react-msaview 8.2.0 → 8.4.0

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 (255) hide show
  1. package/bundle/index.js +77 -300
  2. package/bundle/index.js.map +4 -4
  3. package/dist/blockFasta.d.ts +6 -0
  4. package/dist/blockFasta.js +12 -0
  5. package/dist/blockFasta.js.map +1 -0
  6. package/dist/colorSchemes.d.ts +7 -0
  7. package/dist/colorSchemes.js +15 -0
  8. package/dist/colorSchemes.js.map +1 -1
  9. package/dist/columnCounts.d.ts +4 -3
  10. package/dist/columnCounts.js +11 -6
  11. package/dist/columnCounts.js.map +1 -1
  12. package/dist/components/CopyButton.d.ts +1 -1
  13. package/dist/components/CopyButton.js +1 -1
  14. package/dist/components/CopyButton.js.map +1 -1
  15. package/dist/components/DragHandle.js +14 -2
  16. package/dist/components/DragHandle.js.map +1 -1
  17. package/dist/components/Loading.js +10 -11
  18. package/dist/components/Loading.js.map +1 -1
  19. package/dist/components/MSAView.js +15 -9
  20. package/dist/components/MSAView.js.map +1 -1
  21. package/dist/components/MSAViewer.d.ts +39 -7
  22. package/dist/components/MSAViewer.js +72 -22
  23. package/dist/components/MSAViewer.js.map +1 -1
  24. package/dist/components/MetadataTable.d.ts +5 -0
  25. package/dist/components/MetadataTable.js +29 -0
  26. package/dist/components/MetadataTable.js.map +1 -0
  27. package/dist/components/SequenceTextArea.d.ts +11 -0
  28. package/dist/components/SequenceTextArea.js +40 -8
  29. package/dist/components/SequenceTextArea.js.map +1 -1
  30. package/dist/components/StatusMessage.d.ts +12 -0
  31. package/dist/components/StatusMessage.js +43 -0
  32. package/dist/components/StatusMessage.js.map +1 -0
  33. package/dist/components/Track.js +13 -4
  34. package/dist/components/Track.js.map +1 -1
  35. package/dist/components/VerticalScrollbar.js +6 -1
  36. package/dist/components/VerticalScrollbar.js.map +1 -1
  37. package/dist/components/dialogs/ExportSVGDialog.d.ts +3 -2
  38. package/dist/components/dialogs/ExportSVGDialog.js +4 -2
  39. package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
  40. package/dist/components/dialogs/FeatureDialog.js +15 -10
  41. package/dist/components/dialogs/FeatureDialog.js.map +1 -1
  42. package/dist/components/dialogs/MetadataDialog.js +5 -6
  43. package/dist/components/dialogs/MetadataDialog.js.map +1 -1
  44. package/dist/components/getVisibleLeaves.d.ts +1 -1
  45. package/dist/components/header/ColorSchemeMenu.d.ts +6 -0
  46. package/dist/components/header/ColorSchemeMenu.js +23 -5
  47. package/dist/components/header/ColorSchemeMenu.js.map +1 -1
  48. package/dist/components/header/FileMenu.js +9 -0
  49. package/dist/components/header/FileMenu.js.map +1 -1
  50. package/dist/components/header/GappynessSlider.js +15 -3
  51. package/dist/components/header/GappynessSlider.js.map +1 -1
  52. package/dist/components/header/{HeaderStatusArea.d.ts → GoToBox.d.ts} +2 -2
  53. package/dist/components/header/GoToBox.js +21 -0
  54. package/dist/components/header/GoToBox.js.map +1 -0
  55. package/dist/components/header/Header.js +8 -7
  56. package/dist/components/header/Header.js.map +1 -1
  57. package/dist/components/header/SelectionMenu.d.ts +12 -0
  58. package/dist/components/header/SelectionMenu.js +72 -0
  59. package/dist/components/header/SelectionMenu.js.map +1 -0
  60. package/dist/components/header/goTo.d.ts +20 -0
  61. package/dist/components/header/goTo.js +69 -0
  62. package/dist/components/header/goTo.js.map +1 -0
  63. package/dist/components/header/settingsMenuItems.js +57 -1
  64. package/dist/components/header/settingsMenuItems.js.map +1 -1
  65. package/dist/components/import/ImportForm.js +10 -4
  66. package/dist/components/import/ImportForm.js.map +1 -1
  67. package/dist/components/import/ImportFormExamples.js +19 -27
  68. package/dist/components/import/ImportFormExamples.js.map +1 -1
  69. package/dist/components/minimap/Minimap.js +6 -1
  70. package/dist/components/minimap/Minimap.js.map +1 -1
  71. package/dist/components/msa/AnnotationLegend.js +11 -5
  72. package/dist/components/msa/AnnotationLegend.js.map +1 -1
  73. package/dist/components/msa/MSACanvas.js +17 -1
  74. package/dist/components/msa/MSACanvas.js.map +1 -1
  75. package/dist/components/msa/MSACanvasBlock.js +6 -6
  76. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  77. package/dist/components/msa/msaKeys.d.ts +5 -0
  78. package/dist/components/msa/msaKeys.js +41 -0
  79. package/dist/components/msa/msaKeys.js.map +1 -0
  80. package/dist/components/msa/msaRaster.js +1 -0
  81. package/dist/components/msa/msaRaster.js.map +1 -1
  82. package/dist/components/msa/renderHighlights.d.ts +14 -3
  83. package/dist/components/msa/renderHighlights.js +29 -4
  84. package/dist/components/msa/renderHighlights.js.map +1 -1
  85. package/dist/components/msa/tileColor.js +9 -8
  86. package/dist/components/msa/tileColor.js.map +1 -1
  87. package/dist/components/msa/useMsaBlockMouse.d.ts +2 -4
  88. package/dist/components/msa/useMsaBlockMouse.js +34 -14
  89. package/dist/components/msa/useMsaBlockMouse.js.map +1 -1
  90. package/dist/components/overlayColors.d.ts +2 -0
  91. package/dist/components/overlayColors.js +3 -0
  92. package/dist/components/overlayColors.js.map +1 -1
  93. package/dist/components/rowpanels/RowPanelBlock.js +10 -14
  94. package/dist/components/rowpanels/RowPanelBlock.js.map +1 -1
  95. package/dist/components/selectionDrag.d.ts +17 -0
  96. package/dist/components/selectionDrag.js +30 -0
  97. package/dist/components/selectionDrag.js.map +1 -0
  98. package/dist/components/tracks/drawTracks.d.ts +1 -0
  99. package/dist/components/tracks/drawTracks.js +14 -2
  100. package/dist/components/tracks/drawTracks.js.map +1 -1
  101. package/dist/components/tracks/useTrackHover.d.ts +4 -6
  102. package/dist/components/tracks/useTrackHover.js +30 -10
  103. package/dist/components/tracks/useTrackHover.js.map +1 -1
  104. package/dist/components/tree/ScaleBarSVG.d.ts +14 -0
  105. package/dist/components/tree/ScaleBarSVG.js +11 -0
  106. package/dist/components/tree/ScaleBarSVG.js.map +1 -0
  107. package/dist/components/tree/TreeCanvas.js +8 -26
  108. package/dist/components/tree/TreeCanvas.js.map +1 -1
  109. package/dist/components/tree/TreeCanvasBlock.js +11 -20
  110. package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
  111. package/dist/components/tree/{TreeBranchMenu.d.ts → TreeMenu.d.ts} +5 -4
  112. package/dist/components/tree/TreeMenu.js +48 -0
  113. package/dist/components/tree/TreeMenu.js.map +1 -0
  114. package/dist/components/tree/TreeRuler.js +3 -3
  115. package/dist/components/tree/TreeRuler.js.map +1 -1
  116. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js +9 -8
  117. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map +1 -1
  118. package/dist/components/tree/renderTreeCanvas.js +19 -9
  119. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  120. package/dist/components/tree/renderTreeMouseover.d.ts +5 -0
  121. package/dist/components/tree/renderTreeMouseover.js +20 -0
  122. package/dist/components/tree/renderTreeMouseover.js.map +1 -0
  123. package/dist/components/tree/useTreeHover.d.ts +3 -8
  124. package/dist/components/tree/useTreeHover.js +8 -10
  125. package/dist/components/tree/useTreeHover.js.map +1 -1
  126. package/dist/components/useHoverAnchor.d.ts +19 -0
  127. package/dist/components/useHoverAnchor.js +18 -0
  128. package/dist/components/useHoverAnchor.js.map +1 -0
  129. package/dist/constants.d.ts +3 -0
  130. package/dist/constants.js +12 -3
  131. package/dist/constants.js.map +1 -1
  132. package/dist/element.d.ts +7 -3
  133. package/dist/element.js +32 -4
  134. package/dist/element.js.map +1 -1
  135. package/dist/expandSpec.js +3 -3
  136. package/dist/expandSpec.js.map +1 -1
  137. package/dist/exportFileName.d.ts +3 -3
  138. package/dist/exportFileName.js +4 -4
  139. package/dist/exportFileName.js.map +1 -1
  140. package/dist/featuresLayer.d.ts +8 -0
  141. package/dist/featuresLayer.js +42 -0
  142. package/dist/featuresLayer.js.map +1 -0
  143. package/dist/hierarchy.d.ts +51 -0
  144. package/dist/hierarchy.js +125 -0
  145. package/dist/hierarchy.js.map +1 -1
  146. package/dist/index.d.ts +2 -2
  147. package/dist/model/DataModel.d.ts +1 -1
  148. package/dist/model/DataModel.js +3 -3
  149. package/dist/model/DataModel.js.map +1 -1
  150. package/dist/model/msaModel.d.ts +14 -1
  151. package/dist/model/msaModel.js +17 -1
  152. package/dist/model/msaModel.js.map +1 -1
  153. package/dist/model/treeModel.d.ts +12 -0
  154. package/dist/model/treeModel.js +14 -1
  155. package/dist/model/treeModel.js.map +1 -1
  156. package/dist/model.d.ts +285 -53
  157. package/dist/model.js +693 -231
  158. package/dist/model.js.map +1 -1
  159. package/dist/renderToSvg.js +2 -4
  160. package/dist/renderToSvg.js.map +1 -1
  161. package/dist/rerootTree.d.ts +33 -0
  162. package/dist/rerootTree.js +144 -0
  163. package/dist/rerootTree.js.map +1 -0
  164. package/dist/svgTestUtil.d.ts +172 -26
  165. package/dist/types.d.ts +75 -12
  166. package/dist/useMsaSvgFigure.d.ts +2 -1
  167. package/dist/useMsaSvgFigure.js +11 -4
  168. package/dist/useMsaSvgFigure.js.map +1 -1
  169. package/dist/version.d.ts +1 -1
  170. package/dist/version.js +1 -1
  171. package/dist/writeNewick.d.ts +8 -0
  172. package/dist/writeNewick.js +34 -0
  173. package/dist/writeNewick.js.map +1 -0
  174. package/package.json +3 -3
  175. package/src/blockFasta.ts +18 -0
  176. package/src/colorSchemes.ts +20 -0
  177. package/src/columnCounts.ts +14 -6
  178. package/src/components/CopyButton.tsx +2 -2
  179. package/src/components/DragHandle.tsx +21 -1
  180. package/src/components/Loading.tsx +14 -30
  181. package/src/components/MSAView.tsx +16 -9
  182. package/src/components/MSAViewer.tsx +121 -26
  183. package/src/components/MetadataTable.tsx +55 -0
  184. package/src/components/SequenceTextArea.tsx +54 -8
  185. package/src/components/StatusMessage.tsx +70 -0
  186. package/src/components/Track.tsx +21 -4
  187. package/src/components/VerticalScrollbar.tsx +7 -0
  188. package/src/components/dialogs/ExportSVGDialog.tsx +5 -2
  189. package/src/components/dialogs/FeatureDialog.tsx +59 -38
  190. package/src/components/dialogs/MetadataDialog.tsx +9 -8
  191. package/src/components/header/ColorSchemeMenu.tsx +31 -12
  192. package/src/components/header/FileMenu.tsx +9 -0
  193. package/src/components/header/GappynessSlider.tsx +17 -4
  194. package/src/components/header/GoToBox.tsx +50 -0
  195. package/src/components/header/Header.tsx +11 -8
  196. package/src/components/header/SelectionMenu.tsx +117 -0
  197. package/src/components/header/goTo.ts +75 -0
  198. package/src/components/header/settingsMenuItems.ts +66 -0
  199. package/src/components/import/ImportForm.tsx +14 -7
  200. package/src/components/import/ImportFormExamples.tsx +20 -28
  201. package/src/components/minimap/Minimap.tsx +7 -0
  202. package/src/components/msa/AnnotationLegend.tsx +12 -6
  203. package/src/components/msa/MSACanvas.tsx +19 -1
  204. package/src/components/msa/MSACanvasBlock.tsx +9 -11
  205. package/src/components/msa/msaKeys.ts +45 -0
  206. package/src/components/msa/msaRaster.ts +1 -0
  207. package/src/components/msa/renderHighlights.ts +46 -4
  208. package/src/components/msa/tileColor.ts +9 -8
  209. package/src/components/msa/useMsaBlockMouse.ts +44 -31
  210. package/src/components/overlayColors.ts +4 -0
  211. package/src/components/rowpanels/RowPanelBlock.tsx +16 -23
  212. package/src/components/selectionDrag.ts +42 -0
  213. package/src/components/tracks/drawTracks.ts +15 -2
  214. package/src/components/tracks/useTrackHover.ts +32 -10
  215. package/src/components/tree/ScaleBarSVG.tsx +30 -0
  216. package/src/components/tree/TreeCanvas.tsx +9 -40
  217. package/src/components/tree/TreeCanvasBlock.tsx +19 -39
  218. package/src/components/tree/TreeMenu.tsx +129 -0
  219. package/src/components/tree/TreeRuler.tsx +7 -13
  220. package/src/components/tree/dialogs/TreeNodeInfoDialog.tsx +14 -16
  221. package/src/components/tree/renderTreeCanvas.ts +20 -8
  222. package/src/components/tree/renderTreeMouseover.ts +41 -0
  223. package/src/components/tree/useTreeHover.ts +8 -17
  224. package/src/components/useHoverAnchor.ts +31 -0
  225. package/src/constants.ts +14 -3
  226. package/src/element.ts +45 -5
  227. package/src/expandSpec.ts +3 -3
  228. package/src/exportFileName.ts +4 -3
  229. package/src/featuresLayer.ts +48 -0
  230. package/src/hierarchy.ts +151 -4
  231. package/src/index.ts +8 -1
  232. package/src/model/DataModel.ts +3 -3
  233. package/src/model/msaModel.ts +19 -1
  234. package/src/model/treeModel.ts +22 -0
  235. package/src/model.ts +841 -272
  236. package/src/renderToSvg.tsx +6 -9
  237. package/src/rerootTree.ts +172 -0
  238. package/src/types.ts +92 -12
  239. package/src/useMsaSvgFigure.ts +11 -4
  240. package/src/version.ts +1 -1
  241. package/src/writeNewick.ts +38 -0
  242. package/dist/components/PortalTooltip.d.ts +0 -11
  243. package/dist/components/PortalTooltip.js +0 -29
  244. package/dist/components/PortalTooltip.js.map +0 -1
  245. package/dist/components/header/HeaderStatusArea.js +0 -21
  246. package/dist/components/header/HeaderStatusArea.js.map +0 -1
  247. package/dist/components/tree/TreeBranchMenu.js +0 -29
  248. package/dist/components/tree/TreeBranchMenu.js.map +0 -1
  249. package/dist/components/tree/TreeNodeMenu.d.ts +0 -13
  250. package/dist/components/tree/TreeNodeMenu.js +0 -41
  251. package/dist/components/tree/TreeNodeMenu.js.map +0 -1
  252. package/src/components/PortalTooltip.tsx +0 -47
  253. package/src/components/header/HeaderStatusArea.tsx +0 -32
  254. package/src/components/tree/TreeBranchMenu.tsx +0 -68
  255. package/src/components/tree/TreeNodeMenu.tsx +0 -95

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