react-msaview 3.1.7 → 3.1.8

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Files changed (270) hide show
  1. package/bundle/index.js +32 -32
  2. package/dist/components/Checkbox2.d.ts +7 -0
  3. package/dist/components/Checkbox2.js +10 -0
  4. package/dist/components/Checkbox2.js.map +1 -0
  5. package/dist/components/Loading.js +12 -4
  6. package/dist/components/Loading.js.map +1 -1
  7. package/dist/components/MSAView.js +5 -8
  8. package/dist/components/MSAView.js.map +1 -1
  9. package/dist/components/SequenceTextArea.d.ts +4 -0
  10. package/dist/components/SequenceTextArea.js +38 -0
  11. package/dist/components/SequenceTextArea.js.map +1 -0
  12. package/dist/components/Track.js +9 -8
  13. package/dist/components/Track.js.map +1 -1
  14. package/dist/components/dialogs/AddTrackDialog.js +0 -1
  15. package/dist/components/dialogs/AddTrackDialog.js.map +1 -1
  16. package/dist/components/{ExportSVGDialog.d.ts → dialogs/ExportSVGDialog.d.ts} +1 -1
  17. package/dist/components/{ExportSVGDialog.js → dialogs/ExportSVGDialog.js} +3 -4
  18. package/dist/components/dialogs/ExportSVGDialog.js.map +1 -0
  19. package/dist/components/dialogs/FeatureDialog.d.ts +7 -0
  20. package/dist/components/dialogs/FeatureDialog.js +52 -0
  21. package/dist/components/dialogs/FeatureDialog.js.map +1 -0
  22. package/dist/components/dialogs/InterProScanDialog.d.ts +7 -0
  23. package/dist/components/dialogs/InterProScanDialog.js +163 -0
  24. package/dist/components/dialogs/InterProScanDialog.js.map +1 -0
  25. package/dist/components/dialogs/MetadataDialog.js +6 -3
  26. package/dist/components/dialogs/MetadataDialog.js.map +1 -1
  27. package/dist/components/dialogs/SettingsDialog.js +6 -11
  28. package/dist/components/dialogs/SettingsDialog.js.map +1 -1
  29. package/dist/components/{Header.d.ts → header/Header.d.ts} +1 -1
  30. package/dist/components/header/Header.js +30 -0
  31. package/dist/components/header/Header.js.map +1 -0
  32. package/dist/components/{HeaderInfoArea.d.ts → header/HeaderInfoArea.d.ts} +2 -2
  33. package/dist/components/header/HeaderInfoArea.js +20 -0
  34. package/dist/components/header/HeaderInfoArea.js.map +1 -0
  35. package/dist/components/header/HeaderMenu.d.ts +6 -0
  36. package/dist/components/header/HeaderMenu.js +40 -0
  37. package/dist/components/header/HeaderMenu.js.map +1 -0
  38. package/dist/components/header/HeaderMenuExtra.d.ts +6 -0
  39. package/dist/components/header/HeaderMenuExtra.js +92 -0
  40. package/dist/components/header/HeaderMenuExtra.js.map +1 -0
  41. package/dist/components/header/HeaderStatusArea.d.ts +6 -0
  42. package/dist/components/header/HeaderStatusArea.js +20 -0
  43. package/dist/components/header/HeaderStatusArea.js.map +1 -0
  44. package/dist/components/{MultiAlignmentSelector.d.ts → header/MultiAlignmentSelector.d.ts} +1 -1
  45. package/dist/components/header/MultiAlignmentSelector.js.map +1 -0
  46. package/dist/components/{ZoomControls.d.ts → header/ZoomControls.d.ts} +1 -1
  47. package/dist/components/header/ZoomControls.js +15 -0
  48. package/dist/components/header/ZoomControls.js.map +1 -0
  49. package/dist/components/{ImportForm/index.js → import/ImportForm.js} +1 -1
  50. package/dist/components/import/ImportForm.js.map +1 -0
  51. package/dist/components/{ImportForm → import}/ImportFormExamples.js +6 -2
  52. package/dist/components/import/ImportFormExamples.js.map +1 -0
  53. package/dist/components/import/data/seq2.js.map +1 -0
  54. package/dist/components/import/util.js +10 -0
  55. package/dist/components/import/util.js.map +1 -0
  56. package/dist/components/{Minimap.d.ts → minimap/Minimap.d.ts} +1 -1
  57. package/dist/components/minimap/Minimap.js.map +1 -0
  58. package/dist/components/{MinimapSVG.d.ts → minimap/MinimapSVG.d.ts} +1 -1
  59. package/dist/components/minimap/MinimapSVG.js.map +1 -0
  60. package/dist/components/msa/Loading.js.map +1 -0
  61. package/dist/components/{MSAPanel → msa}/MSACanvas.js +3 -2
  62. package/dist/components/msa/MSACanvas.js.map +1 -0
  63. package/dist/components/{MSAPanel/MSABlock.js → msa/MSACanvasBlock.js} +21 -9
  64. package/dist/components/msa/MSACanvasBlock.js.map +1 -0
  65. package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -0
  66. package/dist/components/msa/MSAPanel.d.ts +6 -0
  67. package/dist/components/{MSAPanel/index.js → msa/MSAPanel.js} +6 -3
  68. package/dist/components/msa/MSAPanel.js.map +1 -0
  69. package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts +9 -0
  70. package/dist/components/msa/renderBoxFeatureCanvasBlock.js +44 -0
  71. package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -0
  72. package/dist/components/{MSAPanel → msa}/renderMSABlock.js +24 -20
  73. package/dist/components/msa/renderMSABlock.js.map +1 -0
  74. package/dist/components/msa/renderMSAMouseover.js.map +1 -0
  75. package/dist/components/tree/TreeBranchMenu.js.map +1 -0
  76. package/dist/components/{TreePanel → tree}/TreeCanvas.js +1 -1
  77. package/dist/components/tree/TreeCanvas.js.map +1 -0
  78. package/dist/components/{TreePanel → tree}/TreeCanvasBlock.js +1 -1
  79. package/dist/components/tree/TreeCanvasBlock.js.map +1 -0
  80. package/dist/components/{TreePanel → tree}/TreeNodeMenu.js +2 -33
  81. package/dist/components/tree/TreeNodeMenu.js.map +1 -0
  82. package/dist/components/{TreePanel/index.js → tree/TreePanel.js} +2 -2
  83. package/dist/components/tree/TreePanel.js.map +1 -0
  84. package/dist/components/tree/TreeRuler.js.map +1 -0
  85. package/dist/components/{TreePanel → tree}/dialogs/TreeNodeInfoDialog.js +6 -2
  86. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map +1 -0
  87. package/dist/components/{TreePanel → tree}/renderTreeCanvas.js +23 -37
  88. package/dist/components/tree/renderTreeCanvas.js.map +1 -0
  89. package/dist/fetchUtils.d.ts +5 -0
  90. package/dist/fetchUtils.js +23 -0
  91. package/dist/fetchUtils.js.map +1 -0
  92. package/dist/ggplotPalettes.d.ts +3 -0
  93. package/dist/ggplotPalettes.js +24 -0
  94. package/dist/ggplotPalettes.js.map +1 -0
  95. package/dist/index.d.ts +1 -1
  96. package/dist/index.js +1 -1
  97. package/dist/index.js.map +1 -1
  98. package/dist/launchInterProScan.d.ts +32 -0
  99. package/dist/launchInterProScan.js +47 -0
  100. package/dist/launchInterProScan.js.map +1 -0
  101. package/dist/model/DataModel.js.map +1 -0
  102. package/dist/model/DialogQueue.js.map +1 -0
  103. package/dist/model/msaModel.d.ts +14 -0
  104. package/dist/model/msaModel.js +36 -0
  105. package/dist/model/msaModel.js.map +1 -0
  106. package/dist/model/treeModel.d.ts +46 -0
  107. package/dist/model/treeModel.js +105 -0
  108. package/dist/model/treeModel.js.map +1 -0
  109. package/dist/model.d.ts +261 -273
  110. package/dist/model.js +1043 -1029
  111. package/dist/model.js.map +1 -1
  112. package/dist/parseGFF.d.ts +10 -0
  113. package/dist/parseGFF.js +29 -0
  114. package/dist/parseGFF.js.map +1 -0
  115. package/dist/renderToSvg.js +23 -9
  116. package/dist/renderToSvg.js.map +1 -1
  117. package/dist/reparseTree.d.ts +2 -0
  118. package/dist/reparseTree.js +13 -0
  119. package/dist/reparseTree.js.map +1 -0
  120. package/dist/util.d.ts +4 -10
  121. package/dist/util.js +3 -28
  122. package/dist/util.js.map +1 -1
  123. package/dist/version.d.ts +1 -1
  124. package/dist/version.js +1 -1
  125. package/package.json +12 -2
  126. package/src/components/Checkbox2.tsx +34 -0
  127. package/src/components/Loading.tsx +27 -11
  128. package/src/components/MSAView.tsx +6 -10
  129. package/src/components/SequenceTextArea.tsx +63 -0
  130. package/src/components/Track.tsx +8 -13
  131. package/src/components/dialogs/AddTrackDialog.tsx +0 -1
  132. package/src/components/{ExportSVGDialog.tsx → dialogs/ExportSVGDialog.tsx} +9 -16
  133. package/src/components/dialogs/FeatureDialog.tsx +109 -0
  134. package/src/components/dialogs/InterProScanDialog.tsx +230 -0
  135. package/src/components/dialogs/MetadataDialog.tsx +9 -2
  136. package/src/components/dialogs/SettingsDialog.tsx +10 -30
  137. package/src/components/header/Header.tsx +44 -0
  138. package/src/components/header/HeaderInfoArea.tsx +27 -0
  139. package/src/components/header/HeaderMenu.tsx +54 -0
  140. package/src/components/header/HeaderMenuExtra.tsx +108 -0
  141. package/src/components/header/HeaderStatusArea.tsx +31 -0
  142. package/src/components/{MultiAlignmentSelector.tsx → header/MultiAlignmentSelector.tsx} +1 -1
  143. package/src/components/header/ZoomControls.tsx +28 -0
  144. package/src/components/{ImportForm → import}/ImportFormExamples.tsx +12 -1
  145. package/src/components/{ImportForm → import}/util.ts +5 -10
  146. package/src/components/{Minimap.tsx → minimap/Minimap.tsx} +1 -1
  147. package/src/components/{MinimapSVG.tsx → minimap/MinimapSVG.tsx} +1 -1
  148. package/src/components/{MSAPanel → msa}/MSACanvas.tsx +3 -2
  149. package/src/components/{MSAPanel/MSABlock.tsx → msa/MSACanvasBlock.tsx} +25 -12
  150. package/src/components/{MSAPanel/index.tsx → msa/MSAPanel.tsx} +8 -2
  151. package/src/components/msa/renderBoxFeatureCanvasBlock.ts +88 -0
  152. package/src/components/{MSAPanel → msa}/renderMSABlock.ts +26 -20
  153. package/src/components/{TreePanel → tree}/TreeCanvas.tsx +1 -1
  154. package/src/components/{TreePanel → tree}/TreeCanvasBlock.tsx +1 -1
  155. package/src/components/{TreePanel → tree}/TreeNodeMenu.tsx +1 -53
  156. package/src/components/{TreePanel/index.tsx → tree/TreePanel.tsx} +1 -1
  157. package/src/components/{TreePanel → tree}/dialogs/TreeNodeInfoDialog.tsx +9 -2
  158. package/src/components/{TreePanel → tree}/renderTreeCanvas.ts +25 -41
  159. package/src/fetchUtils.ts +30 -0
  160. package/src/ggplotPalettes.ts +25 -0
  161. package/src/index.ts +1 -1
  162. package/src/launchInterProScan.ts +98 -0
  163. package/src/model/msaModel.ts +39 -0
  164. package/src/model/treeModel.ts +116 -0
  165. package/src/model.ts +1124 -1126
  166. package/src/parseGFF.ts +32 -0
  167. package/src/renderToSvg.tsx +27 -8
  168. package/src/reparseTree.ts +16 -0
  169. package/src/util.ts +4 -33
  170. package/src/version.ts +1 -1
  171. package/dist/DataModel.js.map +0 -1
  172. package/dist/DialogQueue.js.map +0 -1
  173. package/dist/SelectedStructuresMixin.d.ts +0 -46
  174. package/dist/SelectedStructuresMixin.js +0 -52
  175. package/dist/SelectedStructuresMixin.js.map +0 -1
  176. package/dist/StructureModel.d.ts +0 -9
  177. package/dist/StructureModel.js +0 -11
  178. package/dist/StructureModel.js.map +0 -1
  179. package/dist/UniprotTrack.d.ts +0 -27
  180. package/dist/UniprotTrack.js +0 -53
  181. package/dist/UniprotTrack.js.map +0 -1
  182. package/dist/components/BoxTrack.d.ts +0 -7
  183. package/dist/components/BoxTrack.js +0 -15
  184. package/dist/components/BoxTrack.js.map +0 -1
  185. package/dist/components/BoxTrackBlock.d.ts +0 -8
  186. package/dist/components/BoxTrackBlock.js +0 -136
  187. package/dist/components/BoxTrackBlock.js.map +0 -1
  188. package/dist/components/ExportSVGDialog.js.map +0 -1
  189. package/dist/components/Header.js +0 -62
  190. package/dist/components/Header.js.map +0 -1
  191. package/dist/components/HeaderInfoArea.js +0 -12
  192. package/dist/components/HeaderInfoArea.js.map +0 -1
  193. package/dist/components/ImportForm/ImportFormExamples.js.map +0 -1
  194. package/dist/components/ImportForm/data/seq2.js.map +0 -1
  195. package/dist/components/ImportForm/index.js.map +0 -1
  196. package/dist/components/ImportForm/util.js +0 -16
  197. package/dist/components/ImportForm/util.js.map +0 -1
  198. package/dist/components/MSAPanel/Loading.js.map +0 -1
  199. package/dist/components/MSAPanel/MSABlock.js.map +0 -1
  200. package/dist/components/MSAPanel/MSACanvas.js.map +0 -1
  201. package/dist/components/MSAPanel/MSAMouseoverCanvas.js.map +0 -1
  202. package/dist/components/MSAPanel/index.d.ts +0 -5
  203. package/dist/components/MSAPanel/index.js.map +0 -1
  204. package/dist/components/MSAPanel/renderMSABlock.js.map +0 -1
  205. package/dist/components/MSAPanel/renderMSAMouseover.js.map +0 -1
  206. package/dist/components/Minimap.js.map +0 -1
  207. package/dist/components/MinimapSVG.js.map +0 -1
  208. package/dist/components/MultiAlignmentSelector.js.map +0 -1
  209. package/dist/components/TreePanel/TreeBranchMenu.js.map +0 -1
  210. package/dist/components/TreePanel/TreeCanvas.js.map +0 -1
  211. package/dist/components/TreePanel/TreeCanvasBlock.js.map +0 -1
  212. package/dist/components/TreePanel/TreeNodeMenu.js.map +0 -1
  213. package/dist/components/TreePanel/TreeRuler.js.map +0 -1
  214. package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.js.map +0 -1
  215. package/dist/components/TreePanel/index.js.map +0 -1
  216. package/dist/components/TreePanel/renderTreeCanvas.js.map +0 -1
  217. package/dist/components/VerticalGuide.d.ts +0 -7
  218. package/dist/components/VerticalGuide.js +0 -30
  219. package/dist/components/VerticalGuide.js.map +0 -1
  220. package/dist/components/ZoomControls.js +0 -59
  221. package/dist/components/ZoomControls.js.map +0 -1
  222. package/src/SelectedStructuresMixin.ts +0 -59
  223. package/src/StructureModel.ts +0 -11
  224. package/src/UniprotTrack.ts +0 -59
  225. package/src/components/BoxTrack.tsx +0 -33
  226. package/src/components/BoxTrackBlock.tsx +0 -200
  227. package/src/components/Header.tsx +0 -99
  228. package/src/components/HeaderInfoArea.tsx +0 -21
  229. package/src/components/VerticalGuide.tsx +0 -50
  230. package/src/components/ZoomControls.tsx +0 -86
  231. package/dist/components/{MultiAlignmentSelector.js → header/MultiAlignmentSelector.js} +0 -0
  232. package/dist/components/{ImportForm/index.d.ts → import/ImportForm.d.ts} +0 -0
  233. package/dist/components/{ImportForm → import}/ImportFormExamples.d.ts +0 -0
  234. package/dist/components/{ImportForm → import}/data/seq2.d.ts +0 -0
  235. package/dist/components/{ImportForm → import}/data/seq2.js +0 -0
  236. package/dist/components/{ImportForm → import}/util.d.ts +0 -0
  237. package/dist/components/{Minimap.js → minimap/Minimap.js} +0 -0
  238. package/dist/components/{MinimapSVG.js → minimap/MinimapSVG.js} +0 -0
  239. package/dist/components/{MSAPanel → msa}/Loading.d.ts +0 -0
  240. package/dist/components/{MSAPanel → msa}/Loading.js +0 -0
  241. package/dist/components/{MSAPanel → msa}/MSACanvas.d.ts +0 -0
  242. package/dist/components/{MSAPanel/MSABlock.d.ts → msa/MSACanvasBlock.d.ts} +0 -0
  243. package/dist/components/{MSAPanel → msa}/MSAMouseoverCanvas.d.ts +0 -0
  244. package/dist/components/{MSAPanel → msa}/MSAMouseoverCanvas.js +0 -0
  245. package/dist/components/{MSAPanel → msa}/renderMSABlock.d.ts +1 -1
  246. /package/dist/components/{MSAPanel → msa}/renderMSAMouseover.d.ts +0 -0
  247. /package/dist/components/{MSAPanel → msa}/renderMSAMouseover.js +0 -0
  248. /package/dist/components/{TreePanel → tree}/TreeBranchMenu.d.ts +0 -0
  249. /package/dist/components/{TreePanel → tree}/TreeBranchMenu.js +0 -0
  250. /package/dist/components/{TreePanel → tree}/TreeCanvas.d.ts +0 -0
  251. /package/dist/components/{TreePanel → tree}/TreeCanvasBlock.d.ts +0 -0
  252. /package/dist/components/{TreePanel → tree}/TreeNodeMenu.d.ts +0 -0
  253. /package/dist/components/{TreePanel/index.d.ts → tree/TreePanel.d.ts} +0 -0
  254. /package/dist/components/{TreePanel → tree}/TreeRuler.d.ts +0 -0
  255. /package/dist/components/{TreePanel → tree}/TreeRuler.js +0 -0
  256. /package/dist/components/{TreePanel → tree}/dialogs/TreeNodeInfoDialog.d.ts +0 -0
  257. /package/dist/components/{TreePanel → tree}/renderTreeCanvas.d.ts +0 -0
  258. /package/dist/{DataModel.d.ts → model/DataModel.d.ts} +0 -0
  259. /package/dist/{DataModel.js → model/DataModel.js} +0 -0
  260. /package/dist/{DialogQueue.d.ts → model/DialogQueue.d.ts} +0 -0
  261. /package/dist/{DialogQueue.js → model/DialogQueue.js} +0 -0
  262. /package/src/components/{ImportForm/index.tsx → import/ImportForm.tsx} +0 -0
  263. /package/src/components/{ImportForm → import}/data/seq2.ts +0 -0
  264. /package/src/components/{MSAPanel → msa}/Loading.tsx +0 -0
  265. /package/src/components/{MSAPanel → msa}/MSAMouseoverCanvas.tsx +0 -0
  266. /package/src/components/{MSAPanel → msa}/renderMSAMouseover.ts +0 -0
  267. /package/src/components/{TreePanel → tree}/TreeBranchMenu.tsx +0 -0
  268. /package/src/components/{TreePanel → tree}/TreeRuler.tsx +0 -0
  269. /package/src/{DataModel.ts → model/DataModel.ts} +0 -0
  270. /package/src/{DialogQueue.ts → model/DialogQueue.ts} +0 -0
@@ -0,0 +1,7 @@
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+ import React from 'react';
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+ export default function Checkbox2({ checked, label, disabled, onChange, }: {
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+ checked: boolean;
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+ label: string;
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+ disabled?: boolean;
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+ onChange: () => void;
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+ }): React.JSX.Element;
@@ -0,0 +1,10 @@
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+ import React from 'react';
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+ import { Checkbox, FormControlLabel, } from '@mui/material';
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+ function FormControlLabel2(rest) {
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+ return (React.createElement("div", null,
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+ React.createElement(FormControlLabel, { ...rest })));
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+ }
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+ export default function Checkbox2({ checked, label, disabled, onChange, }) {
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+ return (React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { disabled: disabled, checked: checked, onChange: onChange }), label: label }));
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+ }
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+ //# sourceMappingURL=Checkbox2.js.map
@@ -0,0 +1 @@
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+ {"version":3,"file":"Checkbox2.js","sourceRoot":"","sources":["../../src/components/Checkbox2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,QAAQ,EACR,gBAAgB,GAEjB,MAAM,eAAe,CAAA;AAEtB,SAAS,iBAAiB,CAAC,IAA2B;IACpD,OAAO,CACL;QACE,oBAAC,gBAAgB,OAAK,IAAI,GAAI,CAC1B,CACP,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,OAAO,EACP,KAAK,EACL,QAAQ,EACR,QAAQ,GAMT;IACC,OAAO,CACL,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IAAC,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,QAAQ,GAAI,EAExE,KAAK,EAAE,KAAK,GACZ,CACH,CAAA;AACH,CAAC"}
@@ -1,12 +1,20 @@
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1
  import React from 'react';
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2
  import { observer } from 'mobx-react';
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- import { Typography } from '@mui/material';
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+ import { Button, Typography } from '@mui/material';
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+ import { ErrorBoundary } from 'react-error-boundary';
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+ import { ErrorMessage } from '@jbrowse/core/ui';
4
6
  // locals
5
- import ImportForm from './ImportForm';
7
+ import ImportForm from './import/ImportForm';
6
8
  import MSAView from './MSAView';
9
+ function Reset({ model, error }) {
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+ return (React.createElement("div", null,
11
+ React.createElement(ErrorMessage, { error: error }),
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+ React.createElement(Button, { variant: "contained", color: "primary", onClick: () => model.reset() }, "Return to import form")));
13
+ }
7
14
  const Loading = observer(function ({ model }) {
8
- const { done, initialized } = model;
9
- return (React.createElement("div", null, !initialized ? (React.createElement(ImportForm, { model: model })) : !done ? (React.createElement(Typography, { variant: "h4" }, "Loading...")) : (React.createElement(MSAView, { model: model }))));
15
+ const { isLoading, initialized } = model;
16
+ return (React.createElement("div", null,
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+ React.createElement(ErrorBoundary, { fallbackRender: props => React.createElement(Reset, { model: model, error: props.error }) }, !initialized ? (React.createElement(ImportForm, { model: model })) : isLoading ? (React.createElement(Typography, { variant: "h4" }, "Loading...")) : (React.createElement(MSAView, { model: model })))));
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  });
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  export default Loading;
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  //# sourceMappingURL=Loading.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,OAAO,MAAM,WAAW,CAAA;AAG/B,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAEnC,OAAO,CACL,iCACG,CAAC,WAAW,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACV,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,iBAAwB,CACjD,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
1
+ {"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AACpD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAE/C,SAAS;AACT,OAAO,UAAU,MAAM,qBAAqB,CAAA;AAC5C,OAAO,OAAO,MAAM,WAAW,CAAA;AAG/B,SAAS,KAAK,CAAC,EAAE,KAAK,EAAE,KAAK,EAA2C;IACtE,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,SAAS,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,4BAE/D,CACL,CACP,CAAA;AACH,CAAC;AAED,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAExC,OAAO,CACL;QACE,oBAAC,aAAa,IACZ,cAAc,EAAE,KAAK,CAAC,EAAE,CAAC,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,GAAI,IAEnE,CAAC,WAAW,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,iBAAwB,CACjD,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
@@ -2,12 +2,11 @@ import React, { Suspense } from 'react';
2
2
  import { observer } from 'mobx-react';
3
3
  // locals
4
4
  import { HorizontalResizeHandle, VerticalResizeHandle } from './ResizeHandles';
5
- import TreeRuler from './TreePanel/TreeRuler';
6
- import Header from './Header';
7
- import Track from './Track';
8
- import MSAPanel from './MSAPanel';
9
- import TreePanel from './TreePanel';
10
- import Minimap from './Minimap';
5
+ import TreeRuler from './tree/TreeRuler';
6
+ import Header from './header/Header';
7
+ import MSAPanel from './msa/MSAPanel';
8
+ import TreePanel from './tree/TreePanel';
9
+ import Minimap from './minimap/Minimap';
11
10
  function TopArea({ model }) {
12
11
  return (React.createElement("div", { style: { display: 'flex' } },
13
12
  React.createElement(TreeRuler, { model: model }),
@@ -20,10 +19,8 @@ function MainArea({ model }) {
20
19
  React.createElement(MSAPanel, { model: model })));
21
20
  }
22
21
  const View = observer(function ({ model }) {
23
- const { turnedOnTracks } = model;
24
22
  return (React.createElement("div", { style: { position: 'relative' } },
25
23
  React.createElement(TopArea, { model: model }),
26
- turnedOnTracks?.map(track => (React.createElement(Track, { key: track.model.id, model: model, track: track }))),
27
24
  React.createElement(MainArea, { model: model })));
28
25
  });
29
26
  const MSAView = observer(function ({ model }) {
@@ -1 +1 @@
1
- {"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,SAAS;AACT,OAAO,EAAE,sBAAsB,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAA;AAE9E,OAAO,SAAS,MAAM,uBAAuB,CAAA;AAC7C,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,OAAO,MAAM,WAAW,CAAA;AAE/B,SAAS,OAAO,CAAC,EAAE,KAAK,EAA2B;IACjD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrB,CACP,CAAA;AACH,CAAC;AACD,SAAS,QAAQ,CAAC,EAAE,KAAK,EAA2B;IAClD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC;AAED,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAChE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACxB,cAAc,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAC5B,oBAAC,KAAK,IAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC3D,CAAC;QACF,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACtD,OAAO,CACL;QACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE;YACxC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;YACxB,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB;QACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QAEvC,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,OAAK,WAAW,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
1
+ {"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,SAAS;AACT,OAAO,EAAE,sBAAsB,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAA;AAE9E,OAAO,SAAS,MAAM,kBAAkB,CAAA;AACxC,OAAO,MAAM,MAAM,iBAAiB,CAAA;AACpC,OAAO,QAAQ,MAAM,gBAAgB,CAAA;AACrC,OAAO,SAAS,MAAM,kBAAkB,CAAA;AACxC,OAAO,OAAO,MAAM,mBAAmB,CAAA;AAEvC,SAAS,OAAO,CAAC,EAAE,KAAK,EAA2B;IACjD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrB,CACP,CAAA;AACH,CAAC;AACD,SAAS,QAAQ,CAAC,EAAE,KAAK,EAA2B;IAClD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC;AAED,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAChE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QAEzB,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACtD,OAAO,CACL;QACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE;YACxC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;YACxB,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB;QACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QAEvC,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,OAAK,WAAW,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
@@ -0,0 +1,4 @@
1
+ import React from 'react';
2
+ export default function SequenceTextArea({ str }: {
3
+ str: [string, string][];
4
+ }): React.JSX.Element;
@@ -0,0 +1,38 @@
1
+ import React, { useState } from 'react';
2
+ import { Button, TextField } from '@mui/material';
3
+ import { makeStyles } from 'tss-react/mui';
4
+ import copy from 'copy-to-clipboard';
5
+ // locals
6
+ import Checkbox2 from './Checkbox2';
7
+ const useStyles = makeStyles()({
8
+ textAreaFont: {
9
+ fontFamily: 'Courier New',
10
+ },
11
+ dialogContent: {
12
+ background: 'lightgrey',
13
+ margin: 4,
14
+ minWidth: '80em',
15
+ },
16
+ });
17
+ export default function SequenceTextArea({ str }) {
18
+ const { classes } = useStyles();
19
+ const [copied, setCopied] = useState(false);
20
+ const [showGaps, setShowGaps] = useState(false);
21
+ const disp = str
22
+ .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : s2.replaceAll('-', '')}`)
23
+ .join('\n');
24
+ return (React.createElement(React.Fragment, null,
25
+ React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
26
+ copy(disp);
27
+ setCopied(true);
28
+ setTimeout(() => setCopied(false), 500);
29
+ } }, copied ? 'Copied!' : 'Copy to clipboard'),
30
+ React.createElement(Checkbox2, { label: "Show gaps", checked: showGaps, onChange: () => setShowGaps(!showGaps) }),
31
+ React.createElement(TextField, { variant: "outlined", multiline: true, className: classes.dialogContent, minRows: 5, maxRows: 10, fullWidth: true, value: disp, InputProps: {
32
+ readOnly: true,
33
+ classes: {
34
+ input: classes.textAreaFont,
35
+ },
36
+ } })));
37
+ }
38
+ //# sourceMappingURL=SequenceTextArea.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"SequenceTextArea.js","sourceRoot":"","sources":["../../src/components/SequenceTextArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,IAAI,MAAM,mBAAmB,CAAA;AAEpC,SAAS;AACT,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IACD,aAAa,EAAE;QACb,UAAU,EAAE,WAAW;QACvB,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,MAAM;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,EAAE,GAAG,EAA+B;IAC3E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE/C,MAAM,IAAI,GAAG,GAAG;SACb,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,CAAC;SACtE,IAAI,CAAC,IAAI,CAAC,CAAA;IACb,OAAO,CACL;QACE,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,CAAC,IAAI,CAAC,CAAA;gBACV,SAAS,CAAC,IAAI,CAAC,CAAA;gBACf,UAAU,CAAC,GAAG,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAA;YACzC,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,mBAAmB,CAClC;QACT,oBAAC,SAAS,IACR,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,GACtC;QACF,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,IAAI,EACX,UAAU,EAAE;gBACV,QAAQ,EAAE,IAAI;gBACd,OAAO,EAAE;oBACP,KAAK,EAAE,OAAO,CAAC,YAAY;iBAC5B;aACF,GACD,CACD,CACJ,CAAA;AACH,CAAC"}
@@ -1,10 +1,11 @@
1
- import React, { useState, useRef, useEffect, lazy, Suspense } from 'react';
1
+ import React, { useState, useRef, useEffect, lazy } from 'react';
2
2
  import normalizeWheel from 'normalize-wheel';
3
3
  import { observer } from 'mobx-react';
4
4
  import { IconButton, Menu, MenuItem } from '@mui/material';
5
5
  import { makeStyles } from 'tss-react/mui';
6
6
  // icons
7
7
  import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
8
+ // lazies
8
9
  const TrackInfoDialog = lazy(() => import('./dialogs/TrackInfoDialog'));
9
10
  const useStyles = makeStyles()({
10
11
  button: {
@@ -13,8 +14,7 @@ const useStyles = makeStyles()({
13
14
  });
14
15
  export const TrackLabel = observer(function ({ model, track, }) {
15
16
  const [anchorEl, setAnchorEl] = useState();
16
- const [trackInfoDialogOpen, setTrackInfoDialogOpen] = useState(false);
17
- const { rowHeight, treeAreaWidth: width } = model;
17
+ const { drawLabels, rowHeight, treeAreaWidth: width } = model;
18
18
  const { height, model: { name }, } = track;
19
19
  const { classes } = useStyles();
20
20
  const trackLabelHeight = Math.max(8, rowHeight - 8);
@@ -25,7 +25,7 @@ export const TrackLabel = observer(function ({ model, track, }) {
25
25
  textAlign: 'right',
26
26
  fontSize: trackLabelHeight,
27
27
  } },
28
- name,
28
+ drawLabels ? name : '',
29
29
  ' ',
30
30
  React.createElement(IconButton, { className: classes.button, style: {
31
31
  width: trackLabelHeight,
@@ -38,11 +38,12 @@ export const TrackLabel = observer(function ({ model, track, }) {
38
38
  setAnchorEl(undefined);
39
39
  } }, "Close"),
40
40
  React.createElement(MenuItem, { dense: true, onClick: () => {
41
- setTrackInfoDialogOpen(true);
41
+ model.queueDialog(onClose => [
42
+ TrackInfoDialog,
43
+ { onClose, model: track.model },
44
+ ]);
42
45
  setAnchorEl(undefined);
43
- } }, "Get info"))) : null,
44
- trackInfoDialogOpen ? (React.createElement(Suspense, { fallback: null },
45
- React.createElement(TrackInfoDialog, { model: track.model, onClose: () => setTrackInfoDialogOpen(false) }))) : null));
46
+ } }, "Get info"))) : null));
46
47
  });
47
48
  const Track = observer(function ({ model, track, }) {
48
49
  const { resizeHandleWidth } = model;
@@ -1 +1 @@
1
- {"version":3,"file":"Track.js","sourceRoot":"","sources":["../../src/components/Track.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1E,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,QAAQ;AACR,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AAKjE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AAEvE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,OAAO,EAAE,CAAC;KACX;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAC3C,KAAK,EACL,KAAK,GAKN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAqB,CAAA;IAC7D,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACrE,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EACJ,MAAM,EACN,KAAK,EAAE,EAAE,IAAI,EAAE,GAChB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,GAAG,CAAC,CAAC,CAAA;IAEnD,OAAO,CACL,6BACE,KAAK,EAAE;YACL,KAAK;YACL,MAAM;YACN,UAAU,EAAE,CAAC;YACb,SAAS,EAAE,OAAO;YAClB,QAAQ,EAAE,gBAAgB;SAC3B;QAEA,IAAI;QAAE,GAAG;QACV,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE;gBACL,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,gBAAgB;aACzB,EACD,OAAO,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC;YAElD,oBAAC,iBAAiB,OAAG,CACV;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,SAAS,CAAC;YAErC,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACjC,WAAW,CAAC,SAAS,CAAC,CAAA;gBACxB,CAAC,YAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,sBAAsB,CAAC,IAAI,CAAC,CAAA;oBAC5B,WAAW,CAAC,SAAS,CAAC,CAAA;gBACxB,CAAC,eAGQ,CACN,CACR,CAAC,CAAC,CAAC,IAAI;QACP,mBAAmB,CAAC,CAAC,CAAC,CACrB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,IACd,KAAK,EAAE,KAAK,CAAC,KAAK,EAClB,OAAO,EAAE,GAAG,EAAE,CAAC,sBAAsB,CAAC,KAAK,CAAC,GAC5C,CACO,CACZ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAKN;IACC,MAAM,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IACnC,MAAM,EACJ,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,GACzB,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAM;QACR,CAAC;QACD,SAAS,OAAO,CAAC,SAAqB;YACpC,MAAM,KAAK,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;YACvC,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAE9B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;gBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;gBACxB,qBAAqB,CAAC,GAAG,EAAE;oBACzB,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;gBAC3B,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,SAAS,CAAC,cAAc,EAAE,CAAA;QAC5B,CAAC;QACD,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACvC,OAAO,GAAG,EAAE;YACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IACX,OAAO,CACL,6BAAK,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE;QACpD,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;QAC1C,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GAAI;QAC3D,6BAAK,GAAG,EAAE,GAAG,IACV,KAAK,CAAC,CAAC,CAAC,CACP,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,EAAE,EAAE,IAAG,GAAG,KAAK,EAAE,CAAO,CAC/D,CAAC,CAAC,CAAC,CACF,oBAAC,KAAK,CAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACrD,CACG,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,KAAK,CAAA"}
1
+ {"version":3,"file":"Track.js","sourceRoot":"","sources":["../../src/components/Track.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAChE,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,QAAQ;AACR,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AAKjE,SAAS;AACT,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AAEvE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,OAAO,EAAE,CAAC;KACX;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAC3C,KAAK,EACL,KAAK,GAKN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAqB,CAAA;IAC7D,MAAM,EAAE,UAAU,EAAE,SAAS,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC7D,MAAM,EACJ,MAAM,EACN,KAAK,EAAE,EAAE,IAAI,EAAE,GAChB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,GAAG,CAAC,CAAC,CAAA;IAEnD,OAAO,CACL,6BACE,KAAK,EAAE;YACL,KAAK;YACL,MAAM;YACN,UAAU,EAAE,CAAC;YACb,SAAS,EAAE,OAAO;YAClB,QAAQ,EAAE,gBAAgB;SAC3B;QAEA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;QAAE,GAAG;QAC5B,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE;gBACL,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,gBAAgB;aACzB,EACD,OAAO,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC;YAElD,oBAAC,iBAAiB,OAAG,CACV;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,SAAS,CAAC;YAErC,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACjC,WAAW,CAAC,SAAS,CAAC,CAAA;gBACxB,CAAC,YAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE;qBAChC,CAAC,CAAA;oBACF,WAAW,CAAC,SAAS,CAAC,CAAA;gBACxB,CAAC,eAGQ,CACN,CACR,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAKN;IACC,MAAM,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IACnC,MAAM,EACJ,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,GACzB,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAM;QACR,CAAC;QACD,SAAS,OAAO,CAAC,SAAqB;YACpC,MAAM,KAAK,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;YACvC,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAE9B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;gBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;gBACxB,qBAAqB,CAAC,GAAG,EAAE;oBACzB,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;gBAC3B,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,SAAS,CAAC,cAAc,EAAE,CAAA;QAC5B,CAAC;QACD,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACvC,OAAO,GAAG,EAAE;YACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IACX,OAAO,CACL,6BAAK,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE;QACpD,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;QAC1C,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GAAI;QAC3D,6BAAK,GAAG,EAAE,GAAG,IACV,KAAK,CAAC,CAAC,CAAC,CACP,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,EAAE,EAAE,IAAG,GAAG,KAAK,EAAE,CAAO,CAC/D,CAAC,CAAC,CAAC,CACF,oBAAC,KAAK,CAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACrD,CACG,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,KAAK,CAAA"}
@@ -17,7 +17,6 @@ export default observer(function ({ model, onClose, open, }) {
17
17
  React.createElement(Button, { onClick: () => {
18
18
  model.setError(undefined);
19
19
  if (trackFile) {
20
- // eslint-disable-next-line @typescript-eslint/no-floating-promises
21
20
  model.setMSAFilehandle(trackFile);
22
21
  }
23
22
  }, variant: "contained", color: "primary" }, "Open"),
@@ -1 +1 @@
1
- {"version":3,"file":"AddTrackDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/AddTrackDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,aAAa,EACb,aAAa,EACb,MAAM,EACN,SAAS,EACT,QAAQ,EACR,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAEvD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,eAAe,QAAQ,CAAC,UAAU,EAChC,KAAK,EACL,OAAO,EACP,IAAI,GAKL;IACC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACzC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAC1D,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAC,WAAW;QAC7D,oBAAC,aAAa;YACZ,oBAAC,UAAU,kEAEE;YACb,oBAAC,SAAS,IACR,MAAM,QACN,UAAU,EAAC,qCAAqC,EAChD,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACtC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,CAC9B,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,MAAM,IAAI,KAAK,EAAE,EAAE,KAAK,EAAE,MAAM,IAC/C,MAAM,CACE,CACZ,CAAC,CACQ;YACZ,oBAAC,YAAY,IAAC,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,YAAY,GAAI;YAChE,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;wBACzB,IAAI,SAAS,EAAE,CAAC;4BACd,mEAAmE;4BACnE,KAAK,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;wBACnC,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,WAGR;gBACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,aAGjB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA"}
1
+ {"version":3,"file":"AddTrackDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/AddTrackDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,aAAa,EACb,aAAa,EACb,MAAM,EACN,SAAS,EACT,QAAQ,EACR,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAEvD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,eAAe,QAAQ,CAAC,UAAU,EAChC,KAAK,EACL,OAAO,EACP,IAAI,GAKL;IACC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACzC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAC1D,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAC,WAAW;QAC7D,oBAAC,aAAa;YACZ,oBAAC,UAAU,kEAEE;YACb,oBAAC,SAAS,IACR,MAAM,QACN,UAAU,EAAC,qCAAqC,EAChD,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACtC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,CAC9B,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,MAAM,IAAI,KAAK,EAAE,EAAE,KAAK,EAAE,MAAM,IAC/C,MAAM,CACE,CACZ,CAAC,CACQ;YACZ,oBAAC,YAAY,IAAC,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,YAAY,GAAI;YAChE,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;wBACzB,IAAI,SAAS,EAAE,CAAC;4BACd,KAAK,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;wBACnC,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,WAGR;gBACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,aAGjB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA"}
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { MsaViewModel } from '../model';
2
+ import { MsaViewModel } from '../../model';
3
3
  export default function ExportSVGDialog({ model, onClose, }: {
4
4
  model: MsaViewModel;
5
5
  onClose: () => void;
@@ -1,6 +1,7 @@
1
1
  import React, { useState } from 'react';
2
2
  import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
3
- import { Button, Checkbox, DialogContent, DialogActions, FormControlLabel, FormControl, FormLabel, RadioGroup, Radio, Typography, useTheme, } from '@mui/material';
3
+ import { Button, DialogContent, DialogActions, FormControlLabel, FormControl, FormLabel, RadioGroup, Radio, Typography, useTheme, } from '@mui/material';
4
+ import Checkbox2 from '../Checkbox2';
4
5
  export default function ExportSVGDialog({ model, onClose, }) {
5
6
  const [includeMinimap, setIncludeMinimap] = useState(true);
6
7
  const [exportType, setExportType] = useState('viewport');
@@ -10,9 +11,7 @@ export default function ExportSVGDialog({ model, onClose, }) {
10
11
  React.createElement(DialogContent, null,
11
12
  error ? React.createElement(ErrorMessage, { error: error }) : null,
12
13
  React.createElement(Typography, null, "Settings:"),
13
- React.createElement("div", null,
14
- React.createElement(FormControl, null,
15
- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: includeMinimap, onChange: event => setIncludeMinimap(event.target.checked) }), disabled: exportType === 'entire', label: "Include minimap?" }))),
14
+ React.createElement(Checkbox2, { label: "Include minimap?", disabled: exportType === 'entire', checked: includeMinimap, onChange: () => setIncludeMinimap(!includeMinimap) }),
16
15
  React.createElement("div", null,
17
16
  React.createElement(FormControl, null,
18
17
  React.createElement(FormLabel, null, "Export type"),
@@ -0,0 +1 @@
1
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@@ -0,0 +1,7 @@
1
+ import React from 'react';
2
+ import { MsaViewModel } from '../../model';
3
+ declare const FeatureTypeDialog: ({ onClose, model, }: {
4
+ onClose: () => void;
5
+ model: MsaViewModel;
6
+ }) => React.JSX.Element;
7
+ export default FeatureTypeDialog;
@@ -0,0 +1,52 @@
1
+ import React from 'react';
2
+ import { observer } from 'mobx-react';
3
+ import { Dialog } from '@jbrowse/core/ui';
4
+ import { Button, DialogContent } from '@mui/material';
5
+ import { getPalette } from '../../ggplotPalettes';
6
+ const Toggles = observer(function ({ model }) {
7
+ const { featureFilters } = model;
8
+ return (React.createElement("div", null,
9
+ React.createElement(Button, { onClick: () => {
10
+ for (const key of featureFilters.keys()) {
11
+ model.setFilter(key, true);
12
+ }
13
+ } }, "Toggle all on"),
14
+ React.createElement(Button, { onClick: () => {
15
+ for (const key of featureFilters.keys()) {
16
+ model.setFilter(key, false);
17
+ }
18
+ } }, "Toggle all off")));
19
+ });
20
+ const Table = observer(function ({ model }) {
21
+ const { tidyTypes, featureFilters } = model;
22
+ const values = [...tidyTypes.values()];
23
+ const palette = getPalette(values.length - 1);
24
+ return (React.createElement(React.Fragment, null,
25
+ React.createElement(Toggles, { model: model }),
26
+ React.createElement("table", null,
27
+ React.createElement("thead", null,
28
+ React.createElement("tr", null,
29
+ React.createElement("td", null),
30
+ React.createElement("td", null, "accession"),
31
+ React.createElement("td", null, "name"),
32
+ React.createElement("td", null, "description"))),
33
+ React.createElement("tbody", null, values.map(({ accession, name, description }, idx) => (React.createElement("tr", { key: accession },
34
+ React.createElement("td", null,
35
+ React.createElement("input", { type: "checkbox", checked: featureFilters.get(accession) ?? false, onChange: () => model.setFilter(accession, !model.featureFilters.get(accession)) })),
36
+ React.createElement("td", null, accession),
37
+ React.createElement("td", null, name),
38
+ React.createElement("td", null, description),
39
+ React.createElement("td", null,
40
+ React.createElement("div", { style: {
41
+ width: 20,
42
+ height: 20,
43
+ background: palette[idx] || 'black',
44
+ } })))))))));
45
+ });
46
+ const FeatureTypeDialog = observer(function ({ onClose, model, }) {
47
+ return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Feature filters", maxWidth: "xl" },
48
+ React.createElement(DialogContent, null,
49
+ React.createElement(Table, { model: model }))));
50
+ });
51
+ export default FeatureTypeDialog;
52
+ //# sourceMappingURL=FeatureDialog.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"FeatureDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/FeatureDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAIrD,OAAO,EAAE,UAAU,EAAE,MAAM,sBAAsB,CAAA;AAEjD,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,MAAM,GAAG,IAAI,cAAc,CAAC,IAAI,EAAE,EAAE,CAAC;oBACxC,KAAK,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBAC5B,CAAC;YACH,CAAC,oBAGM;QAET,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,MAAM,GAAG,IAAI,cAAc,CAAC,IAAI,EAAE,EAAE,CAAC;oBACxC,KAAK,CAAC,SAAS,CAAC,GAAG,EAAE,KAAK,CAAC,CAAA;gBAC7B,CAAC;YACH,CAAC,qBAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACjE,MAAM,EAAE,SAAS,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAC3C,MAAM,MAAM,GAAG,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,CAAA;IACtC,MAAM,OAAO,GAAG,UAAU,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IAC7C,OAAO,CACL;QACE,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB;YACE;gBACE;oBACE,+BAAS;oBACT,4CAAkB;oBAClB,uCAAa;oBACb,8CAAoB,CACjB,CACC;YACR,mCACG,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,GAAG,EAAE,EAAE,CAAC,CACrD,4BAAI,GAAG,EAAE,SAAS;gBAChB;oBACE,+BACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,KAAK,EAC/C,QAAQ,EAAE,GAAG,EAAE,CACb,KAAK,CAAC,SAAS,CACb,SAAS,EACT,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,CACrC,GAEH,CACC;gBACL,gCAAK,SAAS,CAAM;gBACpB,gCAAK,IAAI,CAAM;gBACf,gCAAK,WAAW,CAAM;gBACtB;oBACE,6BACE,KAAK,EAAE;4BACL,KAAK,EAAE,EAAE;4BACT,MAAM,EAAE,EAAE;4BACV,UAAU,EAAE,OAAO,CAAC,GAAG,CAAC,IAAI,OAAO;yBACpC,GACI,CACJ,CACF,CACN,CAAC,CACI,CACF,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,OAAO,EACP,KAAK,GAIN;IACC,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EACxB,IAAI,QACJ,KAAK,EAAC,iBAAiB,EACvB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACZ,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,GAAI,CACT,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}
@@ -0,0 +1,7 @@
1
+ import React from 'react';
2
+ import { MsaViewModel } from '../../model';
3
+ declare const FeatureTypeDialog: ({ onClose, model, }: {
4
+ onClose: () => void;
5
+ model: MsaViewModel;
6
+ }) => React.JSX.Element;
7
+ export default FeatureTypeDialog;
@@ -0,0 +1,163 @@
1
+ import React, { useState } from 'react';
2
+ import { observer } from 'mobx-react';
3
+ import { Dialog } from '@jbrowse/core/ui';
4
+ import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
5
+ const FeatureTypeDialog = observer(function ({ onClose, model, }) {
6
+ const [vals, setVals] = useState([
7
+ {
8
+ name: 'NCBIfam',
9
+ description: 'NCBI RefSeq FAMs including TIGRFAMs',
10
+ category: 'Families, domains, sites & repeats',
11
+ checked: true,
12
+ },
13
+ {
14
+ name: 'SFLD',
15
+ description: 'Structure function linkage database',
16
+ category: 'Families, domains, sites & repeats',
17
+ checked: true,
18
+ },
19
+ {
20
+ name: 'Phobius',
21
+ checked: true,
22
+ description: 'A combined transmembrane topology and signal peptide predictor',
23
+ category: 'Other sequence features',
24
+ },
25
+ {
26
+ name: 'SignalP',
27
+ checked: true,
28
+ category: 'Other sequence features',
29
+ },
30
+ {
31
+ name: 'SignalP_EUK',
32
+ category: 'Other category',
33
+ checked: true,
34
+ },
35
+ {
36
+ name: 'SignalP_GRAM_POSITIVE',
37
+ category: 'Other category',
38
+ checked: true,
39
+ },
40
+ {
41
+ name: 'SignalP_GRAM_NEGATIVE',
42
+ checked: true,
43
+ category: 'Other category',
44
+ },
45
+ {
46
+ name: 'SUPERFAMILY',
47
+ category: 'Structural domains',
48
+ checked: true,
49
+ },
50
+ {
51
+ name: 'PANTHER',
52
+ category: 'Families, domains, sites & repeats',
53
+ checked: true,
54
+ },
55
+ {
56
+ name: 'Gene3D',
57
+ category: 'Structural domains',
58
+ checked: true,
59
+ },
60
+ {
61
+ name: 'Hamap',
62
+ category: 'Families, domains, sites & repeats',
63
+ checked: true,
64
+ },
65
+ {
66
+ name: 'ProSiteProfiles',
67
+ category: 'Families, domains, sites & repeats',
68
+ checked: true,
69
+ },
70
+ {
71
+ name: 'ProSitePatterns',
72
+ category: 'Families, domains, sites & repeats',
73
+ checked: true,
74
+ },
75
+ {
76
+ name: 'Coils',
77
+ category: 'Other sequence features',
78
+ checked: true,
79
+ },
80
+ {
81
+ name: 'SMART',
82
+ category: 'Families, domains, sites & repeats',
83
+ checked: true,
84
+ },
85
+ {
86
+ name: 'CDD',
87
+ description: 'Conserved Domains Database',
88
+ category: 'Families, domains, sites & repeats',
89
+ checked: true,
90
+ },
91
+ {
92
+ name: 'PRINTS',
93
+ category: 'Families, domains, sites & repeats',
94
+ checked: true,
95
+ },
96
+ {
97
+ name: 'Pfam',
98
+ category: 'Families, domains, sites & repeats',
99
+ checked: true,
100
+ },
101
+ {
102
+ name: 'MobiDBLite',
103
+ checked: true,
104
+ category: 'Other sequence features',
105
+ },
106
+ {
107
+ name: 'PIRSF',
108
+ checked: true,
109
+ category: 'Other category',
110
+ },
111
+ {
112
+ name: 'TMHMM',
113
+ checked: true,
114
+ category: 'Other sequence features',
115
+ },
116
+ {
117
+ name: 'AntiFam',
118
+ checked: true,
119
+ category: 'Other category',
120
+ },
121
+ {
122
+ name: 'FunFam',
123
+ checked: true,
124
+ category: 'Other category',
125
+ },
126
+ {
127
+ name: 'PIRSR',
128
+ checked: true,
129
+ category: 'Families, domains, sites & repeats',
130
+ },
131
+ ]);
132
+ const programs = vals.filter(e => e.checked).map(e => e.name);
133
+ const [show, setShow] = useState(false);
134
+ return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Feature types", maxWidth: "xl" },
135
+ React.createElement(DialogContent, null,
136
+ React.createElement(Typography, null, "This will run InterProScan on all rows of the current MSA"),
137
+ React.createElement(Button, { onClick: () => setShow(!show) },
138
+ show ? 'Hide' : 'Show',
139
+ " advanced options"),
140
+ show ? (React.createElement("div", null,
141
+ React.createElement(Typography, null, "Select algorithms for InterProScan to run"),
142
+ React.createElement("div", null,
143
+ React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => setVals(vals.map(v => ({ ...v, checked: false }))) }, "Select none"),
144
+ React.createElement(Button, { variant: "contained", color: "primary", onClick: () => setVals(vals.map(v => ({ ...v, checked: true }))) }, "Select all")),
145
+ React.createElement("table", null,
146
+ React.createElement("tbody", null, vals
147
+ .sort((a, b) => a.category.localeCompare(b.category))
148
+ .map(({ name, checked, category }) => (React.createElement("tr", { key: name },
149
+ React.createElement("td", null,
150
+ React.createElement("input", { type: "checkbox", key: name, checked: checked, onChange: () => setVals(vals.map(e => e.name === name
151
+ ? { ...e, checked: !e.checked }
152
+ : e)) })),
153
+ React.createElement("td", null, name),
154
+ React.createElement("td", null, category)))))))) : null),
155
+ React.createElement(DialogActions, null,
156
+ React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"),
157
+ React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
158
+ model.queryInterProScan(programs).catch(e => model.setError(e));
159
+ onClose();
160
+ } }, "Send sequences to InterProScan"))));
161
+ });
162
+ export default FeatureTypeDialog;
163
+ //# sourceMappingURL=InterProScanDialog.js.map
@@ -0,0 +1 @@
1
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@@ -2,12 +2,15 @@ import React from 'react';
2
2
  import { DialogContent } from '@mui/material';
3
3
  import { observer } from 'mobx-react';
4
4
  import { Dialog } from '@jbrowse/core/ui';
5
- import { Attributes } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
5
+ import { Attributes, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
6
+ import SequenceTextArea from '../SequenceTextArea';
6
7
  const MetadataDialog = observer(function ({ model, onClose, }) {
7
8
  const { header } = model;
8
- return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Metadata" },
9
+ return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Metadata", maxWidth: "xl" },
9
10
  React.createElement(DialogContent, null,
10
- React.createElement(Attributes, { attributes: header }))));
11
+ React.createElement(Attributes, { attributes: header }),
12
+ React.createElement(BaseCard, { title: "sequence" },
13
+ React.createElement(SequenceTextArea, { str: model.rows })))));
11
14
  });
12
15
  export default MetadataDialog;
13
16
  //# sourceMappingURL=MetadataDialog.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,mDAAmD,CAAA;AAK9E,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAExB,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,QAAC,KAAK,EAAC,UAAU;QACrD,oBAAC,aAAa;YACZ,oBAAC,UAAU,IAAC,UAAU,EAAE,MAAM,GAAI,CACpB,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
1
+ {"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,UAAU,EACV,QAAQ,GACT,MAAM,mDAAmD,CAAA;AAI1D,OAAO,gBAAgB,MAAM,qBAAqB,CAAA;AAElD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAExB,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,QAAC,KAAK,EAAC,UAAU,EAAC,QAAQ,EAAC,IAAI;QACnE,oBAAC,aAAa;YACZ,oBAAC,UAAU,IAAC,UAAU,EAAE,MAAM,GAAI;YAClC,oBAAC,QAAQ,IAAC,KAAK,EAAC,UAAU;gBACxB,oBAAC,gBAAgB,IAAC,GAAG,EAAE,KAAK,CAAC,IAAI,GAAI,CAC5B,CACG,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
@@ -2,8 +2,9 @@ import React from 'react';
2
2
  import { observer } from 'mobx-react';
3
3
  import { makeStyles } from 'tss-react/mui';
4
4
  import { Dialog } from '@jbrowse/core/ui';
5
- import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, MenuItem, Slider, TextField, Typography, } from '@mui/material';
5
+ import { Button, DialogActions, DialogContent, MenuItem, Slider, TextField, Typography, } from '@mui/material';
6
6
  import colorSchemes from '../../colorSchemes';
7
+ import Checkbox2 from '../Checkbox2';
7
8
  const useStyles = makeStyles()(theme => ({
8
9
  field: {
9
10
  margin: theme.spacing(4),
@@ -12,13 +13,6 @@ const useStyles = makeStyles()(theme => ({
12
13
  display: 'flex',
13
14
  },
14
15
  }));
15
- function FormControlLabel2(rest) {
16
- return (React.createElement("div", null,
17
- React.createElement(FormControlLabel, { ...rest })));
18
- }
19
- function Checkbox2({ checked, label, onChange, }) {
20
- return (React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: checked, onChange: onChange }), label: label }));
21
- }
22
16
  const SettingsContent = observer(function ({ model }) {
23
17
  return (React.createElement(React.Fragment, null,
24
18
  React.createElement(TreeSettings, { model: model }),
@@ -26,13 +20,14 @@ const SettingsContent = observer(function ({ model }) {
26
20
  });
27
21
  const TreeSettings = observer(function TreeSettings({ model, }) {
28
22
  const { classes } = useStyles();
29
- const { drawTree, drawNodeBubbles, labelsAlignRight, noTree, showBranchLen, treeWidthMatchesArea, treeWidth, } = model;
23
+ const { drawTree, drawLabels, drawNodeBubbles, labelsAlignRight, noTree, showBranchLen, treeWidthMatchesArea, treeWidth, } = model;
30
24
  return (React.createElement("div", null,
31
25
  React.createElement("h1", null, "Tree options"),
32
26
  React.createElement(Checkbox2, { checked: showBranchLen, onChange: () => model.setShowBranchLen(!showBranchLen), label: "Show branch length?" }),
33
27
  React.createElement(Checkbox2, { checked: drawNodeBubbles, onChange: () => model.setDrawNodeBubbles(!drawNodeBubbles), label: "Draw clickable bubbles on tree branches?" }),
34
28
  React.createElement(Checkbox2, { checked: drawTree, onChange: () => model.setDrawTree(!drawTree), label: "Show tree?" }),
35
29
  React.createElement(Checkbox2, { checked: labelsAlignRight, onChange: () => model.setLabelsAlignRight(!labelsAlignRight), label: "Tree labels align right?" }),
30
+ React.createElement(Checkbox2, { checked: drawLabels, onChange: () => model.setDrawLabels(!drawLabels), label: "Draw labels" }),
36
31
  !noTree ? (React.createElement("div", null,
37
32
  React.createElement(Checkbox2, { checked: treeWidthMatchesArea, onChange: () => model.setTreeWidthMatchesArea(!treeWidthMatchesArea), label: "Make tree width fit to tree area?" }),
38
33
  !treeWidthMatchesArea ? (React.createElement("div", { className: classes.flex },
@@ -63,8 +58,8 @@ const MSASettings = observer(function MSASettings({ model, }) {
63
58
  React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: event => model.setColorSchemeName(event.target.value) }, Object.keys(colorSchemes).map(option => (React.createElement(MenuItem, { key: option, value: option }, option))))));
64
59
  });
65
60
  const SettingsDialog = observer(function ({ model, onClose, }) {
66
- return (React.createElement(Dialog, { open: true, onClose: () => onClose(), title: "Settings" },
67
- React.createElement(DialogContent, null,
61
+ return (React.createElement(Dialog, { open: true, onClose: () => onClose(), title: "Settings", maxWidth: "xl" },
62
+ React.createElement(DialogContent, { style: { width: '80em' } },
68
63
  React.createElement(SettingsContent, { model: model }),
69
64
  React.createElement(DialogActions, null,
70
65
  React.createElement(Button, { onClick: () => onClose(), variant: "contained", color: "primary" }, "Submit")))));