/RowPanelBlock.d.ts +9 -0
  112. package/dist/components/rowpanels/RowPanelBlock.js +86 -0
  113. package/dist/components/rowpanels/RowPanelBlock.js.map +1 -0
  114. package/dist/components/rowpanels/RowPanelHeaders.d.ts +12 -0
  115. package/dist/components/rowpanels/RowPanelHeaders.js +38 -0
  116. package/dist/components/rowpanels/RowPanelHeaders.js.map +1 -0
  117. package/dist/components/{msa/ColumnStats.d.ts → rowpanels/RowPanels.d.ts} +2 -2
  118. package/dist/components/rowpanels/RowPanels.js +32 -0
  119. package/dist/components/rowpanels/RowPanels.js.map +1 -0
  120. package/dist/components/rowpanels/headerLayout.d.ts +1 -0
  121. package/dist/components/rowpanels/headerLayout.js +5 -0
  122. package/dist/components/rowpanels/headerLayout.js.map +1 -0
  123. package/dist/components/rowpanels/renderFeaturePanel.d.ts +21 -0
  124. package/dist/components/rowpanels/renderFeaturePanel.js +37 -0
  125. package/dist/components/rowpanels/renderFeaturePanel.js.map +1 -0
  126. package/dist/components/rowpanels/renderRowPanel.d.ts +23 -0
  127. package/dist/components/rowpanels/renderRowPanel.js +22 -0
  128. package/dist/components/rowpanels/renderRowPanel.js.map +1 -0
  129. package/dist/components/rowpanels/renderStrip.d.ts +20 -0
  130. package/dist/components/rowpanels/renderStrip.js +26 -0
  131. package/dist/components/rowpanels/renderStrip.js.map +1 -0
  132. package/dist/components/tracks/TrackBlocks.js +13 -16
  133. package/dist/components/tracks/TrackBlocks.js.map +1 -1
  134. package/dist/components/tracks/TrackTooltipContent.d.ts +15 -0
  135. package/dist/components/tracks/TrackTooltipContent.js +109 -0
  136. package/dist/components/tracks/TrackTooltipContent.js.map +1 -0
  137. package/dist/components/tracks/drawTracks.d.ts +30 -12
  138. package/dist/components/tracks/drawTracks.js +127 -34
  139. package/dist/components/tracks/drawTracks.js.map +1 -1
  140. package/dist/components/tracks/useTrackHover.d.ts +22 -0
  141. package/dist/components/tracks/useTrackHover.js +30 -0
  142. package/dist/components/tracks/useTrackHover.js.map +1 -0
  143. package/dist/components/tree/CladeLabels.d.ts +12 -0
  144. package/dist/components/tree/CladeLabels.js +48 -0
  145. package/dist/components/tree/CladeLabels.js.map +1 -0
  146. package/dist/components/tree/TreeCanvas.js +6 -4
  147. package/dist/components/tree/TreeCanvas.js.map +1 -1
  148. package/dist/components/tree/TreeCanvasBlock.js +6 -21
  149. package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
  150. package/dist/components/tree/TreeOverview.d.ts +14 -0
  151. package/dist/components/tree/TreeOverview.js +75 -0
  152. package/dist/components/tree/TreeOverview.js.map +1 -0
  153. package/dist/components/tree/TreeRuler.js +11 -5
  154. package/dist/components/tree/TreeRuler.js.map +1 -1
  155. package/dist/components/tree/cladeBrackets.d.ts +25 -0
  156. package/dist/components/tree/cladeBrackets.js +51 -0
  157. package/dist/components/tree/cladeBrackets.js.map +1 -0
  158. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js +2 -2
  159. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map +1 -1
  160. package/dist/components/tree/renderTreeCanvas.d.ts +0 -1
  161. package/dist/components/tree/renderTreeCanvas.js +221 -47
  162. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  163. package/dist/components/tree/renderTreeOverview.d.ts +52 -0
  164. package/dist/components/tree/renderTreeOverview.js +138 -0
  165. package/dist/components/tree/renderTreeOverview.js.map +1 -0
  166. package/dist/components/tree/scaleBar.d.ts +10 -0
  167. package/dist/components/tree/scaleBar.js +24 -0
  168. package/dist/components/tree/scaleBar.js.map +1 -0
  169. package/dist/components/tree/useTreeHover.js +2 -4
  170. package/dist/components/tree/useTreeHover.js.map +1 -1
  171. package/dist/constants.d.ts +18 -1
  172. package/dist/constants.js +51 -8
  173. package/dist/constants.js.map +1 -1
  174. package/dist/createPaletteMap.d.ts +7 -6
  175. package/dist/createPaletteMap.js +10 -9
  176. package/dist/createPaletteMap.js.map +1 -1
  177. package/dist/element.d.ts +13 -0
  178. package/dist/element.js +269 -0
  179. package/dist/element.js.map +1 -0
  180. package/dist/featureFields.d.ts +11 -0
  181. package/dist/featureFields.js +17 -0
  182. package/dist/featureFields.js.map +1 -0
  183. package/dist/fetchUtils.d.ts +7 -7
  184. package/dist/fetchUtils.js +4 -32
  185. package/dist/fetchUtils.js.map +1 -1
  186. package/dist/flatToTree.js +1 -2
  187. package/dist/flatToTree.js.map +1 -1
  188. package/dist/ggplotPalettes.d.ts +10 -0
  189. package/dist/ggplotPalettes.js +58 -0
  190. package/dist/ggplotPalettes.js.map +1 -1
  191. package/dist/hierarchy.d.ts +29 -1
  192. package/dist/hierarchy.js +82 -19
  193. package/dist/hierarchy.js.map +1 -1
  194. package/dist/index.d.ts +10 -1
  195. package/dist/index.js +10 -2
  196. package/dist/index.js.map +1 -1
  197. package/dist/model/DataModel.js +4 -4
  198. package/dist/model/DataModel.js.map +1 -1
  199. package/dist/model/msaModel.d.ts +3 -2
  200. package/dist/model/msaModel.js +3 -2
  201. package/dist/model/msaModel.js.map +1 -1
  202. package/dist/model/treeModel.d.ts +30 -0
  203. package/dist/model/treeModel.js +37 -1
  204. package/dist/model/treeModel.js.map +1 -1
  205. package/dist/model.d.ts +792 -259
  206. package/dist/model.js +2092 -675
  207. package/dist/model.js.map +1 -1
  208. package/dist/mount.d.ts +11 -0
  209. package/dist/mount.js +22 -0
  210. package/dist/mount.js.map +1 -0
  211. package/dist/neighborJoining.js +8 -32
  212. package/dist/neighborJoining.js.map +1 -1
  213. package/dist/renderToStaticMarkup.d.ts +15 -13
  214. package/dist/renderToStaticMarkup.js +37 -25
  215. package/dist/renderToStaticMarkup.js.map +1 -1
  216. package/dist/renderToSvg.js +198 -68
  217. package/dist/renderToSvg.js.map +1 -1
  218. package/dist/rowCoordinateCalculations.d.ts +26 -28
  219. package/dist/rowCoordinateCalculations.js +13 -39
  220. package/dist/rowCoordinateCalculations.js.map +1 -1
  221. package/dist/scales.d.ts +22 -0
  222. package/dist/scales.js +30 -0
  223. package/dist/scales.js.map +1 -0
  224. package/dist/seqPosToGlobalCol.d.ts +2 -3
  225. package/dist/seqPosToGlobalCol.js +5 -4
  226. package/dist/seqPosToGlobalCol.js.map +1 -1
  227. package/dist/sequenceLogo.d.ts +6 -11
  228. package/dist/sequenceLogo.js +6 -11
  229. package/dist/sequenceLogo.js.map +1 -1
  230. package/dist/stripDefault.d.ts +7 -14
  231. package/dist/stripDefault.js +7 -14
  232. package/dist/stripDefault.js.map +1 -1
  233. package/dist/svgTestUtil.d.ts +306 -124
  234. package/dist/types.d.ts +295 -3
  235. package/dist/umd.d.ts +2 -0
  236. package/dist/umd.js +4 -2
  237. package/dist/umd.js.map +1 -1
  238. package/dist/useCanvasAutorun.d.ts +5 -10
  239. package/dist/useCanvasAutorun.js +5 -10
  240. package/dist/useCanvasAutorun.js.map +1 -1
  241. package/dist/useMsaSvgFigure.d.ts +20 -0
  242. package/dist/useMsaSvgFigure.js +46 -0
  243. package/dist/useMsaSvgFigure.js.map +1 -0
  244. package/dist/util.d.ts +10 -4
  245. package/dist/util.js +37 -10
  246. package/dist/util.js.map +1 -1
  247. package/dist/version.d.ts +1 -1
  248. package/dist/version.js +1 -1
  249. package/dist/wuss.d.ts +14 -0
  250. package/dist/wuss.js +55 -0
  251. package/dist/wuss.js.map +1 -0
  252. package/package.json +23 -14
  253. package/src/colorSchemes.ts +1 -2
  254. package/src/columnStats.ts +58 -0
  255. package/src/components/DragHandle.tsx +18 -7
  256. package/src/components/Loading.tsx +14 -8
  257. package/src/components/MSAView.tsx +19 -5
  258. package/src/components/MSAViewer.tsx +326 -10
  259. package/src/components/PortalTooltip.tsx +47 -0
  260. package/src/components/ResizeHandles.tsx +21 -36
  261. package/src/components/SequenceTextArea.tsx +3 -3
  262. package/src/components/Track.tsx +55 -18
  263. package/src/components/dialogs/AnnotationFileDialog.tsx +162 -0
  264. package/src/components/dialogs/ExportSVGDialog.tsx +7 -2
  265. package/src/components/dialogs/FeatureDialog.tsx +13 -9
  266. package/src/components/dialogs/TrackInfoDialog.tsx +1 -1
  267. package/src/components/header/GappynessSlider.tsx +6 -11
  268. package/src/components/header/Header.tsx +10 -0
  269. package/src/components/header/HeaderStatusArea.tsx +0 -5
  270. package/src/components/header/LoadWarnings.tsx +48 -0
  271. package/src/components/header/MultiAlignmentSelector.tsx +0 -0
  272. package/src/components/header/ScrollZoomIcons.tsx +52 -0
  273. package/src/components/header/TreeSettingsMenu.tsx +7 -1
  274. package/src/components/header/UnshareableDataWarning.tsx +56 -0
  275. package/src/components/header/ZoomControls.tsx +74 -14
  276. package/src/components/header/getAnnotationsMenu.ts +13 -17
  277. package/src/components/header/settingsMenuItems.ts +11 -6
  278. package/src/components/import/ImportForm.tsx +2 -2
  279. package/src/components/import/ImportFormExamples.tsx +4 -8
  280. package/src/components/import/util.ts +2 -0
  281. package/src/components/minimap/Minimap.tsx +1 -2
  282. package/src/components/msa/AnnotationLegend.tsx +48 -38
  283. package/src/components/msa/MSACanvas.tsx +3 -5
  284. package/src/components/msa/MSACanvasBlock.tsx +17 -21
  285. package/src/components/msa/MSAMouseoverCanvas.tsx +2 -1
  286. package/src/components/msa/domainBandCursor.ts +7 -11
  287. package/src/components/msa/drawFeatureSpans.ts +150 -0
  288. package/src/components/msa/legendRows.ts +24 -0
  289. package/src/components/msa/msaRaster.ts +236 -88
  290. package/src/components/msa/packDomainLanes.ts +36 -0
  291. package/src/components/msa/renderBoxFeatureCanvasBlock.ts +69 -123
  292. package/src/components/msa/renderHighlights.ts +141 -10
  293. package/src/components/msa/renderMSABlock.ts +29 -38
  294. package/src/components/msa/renderMSAMouseover.ts +9 -39
  295. package/src/components/msa/tileColor.ts +4 -7
  296. package/src/components/msa/useMsaBlockMouse.ts +6 -6
  297. package/src/components/renderCtx.ts +1 -0
  298. package/src/components/rowpanels/RowPanelBlock.tsx +139 -0
  299. package/src/components/rowpanels/RowPanelHeaders.tsx +57 -0
  300. package/src/components/rowpanels/RowPanels.tsx +77 -0
  301. package/src/components/rowpanels/headerLayout.ts +5 -0
  302. package/src/components/rowpanels/renderFeaturePanel.ts +66 -0
  303. package/src/components/rowpanels/renderRowPanel.ts +41 -0
  304. package/src/components/rowpanels/renderStrip.ts +46 -0
  305. package/src/components/tracks/TrackBlocks.tsx +13 -18
  306. package/src/components/tracks/TrackTooltipContent.tsx +156 -0
  307. package/src/components/tracks/drawTracks.ts +169 -38
  308. package/src/components/tracks/useTrackHover.ts +42 -0
  309. package/src/components/tree/CladeLabels.tsx +77 -0
  310. package/src/components/tree/TreeCanvas.tsx +4 -3
  311. package/src/components/tree/TreeCanvasBlock.tsx +10 -32
  312. package/src/components/tree/TreeOverview.tsx +106 -0
  313. package/src/components/tree/TreeRuler.tsx +29 -5
  314. package/src/components/tree/cladeBrackets.ts +73 -0
  315. package/src/components/tree/dialogs/TreeNodeInfoDialog.tsx +2 -2
  316. package/src/components/tree/renderTreeCanvas.ts +312 -48
  317. package/src/components/tree/renderTreeOverview.ts +212 -0
  318. package/src/components/tree/scaleBar.ts +23 -0
  319. package/src/components/tree/useTreeHover.ts +2 -4
  320. package/src/constants.ts +61 -8
  321. package/src/createPaletteMap.ts +10 -9
  322. package/src/element.ts +321 -0
  323. package/src/featureFields.ts +19 -0
  324. package/src/fetchUtils.ts +7 -40
  325. package/src/flatToTree.ts +1 -2
  326. package/src/ggplotPalettes.ts +60 -0
  327. package/src/hierarchy.ts +97 -20
  328. package/src/index.ts +46 -6
  329. package/src/model/DataModel.ts +5 -4
  330. package/src/model/msaModel.ts +3 -2
  331. package/src/model/treeModel.ts +42 -0
  332. package/src/model.ts +2492 -793
  333. package/src/mount.tsx +32 -0
  334. package/src/neighborJoining.ts +8 -32
  335. package/src/rawImports.d.ts +9 -0
  336. package/src/renderToStaticMarkup.ts +41 -25
  337. package/src/renderToSvg.tsx +365 -92
  338. package/src/rowCoordinateCalculations.ts +16 -62
  339. package/src/scales.ts +47 -0
  340. package/src/seqPosToGlobalCol.ts +5 -4
  341. package/src/sequenceLogo.ts +6 -11
  342. package/src/stripDefault.ts +7 -14
  343. package/src/types.ts +352 -12
  344. package/src/umd.ts +4 -2
  345. package/src/useCanvasAutorun.ts +5 -10
  346. package/src/useMsaSvgFigure.ts +72 -0
  347. package/src/util.ts +40 -14
  348. package/src/version.ts +1 -1
  349. package/src/wuss.ts +62 -0
  350. package/dist/components/dialogs/InterProScanDialog.js +0 -137
  351. package/dist/components/dialogs/InterProScanDialog.js.map +0 -1
  352. package/dist/components/dialogs/InterProScanFileDialog.d.ts +0 -7
  353. package/dist/components/dialogs/InterProScanFileDialog.js +0 -64
  354. package/dist/components/dialogs/InterProScanFileDialog.js.map +0 -1
  355. package/dist/components/msa/ColumnStats.js +0 -42
  356. package/dist/components/msa/ColumnStats.js.map +0 -1
  357. package/dist/launchInterProScan.d.ts +0 -13
  358. package/dist/launchInterProScan.js +0 -110
  359. package/dist/launchInterProScan.js.map +0 -1
  360. package/dist/useColorContrast.d.ts +0 -10
  361. package/dist/useColorContrast.js +0 -13
  362. package/dist/useColorContrast.js.map +0 -1
  363. package/src/clustalX.test.ts +0 -74
  364. package/src/colSpace.test.ts +0 -67
  365. package/src/collapseLogic.test.ts +0 -115
  366. package/src/colorSchemes.docs.test.ts +0 -57
  367. package/src/columnCounts.test.ts +0 -73
  368. package/src/columnStats.test.ts +0 -94
  369. package/src/columnTracks.test.ts +0 -97
  370. package/src/components/dialogs/InterProScanDialog.tsx +0 -214
  371. package/src/components/dialogs/InterProScanFileDialog.tsx +0 -138
  372. package/src/components/minimap/minimapLayout.test.ts +0 -71
  373. package/src/components/msa/ColumnStats.tsx +0 -54
  374. package/src/components/msa/msaRaster.test.ts +0 -145
  375. package/src/components/msa/renderBoxFeatureCanvasBlock.test.ts +0 -51
  376. package/src/components/tree/renderTreeCanvas.test.ts +0 -296
  377. package/src/dataInitialized.test.ts +0 -42
  378. package/src/domainBands.test.ts +0 -122
  379. package/src/domainLetterColor.test.ts +0 -80
  380. package/src/exportFileName.test.ts +0 -40
  381. package/src/fetchUtils.test.ts +0 -83
  382. package/src/flatToTree.test.ts +0 -51
  383. package/src/hierarchy.test.ts +0 -228
  384. package/src/highlights.test.ts +0 -70
  385. package/src/impgRender.test.tsx +0 -68
  386. package/src/largeTree.test.ts +0 -67
  387. package/src/launchInterProScan.ts +0 -167
  388. package/src/loadErrorDisplay.test.tsx +0 -102
  389. package/src/modelFilehandleLoaders.test.ts +0 -137
  390. package/src/modelReset.test.ts +0 -120
  391. package/src/neighborJoining.test.ts +0 -164
  392. package/src/parseAsn1.test.ts +0 -36
  393. package/src/propertyConservation.test.ts +0 -36
  394. package/src/renderColumnTracksSvg.test.tsx +0 -108
  395. package/src/renderDomainsSvg.test.tsx +0 -118
  396. package/src/renderHighlightsSvg.test.tsx +0 -85
  397. package/src/renderMinimapSvg.test.tsx +0 -62
  398. package/src/renderRasterSvg.test.tsx +0 -144
  399. package/src/renderSequenceLogoSvg.test.tsx +0 -165
  400. package/src/renderToSvg.test.tsx +0 -65
  401. package/src/reset.test.ts +0 -61
  402. package/src/rowCoordinateCalculations.test.ts +0 -211
  403. package/src/rowSpace.test.ts +0 -46
  404. package/src/segmentOverlay.test.ts +0 -70
  405. package/src/seqPosToGlobalCol.test.ts +0 -59
  406. package/src/sequenceLogo.test.ts +0 -88
  407. package/src/setFontSize.test.ts +0 -33
  408. package/src/stripDefault.test.ts +0 -48
  409. package/src/stripDefaultSnapshot.test.ts +0 -87
  410. package/src/treeMetadata.test.ts +0 -39
  411. package/src/useCanvasAutorun.test.tsx +0 -98
  412. package/src/useColorContrast.ts +0 -18
  413. package/src/viewChrome.test.tsx +0 -134
  414. package/src/wheelZoom.test.ts +0 -46
package/README.md CHANGED
@@ -8,9 +8,11 @@ many color schemes, and SVG export.
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9
9
  ## Install
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10
 
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- ```sh
12
- pnpm add react-msaview @jbrowse/core @mui/material @emotion/react @emotion/styled react react-dom
13
- ```
11
+ The viewer shares mobx, mobx-state-tree and MUI with `@jbrowse/core` and needs
12
+ one copy of each, so the install line pins those majors to what your
13
+ `@jbrowse/core` depends on. The
14
+ [usage & embedding guide](../../USAGE.md#zero-config-component-recommended) has
15
+ the install line.
14
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  ## Quick start
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@@ -30,16 +32,16 @@ export default function App() {
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32
  ```
31
33
 
32
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  `MSAViewer` creates the model, measures width, and applies the theme for you.
33
- For full control use the `MSAModelF` / `MSAView` model-based API — see the
34
- [usage & embedding guide](../../USAGE.md).
35
+ For full control, use the `MSAModelF` / `MSAView` model-based API described in
36
+ the [usage & embedding guide](../../USAGE.md).
35
37
 
36
38
  ## Docs & links
37
39
 
38
- - [Usage & embedding guide](../../USAGE.md) — props, model API, UMD bundle, R
39
- - [Live examples](https://jbrowse.org/storybook/msa) — runnable snippets
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+ - [Usage & embedding guide](../../USAGE.md): props, model API, UMD bundle, R
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+ - [Live examples](https://gmod.org/JBrowseMSA/examples): runnable snippets
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  - [Model API reference](apidocs/MsaView.md)
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  - [Main repository](https://github.com/GMOD/JBrowseMSA)
42
- - [CLI](../cli/) — batch InterProScan → GFF domain annotations
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- - [msa-parsers](../msa-parsers/) — standalone parsing library
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- - [ProteinBrowser](https://github.com/GMOD/proteinbrowser) — full protein
45
- analysis suite built on this viewer
44
+ - [CLI](../cli/): domain and exon GFFs, plus headless SVG export
45
+ - [msa-parsers](../msa-parsers/): standalone parsing library
46
+ - [ProteinBrowser](https://github.com/GMOD/proteinbrowser): protein analysis
47
+ suite built on this viewer