react-msaview 7.0.0 → 8.1.0

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 (335) hide show
  1. package/README.md +11 -10
  2. package/bundle/index.js +122 -111
  3. package/bundle/index.js.map +4 -4
  4. package/dist/calculateBlocks.js +5 -3
  5. package/dist/calculateBlocks.js.map +1 -1
  6. package/dist/colorSchemes.js +1 -2
  7. package/dist/colorSchemes.js.map +1 -1
  8. package/dist/columnStats.d.ts +28 -0
  9. package/dist/columnStats.js +34 -0
  10. package/dist/columnStats.js.map +1 -0
  11. package/dist/components/DragHandle.d.ts +3 -2
  12. package/dist/components/DragHandle.js +11 -5
  13. package/dist/components/DragHandle.js.map +1 -1
  14. package/dist/components/Loading.js +2 -8
  15. package/dist/components/Loading.js.map +1 -1
  16. package/dist/components/MSAView.js +17 -6
  17. package/dist/components/MSAView.js.map +1 -1
  18. package/dist/components/MSAViewer.d.ts +64 -7
  19. package/dist/components/MSAViewer.js +128 -23
  20. package/dist/components/MSAViewer.js.map +1 -1
  21. package/dist/components/PortalTooltip.d.ts +11 -0
  22. package/dist/components/PortalTooltip.js +29 -0
  23. package/dist/components/PortalTooltip.js.map +1 -0
  24. package/dist/components/ResizeHandles.js +11 -29
  25. package/dist/components/ResizeHandles.js.map +1 -1
  26. package/dist/components/SequenceTextArea.js +3 -4
  27. package/dist/components/SequenceTextArea.js.map +1 -1
  28. package/dist/components/Track.js +43 -24
  29. package/dist/components/Track.js.map +1 -1
  30. package/dist/components/dialogs/AboutDialog.js +6 -6
  31. package/dist/components/dialogs/AboutDialog.js.map +1 -1
  32. package/dist/components/dialogs/AnnotationFileDialog.js +5 -2
  33. package/dist/components/dialogs/AnnotationFileDialog.js.map +1 -1
  34. package/dist/components/dialogs/ExportSVGDialog.js +6 -4
  35. package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
  36. package/dist/components/dialogs/FeatureDialog.js +8 -3
  37. package/dist/components/dialogs/FeatureDialog.js.map +1 -1
  38. package/dist/components/dialogs/TrackInfoDialog.js +1 -1
  39. package/dist/components/dialogs/TrackInfoDialog.js.map +1 -1
  40. package/dist/components/header/GappynessSlider.js +6 -11
  41. package/dist/components/header/GappynessSlider.js.map +1 -1
  42. package/dist/components/header/Header.js +4 -1
  43. package/dist/components/header/Header.js.map +1 -1
  44. package/dist/components/header/LoadWarnings.js +6 -23
  45. package/dist/components/header/LoadWarnings.js.map +1 -1
  46. package/dist/components/header/ScrollZoomIcons.d.ts +6 -0
  47. package/dist/components/header/ScrollZoomIcons.js +35 -0
  48. package/dist/components/header/ScrollZoomIcons.js.map +1 -0
  49. package/dist/components/header/TreeSettingsMenu.js +1 -3
  50. package/dist/components/header/TreeSettingsMenu.js.map +1 -1
  51. package/dist/components/header/UnshareableDataWarning.js +2 -4
  52. package/dist/components/header/UnshareableDataWarning.js.map +1 -1
  53. package/dist/components/header/ZoomControls.js +49 -6
  54. package/dist/components/header/ZoomControls.js.map +1 -1
  55. package/dist/components/header/getAnnotationsMenu.js +3 -6
  56. package/dist/components/header/getAnnotationsMenu.js.map +1 -1
  57. package/dist/components/header/settingsMenuItems.js +12 -9
  58. package/dist/components/header/settingsMenuItems.js.map +1 -1
  59. package/dist/components/import/ImportForm.js +1 -1
  60. package/dist/components/import/ImportForm.js.map +1 -1
  61. package/dist/components/import/util.js +1 -2
  62. package/dist/components/import/util.js.map +1 -1
  63. package/dist/components/minimap/Minimap.js +1 -2
  64. package/dist/components/minimap/Minimap.js.map +1 -1
  65. package/dist/components/msa/AnnotationLegend.js +27 -19
  66. package/dist/components/msa/AnnotationLegend.js.map +1 -1
  67. package/dist/components/msa/MSACanvas.js +2 -4
  68. package/dist/components/msa/MSACanvas.js.map +1 -1
  69. package/dist/components/msa/MSACanvasBlock.js +13 -15
  70. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  71. package/dist/components/msa/MSAMouseoverCanvas.js +2 -1
  72. package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -1
  73. package/dist/components/msa/domainBandCursor.d.ts +7 -11
  74. package/dist/components/msa/domainBandCursor.js +7 -11
  75. package/dist/components/msa/domainBandCursor.js.map +1 -1
  76. package/dist/components/msa/drawFeatureSpans.d.ts +59 -0
  77. package/dist/components/msa/drawFeatureSpans.js +113 -0
  78. package/dist/components/msa/drawFeatureSpans.js.map +1 -0
  79. package/dist/components/msa/legendRows.d.ts +8 -0
  80. package/dist/components/msa/legendRows.js +16 -0
  81. package/dist/components/msa/legendRows.js.map +1 -0
  82. package/dist/components/msa/msaRaster.d.ts +24 -31
  83. package/dist/components/msa/msaRaster.js +30 -39
  84. package/dist/components/msa/msaRaster.js.map +1 -1
  85. package/dist/components/msa/packDomainLanes.d.ts +20 -0
  86. package/dist/components/msa/packDomainLanes.js +33 -0
  87. package/dist/components/msa/packDomainLanes.js.map +1 -0
  88. package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts +3 -1
  89. package/dist/components/msa/renderBoxFeatureCanvasBlock.js +50 -87
  90. package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
  91. package/dist/components/msa/renderHighlights.d.ts +15 -13
  92. package/dist/components/msa/renderHighlights.js +43 -20
  93. package/dist/components/msa/renderHighlights.js.map +1 -1
  94. package/dist/components/msa/renderMSABlock.js +12 -12
  95. package/dist/components/msa/renderMSABlock.js.map +1 -1
  96. package/dist/components/msa/tileColor.js +4 -7
  97. package/dist/components/msa/tileColor.js.map +1 -1
  98. package/dist/components/msa/useMsaBlockMouse.d.ts +5 -3
  99. package/dist/components/msa/useMsaBlockMouse.js +6 -6
  100. package/dist/components/msa/useMsaBlockMouse.js.map +1 -1
  101. package/dist/components/rowpanels/RowPanelBlock.d.ts +9 -0
  102. package/dist/components/rowpanels/RowPanelBlock.js +86 -0
  103. package/dist/components/rowpanels/RowPanelBlock.js.map +1 -0
  104. package/dist/components/rowpanels/RowPanelHeaders.d.ts +12 -0
  105. package/dist/components/rowpanels/RowPanelHeaders.js +38 -0
  106. package/dist/components/rowpanels/RowPanelHeaders.js.map +1 -0
  107. package/dist/components/{msa/ColumnStats.d.ts → rowpanels/RowPanels.d.ts} +2 -2
  108. package/dist/components/rowpanels/RowPanels.js +32 -0
  109. package/dist/components/rowpanels/RowPanels.js.map +1 -0
  110. package/dist/components/rowpanels/headerLayout.d.ts +1 -0
  111. package/dist/components/rowpanels/headerLayout.js +5 -0
  112. package/dist/components/rowpanels/headerLayout.js.map +1 -0
  113. package/dist/components/rowpanels/renderFeaturePanel.d.ts +21 -0
  114. package/dist/components/rowpanels/renderFeaturePanel.js +37 -0
  115. package/dist/components/rowpanels/renderFeaturePanel.js.map +1 -0
  116. package/dist/components/rowpanels/renderRowPanel.d.ts +23 -0
  117. package/dist/components/rowpanels/renderRowPanel.js +22 -0
  118. package/dist/components/rowpanels/renderRowPanel.js.map +1 -0
  119. package/dist/components/rowpanels/renderStrip.d.ts +20 -0
  120. package/dist/components/rowpanels/renderStrip.js +26 -0
  121. package/dist/components/rowpanels/renderStrip.js.map +1 -0
  122. package/dist/components/tracks/TrackBlocks.js +3 -5
  123. package/dist/components/tracks/TrackBlocks.js.map +1 -1
  124. package/dist/components/tracks/TrackTooltipContent.d.ts +15 -0
  125. package/dist/components/tracks/TrackTooltipContent.js +109 -0
  126. package/dist/components/tracks/TrackTooltipContent.js.map +1 -0
  127. package/dist/components/tracks/drawTracks.d.ts +4 -4
  128. package/dist/components/tracks/drawTracks.js +25 -39
  129. package/dist/components/tracks/drawTracks.js.map +1 -1
  130. package/dist/components/tracks/useTrackHover.d.ts +22 -0
  131. package/dist/components/tracks/useTrackHover.js +30 -0
  132. package/dist/components/tracks/useTrackHover.js.map +1 -0
  133. package/dist/components/tree/CladeLabels.d.ts +12 -0
  134. package/dist/components/tree/CladeLabels.js +48 -0
  135. package/dist/components/tree/CladeLabels.js.map +1 -0
  136. package/dist/components/tree/TreeBranchMenu.js +1 -1
  137. package/dist/components/tree/TreeBranchMenu.js.map +1 -1
  138. package/dist/components/tree/TreeCanvas.js +5 -4
  139. package/dist/components/tree/TreeCanvas.js.map +1 -1
  140. package/dist/components/tree/TreeCanvasBlock.js +4 -21
  141. package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
  142. package/dist/components/tree/TreeNodeMenu.js +1 -1
  143. package/dist/components/tree/TreeNodeMenu.js.map +1 -1
  144. package/dist/components/tree/TreeOverview.d.ts +14 -0
  145. package/dist/components/tree/TreeOverview.js +75 -0
  146. package/dist/components/tree/TreeOverview.js.map +1 -0
  147. package/dist/components/tree/TreeRuler.js +9 -13
  148. package/dist/components/tree/TreeRuler.js.map +1 -1
  149. package/dist/components/tree/cladeBrackets.d.ts +25 -0
  150. package/dist/components/tree/cladeBrackets.js +51 -0
  151. package/dist/components/tree/cladeBrackets.js.map +1 -0
  152. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js +2 -2
  153. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map +1 -1
  154. package/dist/components/tree/renderTreeCanvas.js +160 -25
  155. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  156. package/dist/components/tree/renderTreeOverview.d.ts +52 -0
  157. package/dist/components/tree/renderTreeOverview.js +138 -0
  158. package/dist/components/tree/renderTreeOverview.js.map +1 -0
  159. package/dist/components/tree/useTreeHover.js +2 -4
  160. package/dist/components/tree/useTreeHover.js.map +1 -1
  161. package/dist/constants.d.ts +16 -0
  162. package/dist/constants.js +52 -22
  163. package/dist/constants.js.map +1 -1
  164. package/dist/createPaletteMap.d.ts +7 -6
  165. package/dist/createPaletteMap.js +10 -9
  166. package/dist/createPaletteMap.js.map +1 -1
  167. package/dist/element.d.ts +13 -0
  168. package/dist/element.js +269 -0
  169. package/dist/element.js.map +1 -0
  170. package/dist/featureFields.d.ts +11 -0
  171. package/dist/featureFields.js +17 -0
  172. package/dist/featureFields.js.map +1 -0
  173. package/dist/flatToTree.js +1 -2
  174. package/dist/flatToTree.js.map +1 -1
  175. package/dist/ggplotPalettes.d.ts +10 -0
  176. package/dist/ggplotPalettes.js +58 -0
  177. package/dist/ggplotPalettes.js.map +1 -1
  178. package/dist/hierarchy.d.ts +27 -0
  179. package/dist/hierarchy.js +66 -9
  180. package/dist/hierarchy.js.map +1 -1
  181. package/dist/index.d.ts +9 -1
  182. package/dist/index.js +5 -3
  183. package/dist/index.js.map +1 -1
  184. package/dist/model/DataModel.js +2 -5
  185. package/dist/model/DataModel.js.map +1 -1
  186. package/dist/model/msaModel.d.ts +3 -2
  187. package/dist/model/msaModel.js +3 -2
  188. package/dist/model/msaModel.js.map +1 -1
  189. package/dist/model/treeModel.d.ts +30 -0
  190. package/dist/model/treeModel.js +37 -1
  191. package/dist/model/treeModel.js.map +1 -1
  192. package/dist/model.d.ts +549 -294
  193. package/dist/model.js +1412 -621
  194. package/dist/model.js.map +1 -1
  195. package/dist/mount.d.ts +11 -0
  196. package/dist/mount.js +22 -0
  197. package/dist/mount.js.map +1 -0
  198. package/dist/neighborJoining.js +8 -32
  199. package/dist/neighborJoining.js.map +1 -1
  200. package/dist/renderToStaticMarkup.d.ts +10 -19
  201. package/dist/renderToStaticMarkup.js +13 -24
  202. package/dist/renderToStaticMarkup.js.map +1 -1
  203. package/dist/renderToSvg.js +180 -56
  204. package/dist/renderToSvg.js.map +1 -1
  205. package/dist/rowCoordinateCalculations.d.ts +4 -6
  206. package/dist/rowCoordinateCalculations.js +4 -6
  207. package/dist/rowCoordinateCalculations.js.map +1 -1
  208. package/dist/scales.d.ts +22 -0
  209. package/dist/scales.js +30 -0
  210. package/dist/scales.js.map +1 -0
  211. package/dist/seqPosToGlobalCol.d.ts +2 -3
  212. package/dist/seqPosToGlobalCol.js +2 -3
  213. package/dist/seqPosToGlobalCol.js.map +1 -1
  214. package/dist/sequenceLogo.d.ts +6 -11
  215. package/dist/sequenceLogo.js +6 -11
  216. package/dist/sequenceLogo.js.map +1 -1
  217. package/dist/stripDefault.d.ts +7 -14
  218. package/dist/stripDefault.js +7 -14
  219. package/dist/stripDefault.js.map +1 -1
  220. package/dist/svgTestUtil.d.ts +186 -70
  221. package/dist/types.d.ts +221 -21
  222. package/dist/umd.d.ts +2 -0
  223. package/dist/umd.js +4 -2
  224. package/dist/umd.js.map +1 -1
  225. package/dist/useCanvasAutorun.d.ts +5 -10
  226. package/dist/useCanvasAutorun.js +5 -10
  227. package/dist/useCanvasAutorun.js.map +1 -1
  228. package/dist/useMsaSvgFigure.d.ts +20 -0
  229. package/dist/useMsaSvgFigure.js +46 -0
  230. package/dist/useMsaSvgFigure.js.map +1 -0
  231. package/dist/useWheelScroll.js +0 -4
  232. package/dist/useWheelScroll.js.map +1 -1
  233. package/dist/util.d.ts +5 -6
  234. package/dist/util.js +13 -6
  235. package/dist/util.js.map +1 -1
  236. package/dist/version.d.ts +1 -1
  237. package/dist/version.js +1 -1
  238. package/package.json +19 -12
  239. package/src/calculateBlocks.ts +5 -3
  240. package/src/colorSchemes.ts +1 -2
  241. package/src/columnStats.ts +58 -0
  242. package/src/components/DragHandle.tsx +18 -7
  243. package/src/components/Loading.tsx +4 -36
  244. package/src/components/MSAView.tsx +19 -5
  245. package/src/components/MSAViewer.tsx +240 -28
  246. package/src/components/PortalTooltip.tsx +47 -0
  247. package/src/components/ResizeHandles.tsx +17 -32
  248. package/src/components/SequenceTextArea.tsx +3 -4
  249. package/src/components/Track.tsx +57 -19
  250. package/src/components/dialogs/AboutDialog.tsx +35 -6
  251. package/src/components/dialogs/AnnotationFileDialog.tsx +10 -1
  252. package/src/components/dialogs/ExportSVGDialog.tsx +8 -3
  253. package/src/components/dialogs/FeatureDialog.tsx +11 -3
  254. package/src/components/dialogs/TrackInfoDialog.tsx +1 -1
  255. package/src/components/header/GappynessSlider.tsx +6 -11
  256. package/src/components/header/Header.tsx +7 -1
  257. package/src/components/header/LoadWarnings.tsx +11 -25
  258. package/src/components/header/ScrollZoomIcons.tsx +52 -0
  259. package/src/components/header/TreeSettingsMenu.tsx +1 -3
  260. package/src/components/header/UnshareableDataWarning.tsx +2 -4
  261. package/src/components/header/ZoomControls.tsx +74 -14
  262. package/src/components/header/getAnnotationsMenu.ts +3 -6
  263. package/src/components/header/settingsMenuItems.ts +13 -8
  264. package/src/components/import/ImportForm.tsx +3 -5
  265. package/src/components/import/ImportFormExamples.tsx +2 -2
  266. package/src/components/import/util.ts +1 -2
  267. package/src/components/minimap/Minimap.tsx +1 -2
  268. package/src/components/msa/AnnotationLegend.tsx +48 -38
  269. package/src/components/msa/MSACanvas.tsx +3 -8
  270. package/src/components/msa/MSACanvasBlock.tsx +13 -16
  271. package/src/components/msa/MSAMouseoverCanvas.tsx +2 -1
  272. package/src/components/msa/domainBandCursor.ts +7 -11
  273. package/src/components/msa/drawFeatureSpans.ts +205 -0
  274. package/src/components/msa/legendRows.ts +24 -0
  275. package/src/components/msa/msaRaster.ts +30 -39
  276. package/src/components/msa/packDomainLanes.ts +36 -0
  277. package/src/components/msa/renderBoxFeatureCanvasBlock.ts +67 -123
  278. package/src/components/msa/renderHighlights.ts +53 -20
  279. package/src/components/msa/renderMSABlock.ts +14 -11
  280. package/src/components/msa/tileColor.ts +4 -7
  281. package/src/components/msa/useMsaBlockMouse.ts +6 -6
  282. package/src/components/rowpanels/RowPanelBlock.tsx +139 -0
  283. package/src/components/rowpanels/RowPanelHeaders.tsx +57 -0
  284. package/src/components/rowpanels/RowPanels.tsx +77 -0
  285. package/src/components/rowpanels/headerLayout.ts +5 -0
  286. package/src/components/rowpanels/renderFeaturePanel.ts +66 -0
  287. package/src/components/rowpanels/renderRowPanel.ts +41 -0
  288. package/src/components/rowpanels/renderStrip.ts +46 -0
  289. package/src/components/tracks/TrackBlocks.tsx +3 -5
  290. package/src/components/tracks/TrackTooltipContent.tsx +156 -0
  291. package/src/components/tracks/drawTracks.ts +25 -50
  292. package/src/components/tracks/useTrackHover.ts +42 -0
  293. package/src/components/tree/CladeLabels.tsx +77 -0
  294. package/src/components/tree/TreeBranchMenu.tsx +1 -2
  295. package/src/components/tree/TreeCanvas.tsx +2 -3
  296. package/src/components/tree/TreeCanvasBlock.tsx +8 -32
  297. package/src/components/tree/TreeNodeMenu.tsx +1 -2
  298. package/src/components/tree/TreeOverview.tsx +106 -0
  299. package/src/components/tree/TreeRuler.tsx +11 -22
  300. package/src/components/tree/cladeBrackets.ts +73 -0
  301. package/src/components/tree/dialogs/TreeNodeInfoDialog.tsx +2 -2
  302. package/src/components/tree/renderTreeCanvas.ts +242 -21
  303. package/src/components/tree/renderTreeOverview.ts +212 -0
  304. package/src/components/tree/useTreeHover.ts +2 -4
  305. package/src/constants.ts +61 -22
  306. package/src/createPaletteMap.ts +10 -9
  307. package/src/element.ts +321 -0
  308. package/src/featureFields.ts +19 -0
  309. package/src/flatToTree.ts +1 -2
  310. package/src/ggplotPalettes.ts +60 -0
  311. package/src/hierarchy.ts +77 -9
  312. package/src/index.ts +31 -7
  313. package/src/model/DataModel.ts +2 -5
  314. package/src/model/msaModel.ts +3 -2
  315. package/src/model/treeModel.ts +42 -0
  316. package/src/model.ts +1677 -643
  317. package/src/mount.tsx +32 -0
  318. package/src/neighborJoining.ts +8 -32
  319. package/src/renderToStaticMarkup.ts +13 -24
  320. package/src/renderToSvg.tsx +335 -68
  321. package/src/rowCoordinateCalculations.ts +4 -6
  322. package/src/scales.ts +47 -0
  323. package/src/seqPosToGlobalCol.ts +2 -3
  324. package/src/sequenceLogo.ts +6 -11
  325. package/src/stripDefault.ts +7 -14
  326. package/src/types.ts +260 -45
  327. package/src/umd.ts +4 -2
  328. package/src/useCanvasAutorun.ts +5 -10
  329. package/src/useMsaSvgFigure.ts +72 -0
  330. package/src/useWheelScroll.ts +0 -4
  331. package/src/util.ts +15 -6
  332. package/src/version.ts +1 -1
  333. package/dist/components/msa/ColumnStats.js +0 -42
  334. package/dist/components/msa/ColumnStats.js.map +0 -1
  335. package/src/components/msa/ColumnStats.tsx +0 -54

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