react-msaview 9.0.0 → 9.1.1

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 (352) hide show
  1. package/README.md +19 -10
  2. package/bundle/index.js +111 -115
  3. package/bundle/index.js.map +4 -4
  4. package/dist/blosum62.d.ts +3 -0
  5. package/dist/blosum62.js +43 -0
  6. package/dist/blosum62.js.map +1 -0
  7. package/dist/colorSchemes.js +2 -3
  8. package/dist/colorSchemes.js.map +1 -1
  9. package/dist/columnCounts.d.ts +0 -1
  10. package/dist/columnCounts.js +1 -1
  11. package/dist/columnCounts.js.map +1 -1
  12. package/dist/components/Loading.d.ts +3 -2
  13. package/dist/components/Loading.js +7 -7
  14. package/dist/components/Loading.js.map +1 -1
  15. package/dist/components/MSAView.d.ts +3 -2
  16. package/dist/components/MSAView.js +7 -4
  17. package/dist/components/MSAView.js.map +1 -1
  18. package/dist/components/MSAViewer.d.ts +1941 -4
  19. package/dist/components/MSAViewer.js +144 -201
  20. package/dist/components/MSAViewer.js.map +1 -1
  21. package/dist/components/MetadataTable.d.ts +4 -1
  22. package/dist/components/MetadataTable.js +55 -16
  23. package/dist/components/MetadataTable.js.map +1 -1
  24. package/dist/components/ResizeHandles.js +3 -2
  25. package/dist/components/ResizeHandles.js.map +1 -1
  26. package/dist/components/Track.js +8 -1
  27. package/dist/components/Track.js.map +1 -1
  28. package/dist/components/controls.d.ts +11 -0
  29. package/dist/components/controls.js +49 -0
  30. package/dist/components/controls.js.map +1 -0
  31. package/dist/components/dialogs/AnnotationFileDialog.js +12 -18
  32. package/dist/components/dialogs/AnnotationFileDialog.js.map +1 -1
  33. package/dist/components/dialogs/ExportSVGDialog.js +5 -7
  34. package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
  35. package/dist/components/dialogs/FeatureDialog.js +2 -2
  36. package/dist/components/dialogs/FeatureDialog.js.map +1 -1
  37. package/dist/components/{header/TreeSettingsMenu.d.ts → dialogs/GapThresholdDialog.d.ts} +3 -2
  38. package/dist/components/dialogs/GapThresholdDialog.js +15 -0
  39. package/dist/components/dialogs/GapThresholdDialog.js.map +1 -0
  40. package/dist/components/{header → dialogs}/GappynessSlider.d.ts +1 -1
  41. package/dist/components/{header → dialogs}/GappynessSlider.js +3 -10
  42. package/dist/components/dialogs/GappynessSlider.js.map +1 -0
  43. package/dist/components/{header → dialogs}/GoToBox.d.ts +4 -2
  44. package/dist/components/dialogs/GoToBox.js +48 -0
  45. package/dist/components/dialogs/GoToBox.js.map +1 -0
  46. package/dist/components/dialogs/GoToDialog.d.ts +6 -0
  47. package/dist/components/dialogs/GoToDialog.js +10 -0
  48. package/dist/components/dialogs/GoToDialog.js.map +1 -0
  49. package/dist/components/dialogs/HelpDialog.d.ts +6 -0
  50. package/dist/components/dialogs/HelpDialog.js +30 -0
  51. package/dist/components/dialogs/HelpDialog.js.map +1 -0
  52. package/dist/components/dialogs/MetadataDialog.js +11 -3
  53. package/dist/components/dialogs/MetadataDialog.js.map +1 -1
  54. package/dist/components/dialogs/goTo.d.ts +5 -0
  55. package/dist/components/{header → dialogs}/goTo.js +1 -1
  56. package/dist/components/dialogs/goTo.js.map +1 -0
  57. package/dist/components/dialogs/metadataLabels.d.ts +4 -0
  58. package/dist/components/dialogs/metadataLabels.js +52 -0
  59. package/dist/components/dialogs/metadataLabels.js.map +1 -0
  60. package/dist/components/dialogs/metadataRecord.d.ts +1 -0
  61. package/dist/components/dialogs/metadataRecord.js +38 -0
  62. package/dist/components/dialogs/metadataRecord.js.map +1 -0
  63. package/dist/components/header/Header.d.ts +6 -2
  64. package/dist/components/header/Header.js +30 -34
  65. package/dist/components/header/Header.js.map +1 -1
  66. package/dist/components/header/HiddenColumnsChip.d.ts +6 -0
  67. package/dist/components/header/HiddenColumnsChip.js +15 -0
  68. package/dist/components/header/HiddenColumnsChip.js.map +1 -0
  69. package/dist/components/header/{FileMenu.d.ts → MenuBar.d.ts} +3 -3
  70. package/dist/components/header/MenuBar.js +33 -0
  71. package/dist/components/header/MenuBar.js.map +1 -0
  72. package/dist/components/header/ScrollZoomCheckbox.d.ts +7 -0
  73. package/dist/components/header/ScrollZoomCheckbox.js +19 -0
  74. package/dist/components/header/ScrollZoomCheckbox.js.map +1 -0
  75. package/dist/components/header/ZoomControls.js +12 -48
  76. package/dist/components/header/ZoomControls.js.map +1 -1
  77. package/dist/components/header/colorSchemeMenuItems.d.ts +4 -0
  78. package/dist/components/header/colorSchemeMenuItems.js +106 -0
  79. package/dist/components/header/colorSchemeMenuItems.js.map +1 -0
  80. package/dist/components/header/getAnnotationsMenu.d.ts +3 -30
  81. package/dist/components/header/getAnnotationsMenu.js +48 -54
  82. package/dist/components/header/getAnnotationsMenu.js.map +1 -1
  83. package/dist/components/header/menuBarItems.d.ts +11 -0
  84. package/dist/components/header/menuBarItems.js +277 -0
  85. package/dist/components/header/menuBarItems.js.map +1 -0
  86. package/dist/components/import/ImportForm.js +12 -6
  87. package/dist/components/import/ImportForm.js.map +1 -1
  88. package/dist/components/import/data/seq2.d.ts +0 -1
  89. package/dist/components/import/data/seq2.js +0 -17
  90. package/dist/components/import/data/seq2.js.map +1 -1
  91. package/dist/components/minimap/Minimap.js +7 -3
  92. package/dist/components/minimap/Minimap.js.map +1 -1
  93. package/dist/components/minimap/MinimapSVG.js +2 -1
  94. package/dist/components/minimap/MinimapSVG.js.map +1 -1
  95. package/dist/components/minimap/minimapLayout.d.ts +12 -0
  96. package/dist/components/minimap/minimapLayout.js +20 -0
  97. package/dist/components/minimap/minimapLayout.js.map +1 -1
  98. package/dist/components/msa/MSACanvas.js +28 -10
  99. package/dist/components/msa/MSACanvas.js.map +1 -1
  100. package/dist/components/msa/MSACanvasBlock.js +17 -16
  101. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  102. package/dist/components/msa/MSAMouseoverCanvas.js +2 -2
  103. package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -1
  104. package/dist/components/msa/WheelZoomHint.d.ts +7 -0
  105. package/dist/components/msa/WheelZoomHint.js +38 -0
  106. package/dist/components/msa/WheelZoomHint.js.map +1 -0
  107. package/dist/components/msa/drawFeatureSpans.d.ts +50 -11
  108. package/dist/components/msa/drawFeatureSpans.js +99 -56
  109. package/dist/components/msa/drawFeatureSpans.js.map +1 -1
  110. package/dist/components/msa/msaKeys.js +3 -0
  111. package/dist/components/msa/msaKeys.js.map +1 -1
  112. package/dist/components/msa/msaRaster.d.ts +14 -2
  113. package/dist/components/msa/msaRaster.js +20 -10
  114. package/dist/components/msa/msaRaster.js.map +1 -1
  115. package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts +9 -0
  116. package/dist/components/msa/renderBoxFeatureCanvasBlock.js +39 -8
  117. package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
  118. package/dist/components/msa/renderHighlights.d.ts +2 -5
  119. package/dist/components/msa/renderHighlights.js +5 -6
  120. package/dist/components/msa/renderHighlights.js.map +1 -1
  121. package/dist/components/msa/renderMSABlock.d.ts +6 -1
  122. package/dist/components/msa/renderMSABlock.js +44 -17
  123. package/dist/components/msa/renderMSABlock.js.map +1 -1
  124. package/dist/components/msa/renderMSAMouseover.js +2 -1
  125. package/dist/components/msa/renderMSAMouseover.js.map +1 -1
  126. package/dist/components/msa/tileColor.js +7 -0
  127. package/dist/components/msa/tileColor.js.map +1 -1
  128. package/dist/components/renderCtx.d.ts +1 -1
  129. package/dist/components/rowpanels/RowPanelBlock.js +2 -2
  130. package/dist/components/rowpanels/RowPanelBlock.js.map +1 -1
  131. package/dist/components/rowpanels/renderFeaturePanel.d.ts +5 -1
  132. package/dist/components/rowpanels/renderFeaturePanel.js +12 -5
  133. package/dist/components/rowpanels/renderFeaturePanel.js.map +1 -1
  134. package/dist/components/settings/MenuItemsForm.d.ts +10 -0
  135. package/dist/components/settings/MenuItemsForm.js +80 -0
  136. package/dist/components/settings/MenuItemsForm.js.map +1 -0
  137. package/dist/components/settings/SettingsPanel.d.ts +12 -0
  138. package/dist/components/settings/SettingsPanel.js +92 -0
  139. package/dist/components/settings/SettingsPanel.js.map +1 -0
  140. package/dist/components/{header/ZoomMenu.d.ts → settings/TrackList.d.ts} +2 -2
  141. package/dist/components/settings/TrackList.js +55 -0
  142. package/dist/components/settings/TrackList.js.map +1 -0
  143. package/dist/components/tracks/TrackBlocks.js +2 -2
  144. package/dist/components/tracks/TrackBlocks.js.map +1 -1
  145. package/dist/components/tracks/drawTracks.d.ts +1 -53
  146. package/dist/components/tracks/drawTracks.js +5 -5
  147. package/dist/components/tracks/drawTracks.js.map +1 -1
  148. package/dist/components/tree/CladeLabels.d.ts +1 -1
  149. package/dist/components/tree/CladeLabels.js +22 -34
  150. package/dist/components/tree/CladeLabels.js.map +1 -1
  151. package/dist/components/tree/TreeCanvasBlock.js +2 -2
  152. package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
  153. package/dist/components/tree/TreeMenu.js +4 -6
  154. package/dist/components/tree/TreeMenu.js.map +1 -1
  155. package/dist/components/tree/TreeOverview.js +2 -2
  156. package/dist/components/tree/TreeOverview.js.map +1 -1
  157. package/dist/components/tree/cladeBrackets.d.ts +17 -10
  158. package/dist/components/tree/cladeBrackets.js +33 -3
  159. package/dist/components/tree/cladeBrackets.js.map +1 -1
  160. package/dist/components/tree/renderTreeCanvas.js +2 -8
  161. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  162. package/dist/components/tree/renderTreeOverview.js +4 -11
  163. package/dist/components/tree/renderTreeOverview.js.map +1 -1
  164. package/dist/constants.d.ts +4 -1
  165. package/dist/constants.js +7 -1
  166. package/dist/constants.js.map +1 -1
  167. package/dist/darkReader.d.ts +7 -0
  168. package/dist/darkReader.js +42 -0
  169. package/dist/darkReader.js.map +1 -0
  170. package/dist/element.js +25 -53
  171. package/dist/element.js.map +1 -1
  172. package/dist/exportLayout.d.ts +39 -0
  173. package/dist/exportLayout.js +78 -0
  174. package/dist/exportLayout.js.map +1 -0
  175. package/dist/featurePanels.d.ts +37 -0
  176. package/dist/featurePanels.js +187 -0
  177. package/dist/featurePanels.js.map +1 -0
  178. package/dist/filehandleLoader.d.ts +41 -0
  179. package/dist/filehandleLoader.js +99 -0
  180. package/dist/filehandleLoader.js.map +1 -0
  181. package/dist/headlessRenderEnv.d.ts +12 -39
  182. package/dist/headlessRenderEnv.js +18 -12
  183. package/dist/headlessRenderEnv.js.map +1 -1
  184. package/dist/hierarchy.d.ts +5 -8
  185. package/dist/hierarchy.js +5 -79
  186. package/dist/hierarchy.js.map +1 -1
  187. package/dist/index.d.ts +6 -1
  188. package/dist/index.js +6 -1
  189. package/dist/index.js.map +1 -1
  190. package/dist/measureTextCanvas.d.ts +7 -0
  191. package/dist/measureTextCanvas.js +8 -6
  192. package/dist/measureTextCanvas.js.map +1 -1
  193. package/dist/model/treeModel.d.ts +6 -2
  194. package/dist/model/treeModel.js +8 -4
  195. package/dist/model/treeModel.js.map +1 -1
  196. package/dist/model.d.ts +180 -76
  197. package/dist/model.js +358 -618
  198. package/dist/model.js.map +1 -1
  199. package/dist/neighborJoining.js +1 -40
  200. package/dist/neighborJoining.js.map +1 -1
  201. package/dist/renderToSvg.d.ts +2 -7
  202. package/dist/renderToSvg.js +33 -133
  203. package/dist/renderToSvg.js.map +1 -1
  204. package/dist/rerootTree.d.ts +1 -0
  205. package/dist/rerootTree.js +7 -6
  206. package/dist/rerootTree.js.map +1 -1
  207. package/dist/schemeResidueColor.d.ts +12 -0
  208. package/dist/schemeResidueColor.js +33 -0
  209. package/dist/schemeResidueColor.js.map +1 -0
  210. package/dist/similarityColors.d.ts +11 -0
  211. package/dist/similarityColors.js +90 -0
  212. package/dist/similarityColors.js.map +1 -0
  213. package/dist/svgTestUtil.d.ts +74 -32
  214. package/dist/treeDisplay.d.ts +37 -0
  215. package/dist/treeDisplay.js +209 -0
  216. package/dist/treeDisplay.js.map +1 -0
  217. package/dist/types.d.ts +6 -3
  218. package/dist/useWheelScroll.d.ts +3 -1
  219. package/dist/useWheelScroll.js +36 -17
  220. package/dist/useWheelScroll.js.map +1 -1
  221. package/dist/util.d.ts +2 -0
  222. package/dist/util.js +2 -0
  223. package/dist/util.js.map +1 -1
  224. package/dist/version.d.ts +1 -1
  225. package/dist/version.js +1 -1
  226. package/dist/viewerSnapshot.d.ts +169 -0
  227. package/dist/viewerSnapshot.js +100 -0
  228. package/dist/viewerSnapshot.js.map +1 -0
  229. package/dist/wheelZoom.d.ts +8 -3
  230. package/dist/wheelZoom.js +44 -32
  231. package/dist/wheelZoom.js.map +1 -1
  232. package/dist/zoomSnapshot.d.ts +29 -0
  233. package/dist/zoomSnapshot.js +47 -0
  234. package/dist/zoomSnapshot.js.map +1 -0
  235. package/package.json +11 -11
  236. package/src/blosum62.ts +45 -0
  237. package/src/colorSchemes.ts +2 -4
  238. package/src/columnCounts.ts +1 -1
  239. package/src/components/Loading.tsx +25 -14
  240. package/src/components/MSAView.tsx +22 -5
  241. package/src/components/MSAViewer.tsx +275 -251
  242. package/src/components/MetadataTable.tsx +83 -26
  243. package/src/components/ResizeHandles.tsx +9 -2
  244. package/src/components/Track.tsx +15 -1
  245. package/src/components/controls.ts +62 -0
  246. package/src/components/dialogs/AnnotationFileDialog.tsx +16 -21
  247. package/src/components/dialogs/ExportSVGDialog.tsx +8 -19
  248. package/src/components/dialogs/FeatureDialog.tsx +2 -5
  249. package/src/components/dialogs/GapThresholdDialog.tsx +36 -0
  250. package/src/components/{header → dialogs}/GappynessSlider.tsx +3 -10
  251. package/src/components/{header → dialogs}/GoToBox.tsx +36 -10
  252. package/src/components/dialogs/GoToDialog.tsx +30 -0
  253. package/src/components/dialogs/HelpDialog.tsx +79 -0
  254. package/src/components/dialogs/MetadataDialog.tsx +32 -4
  255. package/src/components/{header → dialogs}/goTo.ts +1 -1
  256. package/src/components/dialogs/metadataLabels.ts +54 -0
  257. package/src/components/dialogs/metadataRecord.tsx +61 -0
  258. package/src/components/header/Header.tsx +75 -44
  259. package/src/components/header/HiddenColumnsChip.tsx +39 -0
  260. package/src/components/header/MenuBar.tsx +64 -0
  261. package/src/components/header/ScrollZoomCheckbox.tsx +46 -0
  262. package/src/components/header/ZoomControls.tsx +23 -74
  263. package/src/components/header/colorSchemeMenuItems.ts +121 -0
  264. package/src/components/header/getAnnotationsMenu.ts +52 -56
  265. package/src/components/header/menuBarItems.ts +357 -0
  266. package/src/components/import/ImportForm.tsx +19 -7
  267. package/src/components/import/data/seq2.ts +0 -18
  268. package/src/components/minimap/Minimap.tsx +11 -3
  269. package/src/components/minimap/MinimapSVG.tsx +17 -1
  270. package/src/components/minimap/minimapLayout.ts +27 -0
  271. package/src/components/msa/MSACanvas.tsx +24 -4
  272. package/src/components/msa/MSACanvasBlock.tsx +20 -17
  273. package/src/components/msa/MSAMouseoverCanvas.tsx +2 -2
  274. package/src/components/msa/WheelZoomHint.tsx +56 -0
  275. package/src/components/msa/drawFeatureSpans.ts +160 -79
  276. package/src/components/msa/msaKeys.ts +3 -0
  277. package/src/components/msa/msaRaster.ts +26 -10
  278. package/src/components/msa/renderBoxFeatureCanvasBlock.ts +62 -24
  279. package/src/components/msa/renderHighlights.ts +5 -6
  280. package/src/components/msa/renderMSABlock.ts +51 -15
  281. package/src/components/msa/renderMSAMouseover.ts +5 -1
  282. package/src/components/msa/tileColor.ts +7 -0
  283. package/src/components/renderCtx.ts +0 -1
  284. package/src/components/rowpanels/RowPanelBlock.tsx +2 -2
  285. package/src/components/rowpanels/renderFeaturePanel.ts +26 -7
  286. package/src/components/settings/MenuItemsForm.tsx +225 -0
  287. package/src/components/settings/SettingsPanel.tsx +156 -0
  288. package/src/components/settings/TrackList.tsx +119 -0
  289. package/src/components/tracks/TrackBlocks.tsx +2 -2
  290. package/src/components/tracks/drawTracks.ts +5 -5
  291. package/src/components/tree/CladeLabels.tsx +30 -54
  292. package/src/components/tree/TreeCanvasBlock.tsx +2 -2
  293. package/src/components/tree/TreeMenu.tsx +4 -6
  294. package/src/components/tree/TreeOverview.tsx +2 -2
  295. package/src/components/tree/cladeBrackets.ts +50 -3
  296. package/src/components/tree/renderTreeCanvas.ts +2 -13
  297. package/src/components/tree/renderTreeOverview.ts +7 -14
  298. package/src/constants.ts +9 -1
  299. package/src/darkReader.ts +57 -0
  300. package/src/element.ts +37 -64
  301. package/src/exportLayout.ts +134 -0
  302. package/src/featurePanels.ts +269 -0
  303. package/src/filehandleLoader.ts +136 -0
  304. package/src/headlessRenderEnv.ts +24 -11
  305. package/src/hierarchy.ts +5 -88
  306. package/src/index.ts +9 -5
  307. package/src/measureTextCanvas.ts +8 -6
  308. package/src/model/treeModel.ts +9 -3
  309. package/src/model.ts +452 -807
  310. package/src/neighborJoining.ts +1 -42
  311. package/src/renderToSvg.tsx +56 -207
  312. package/src/rerootTree.ts +7 -6
  313. package/src/schemeResidueColor.ts +37 -0
  314. package/src/similarityColors.ts +112 -0
  315. package/src/treeDisplay.ts +278 -0
  316. package/src/types.ts +6 -4
  317. package/src/useWheelScroll.ts +43 -22
  318. package/src/util.ts +3 -0
  319. package/src/version.ts +1 -1
  320. package/src/viewerSnapshot.ts +147 -0
  321. package/src/wheelZoom.ts +55 -33
  322. package/src/zoomSnapshot.ts +80 -0
  323. package/dist/components/header/ColorSchemeMenu.d.ts +0 -12
  324. package/dist/components/header/ColorSchemeMenu.js +0 -37
  325. package/dist/components/header/ColorSchemeMenu.js.map +0 -1
  326. package/dist/components/header/FileMenu.js +0 -66
  327. package/dist/components/header/FileMenu.js.map +0 -1
  328. package/dist/components/header/GappynessSlider.js.map +0 -1
  329. package/dist/components/header/GoToBox.js +0 -31
  330. package/dist/components/header/GoToBox.js.map +0 -1
  331. package/dist/components/header/MSASettingsMenu.d.ts +0 -6
  332. package/dist/components/header/MSASettingsMenu.js +0 -11
  333. package/dist/components/header/MSASettingsMenu.js.map +0 -1
  334. package/dist/components/header/ScrollZoomIcons.d.ts +0 -6
  335. package/dist/components/header/ScrollZoomIcons.js +0 -35
  336. package/dist/components/header/ScrollZoomIcons.js.map +0 -1
  337. package/dist/components/header/TreeSettingsMenu.js +0 -42
  338. package/dist/components/header/TreeSettingsMenu.js.map +0 -1
  339. package/dist/components/header/ZoomMenu.js +0 -37
  340. package/dist/components/header/ZoomMenu.js.map +0 -1
  341. package/dist/components/header/goTo.d.ts +0 -20
  342. package/dist/components/header/goTo.js.map +0 -1
  343. package/dist/components/header/settingsMenuItems.d.ts +0 -4
  344. package/dist/components/header/settingsMenuItems.js +0 -127
  345. package/dist/components/header/settingsMenuItems.js.map +0 -1
  346. package/src/components/header/ColorSchemeMenu.tsx +0 -56
  347. package/src/components/header/FileMenu.tsx +0 -81
  348. package/src/components/header/MSASettingsMenu.tsx +0 -26
  349. package/src/components/header/ScrollZoomIcons.tsx +0 -52
  350. package/src/components/header/TreeSettingsMenu.tsx +0 -60
  351. package/src/components/header/ZoomMenu.tsx +0 -48
  352. package/src/components/header/settingsMenuItems.ts +0 -157
@@ -10,6 +10,7 @@ import {
10
10
  defaultShowBranchLen,
11
11
  defaultTreeOrder,
12
12
  defaultShowTreeOverview,
13
+ defaultShowTreeScaleBar,
13
14
  treeOrders,
14
15
  } from '../constants.ts'
15
16
  import { stripDefault } from '../stripDefault.ts'
@@ -93,6 +94,12 @@ export function TreeModelF() {
93
94
  */
94
95
  showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
95
96
 
97
+ /**
98
+ * #property
99
+ * draw the branch-length scale bar above the tree of a phylogram
100
+ */
101
+ showTreeScaleBar: stripDefault(types.boolean, defaultShowTreeScaleBar),
102
+
96
103
  /**
97
104
  * #property
98
105
  * height of the tree overview band, px
@@ -165,10 +172,9 @@ export function TreeModelF() {
165
172
  },
166
173
  /**
167
174
  * #action
168
- * set the height of the tree overview band (px)
169
175
  */
170
- setOverviewHeight(n: number) {
171
- self.overviewHeight = Math.round(n)
176
+ setShowTreeScaleBar(arg: boolean) {
177
+ self.showTreeScaleBar = arg
172
178
  },
173
179
  /**
174
180
  * #action