@teselagen/ove 0.0.14 → 0.0.16

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 (362) hide show
  1. package/index.umd.js +164825 -135871
  2. package/package.json +78 -9
  3. package/src/AlignmentTool/index.js +16 -0
  4. package/src/AlignmentView/AlignmentVisibilityTool.js +105 -0
  5. package/src/AlignmentView/EditTrackNameDialog.js +34 -0
  6. package/src/AlignmentView/HorizontalPanelDragHandle.js +35 -0
  7. package/src/AlignmentView/Minimap.js +520 -0
  8. package/src/AlignmentView/Mismatches.js +134 -0
  9. package/src/AlignmentView/PairwiseAlignmentView.js +68 -0
  10. package/src/AlignmentView/PerformantSelectionLayer.js +32 -0
  11. package/src/AlignmentView/coerceInitialValue.js +7 -0
  12. package/src/AlignmentView/getGapMap.js +12 -0
  13. package/src/AlignmentView/getGaps.js +27 -0
  14. package/src/AlignmentView/getPairwiseOverviewLinearViewOptions.js +38 -0
  15. package/src/AlignmentView/getTrackFromEvent.js +25 -0
  16. package/src/AlignmentView/index.js +2058 -0
  17. package/src/AlignmentView/isTargetWithinEl.js +6 -0
  18. package/src/AlignmentView/style.css +100 -0
  19. package/src/AlignmentView/updateTrackHelper.js +58 -0
  20. package/src/AutoAnnotate.js +500 -0
  21. package/src/AutoAnnotateBpMatchingDialog.js +208 -0
  22. package/src/CircularView/Axis.js +40 -0
  23. package/src/CircularView/AxisNumbers.js +35 -0
  24. package/src/CircularView/Caret.js +63 -0
  25. package/src/CircularView/CircularDnaSequence.js +73 -0
  26. package/src/CircularView/CircularZoomMinimap.js +16 -0
  27. package/src/CircularView/Cutsite.js +18 -0
  28. package/src/CircularView/Cutsites.js +113 -0
  29. package/src/CircularView/DeletionLayer.js +28 -0
  30. package/src/CircularView/Feature.js +83 -0
  31. package/src/CircularView/Labels/index.js +536 -0
  32. package/src/CircularView/Labels/relaxLabelAngles.js +157 -0
  33. package/src/CircularView/Labels/relaxLabels_DEPRECATED.js +105 -0
  34. package/src/CircularView/Labels/style.css +55 -0
  35. package/src/CircularView/Orf.js +25 -0
  36. package/src/CircularView/Part.js +34 -0
  37. package/src/CircularView/PositionAnnotationOnCircle.js +26 -0
  38. package/src/CircularView/Primer.js +41 -0
  39. package/src/CircularView/RotateCircularViewSlider.js +82 -0
  40. package/src/CircularView/SelectionLayer.js +132 -0
  41. package/src/CircularView/VeTopRightContainer.js +12 -0
  42. package/src/CircularView/ZoomCircularViewSlider.js +62 -0
  43. package/src/CircularView/drawAnnotations.js +433 -0
  44. package/src/CircularView/drawDirectedPiePiece.js +142 -0
  45. package/src/CircularView/getAngleForPositionMidpoint.js +3 -0
  46. package/src/CircularView/getInternalLabel.js +40 -0
  47. package/src/CircularView/getRangeAnglesSpecial.js +12 -0
  48. package/src/CircularView/getYOffset.js +15 -0
  49. package/src/CircularView/index.d.ts +20 -0
  50. package/src/CircularView/index.js +930 -0
  51. package/src/CircularView/normalizeAngle.js +3 -0
  52. package/src/CircularView/normalizeAngleRange.js +9 -0
  53. package/src/CircularView/positionCutsites.js +6 -0
  54. package/src/CircularView/shouldFlipText.js +4 -0
  55. package/src/CircularView/style.css +47 -0
  56. package/src/CircularView/utils/polarToSpecialCartesian.js +7 -0
  57. package/src/CreateAnnotationsPage.js +96 -0
  58. package/src/CreateCustomEnzyme/index.js +337 -0
  59. package/src/CreateCustomEnzyme/style.css +100 -0
  60. package/src/CutsiteFilter/AdditionalCutsiteInfoDialog.js +599 -0
  61. package/src/CutsiteFilter/index.js +408 -0
  62. package/src/CutsiteFilter/style.css +23 -0
  63. package/src/CutsiteFilter/withRestrictionEnzymes.js +15 -0
  64. package/src/DigestTool/AddLaddersDialog.js +82 -0
  65. package/src/DigestTool/DigestTool.js +223 -0
  66. package/src/DigestTool/Ladder.css +20 -0
  67. package/src/DigestTool/Ladder.js +303 -0
  68. package/src/DigestTool/createFragmentLines.js +120 -0
  69. package/src/DigestTool/ladderDefaults.js +26 -0
  70. package/src/DigestTool/ruler.css +89 -0
  71. package/src/Editor/CommandHotkeyHandler.js +44 -0
  72. package/src/Editor/DropHandler.css +21 -0
  73. package/src/Editor/DropHandler.js +64 -0
  74. package/src/Editor/FillWindow.js +46 -0
  75. package/src/Editor/darkmode.css +98 -0
  76. package/src/Editor/index.js +1005 -0
  77. package/src/Editor/style.css +235 -0
  78. package/src/Editor/userDefinedHandlersAndOpts.js +56 -0
  79. package/src/EnzymeViewer/index.js +81 -0
  80. package/src/EnzymeViewer/style.css +6 -0
  81. package/src/FindBar/index.js +411 -0
  82. package/src/FindBar/style.css +46 -0
  83. package/src/GlobalDialog.js +66 -0
  84. package/src/GlobalDialogUtils.js +85 -0
  85. package/src/LinearView/SequenceName.js +15 -0
  86. package/src/LinearView/ZoomLinearView.js +47 -0
  87. package/src/LinearView/index.js +374 -0
  88. package/src/LinearView/style.css +12 -0
  89. package/src/ManageEnzymes/index.js +326 -0
  90. package/src/ManageEnzymes/style.css +100 -0
  91. package/src/MenuBar/defaultConfig.js +149 -0
  92. package/src/MenuBar/index.js +98 -0
  93. package/src/MenuBar/viewSubmenu.js +479 -0
  94. package/src/PCRTool/PCRTool.js +173 -0
  95. package/src/Reflex/Browser.js +107 -0
  96. package/src/Reflex/ReflexContainer.js +802 -0
  97. package/src/Reflex/ReflexElement.js +160 -0
  98. package/src/Reflex/ReflexEvents.js +77 -0
  99. package/src/Reflex/ReflexSplitter.js +205 -0
  100. package/src/Reflex/index.js +5 -0
  101. package/src/Reflex/reflex-styles.css +128 -0
  102. package/src/Reflex/reflex-styles.css.map +9 -0
  103. package/src/RowItem/AnnotationContainerHolder.js +20 -0
  104. package/src/RowItem/AnnotationPositioner.js +27 -0
  105. package/src/RowItem/Axis.js +149 -0
  106. package/src/RowItem/Caret/index.js +64 -0
  107. package/src/RowItem/Caret/style.css +8 -0
  108. package/src/RowItem/Chromatograms/Chromatogram.js +289 -0
  109. package/src/RowItem/CutsiteSelectionLayers.js +47 -0
  110. package/src/RowItem/Cutsites.js +271 -0
  111. package/src/RowItem/DeletionLayers/index.js +113 -0
  112. package/src/RowItem/DeletionLayers/style.css +5 -0
  113. package/src/RowItem/Labels.js +327 -0
  114. package/src/RowItem/Orf.js +109 -0
  115. package/src/RowItem/Orfs.js +35 -0
  116. package/src/RowItem/ReplacementLayers/style.css +5 -0
  117. package/src/RowItem/SelectionLayer/index.js +184 -0
  118. package/src/RowItem/SelectionLayer/style.css +21 -0
  119. package/src/RowItem/Sequence.js +269 -0
  120. package/src/RowItem/StackedAnnotations/PointedAnnotation.js +347 -0
  121. package/src/RowItem/StackedAnnotations/getStructuredBases.js +97 -0
  122. package/src/RowItem/StackedAnnotations/index.js +182 -0
  123. package/src/RowItem/StackedAnnotations/primerBases.js +218 -0
  124. package/src/RowItem/StackedAnnotations/style.css +14 -0
  125. package/src/RowItem/Translations/AASliver.js +190 -0
  126. package/src/RowItem/Translations/Translation.js +162 -0
  127. package/src/RowItem/Translations/index.js +54 -0
  128. package/src/RowItem/Translations/style.css +3 -0
  129. package/src/RowItem/constants.js +3 -0
  130. package/src/RowItem/getCutsiteLabelHeights.js +56 -0
  131. package/src/RowItem/getXStartAndWidthFromNonCircularRange.js +12 -0
  132. package/src/RowItem/getXStartAndWidthOfRangeWrtRow.js +27 -0
  133. package/src/RowItem/getXStartAndWidthOfRowAnnotation.js +19 -0
  134. package/src/RowItem/index.js +647 -0
  135. package/src/RowItem/partOverhangs.js +6 -0
  136. package/src/RowItem/style.css +103 -0
  137. package/src/RowItem/utils.js +32 -0
  138. package/src/RowView/estimateRowHeight.js +184 -0
  139. package/src/RowView/index.d.ts +10 -0
  140. package/src/RowView/index.js +554 -0
  141. package/src/RowView/style.css +12 -0
  142. package/src/SimpleCircularOrLinearView.js +379 -0
  143. package/src/SimpleOligoPreview.js +39 -0
  144. package/src/StatusBar/MeltingTemp.js +81 -0
  145. package/src/StatusBar/index.js +275 -0
  146. package/src/StatusBar/style.css +38 -0
  147. package/src/ToolBar/ToolbarItem.js +194 -0
  148. package/src/ToolBar/alignmentTool.js +503 -0
  149. package/src/ToolBar/array_move.js +10 -0
  150. package/src/ToolBar/cutsiteTool.js +88 -0
  151. package/src/ToolBar/downloadTool.js +38 -0
  152. package/src/ToolBar/editTool.js +26 -0
  153. package/src/ToolBar/featureTool.js +34 -0
  154. package/src/ToolBar/findTool.js +2 -0
  155. package/src/ToolBar/importTool.js +27 -0
  156. package/src/ToolBar/index.js +231 -0
  157. package/src/ToolBar/inlineFindTool.js +38 -0
  158. package/src/ToolBar/oligoTool.js +30 -0
  159. package/src/ToolBar/orfTool.js +141 -0
  160. package/src/ToolBar/partTool.js +47 -0
  161. package/src/ToolBar/printTool.js +31 -0
  162. package/src/ToolBar/redoTool.js +30 -0
  163. package/src/ToolBar/saveTool.js +48 -0
  164. package/src/ToolBar/style.css +138 -0
  165. package/src/ToolBar/undoTool.js +30 -0
  166. package/src/ToolBar/veToolbarIcons/find.png +0 -0
  167. package/src/ToolBar/veToolbarIcons/fullscreen.png +0 -0
  168. package/src/ToolBar/veToolbarIcons/linear.png +0 -0
  169. package/src/ToolBar/veToolbarIcons/pie.png +0 -0
  170. package/src/ToolBar/veToolbarIcons/print.png +0 -0
  171. package/src/ToolBar/veToolbarIcons/save.png +0 -0
  172. package/src/ToolBar/veToolbarIcons/show_cut_sites.png +0 -0
  173. package/src/ToolBar/veToolbarIcons/show_features.png +0 -0
  174. package/src/ToolBar/veToolbarIcons/show_orfs.png +0 -0
  175. package/src/ToolBar/veToolbarIcons/show_primers.png +0 -0
  176. package/src/ToolBar/veToolbarIcons/toggle_views.svg +1 -0
  177. package/src/ToolBar/versionHistoryTool.js +20 -0
  178. package/src/ToolBar/visibilityTool.js +39 -0
  179. package/src/VersionHistoryView/index.js +215 -0
  180. package/src/addAlignment.js +6 -0
  181. package/src/commands/getOveHotkeyDefs.js +12 -0
  182. package/src/commands/index.js +1585 -0
  183. package/src/constants/constants.js +2 -0
  184. package/src/constants/dnaToColor.js +17 -0
  185. package/src/constants/draggableClassnames.js +5 -0
  186. package/src/constants/findToolConstants.js +1 -0
  187. package/src/constants/orfFrameToColorMap.js +10 -0
  188. package/src/constants/rowviewContants.js +3 -0
  189. package/src/constants/specialCutsiteFilterOptions.js +22 -0
  190. package/src/constants.js +1 -0
  191. package/src/createVectorEditor/index.js +138 -0
  192. package/src/createVectorEditor/makeStore.js +34 -0
  193. package/src/fileUtils.js +103 -0
  194. package/src/helperComponents/AddOrEditAnnotationDialog/index.js +711 -0
  195. package/src/helperComponents/AddOrEditAnnotationDialog/style.css +11 -0
  196. package/src/helperComponents/AddOrEditFeatureDialog/index.js +58 -0
  197. package/src/helperComponents/AddOrEditPartDialog/index.js +101 -0
  198. package/src/helperComponents/AddOrEditPrimerDialog/EditCaretPosition.js +234 -0
  199. package/src/helperComponents/AddOrEditPrimerDialog/index.js +329 -0
  200. package/src/helperComponents/AddOrEditPrimerDialog/style.css +41 -0
  201. package/src/helperComponents/EnzymesDialog/index.js +904 -0
  202. package/src/helperComponents/EnzymesDialog/style.css +21 -0
  203. package/src/helperComponents/GoToDialog.js +21 -0
  204. package/src/helperComponents/MergeFeaturesDialog/index.js +253 -0
  205. package/src/helperComponents/MergeFeaturesDialog/style.css +3 -0
  206. package/src/helperComponents/MultipleSeqsDetectedOnImportDialog.js +74 -0
  207. package/src/helperComponents/PinchHelper/PinchHelper.js +24 -0
  208. package/src/helperComponents/PrintDialog/index.js +396 -0
  209. package/src/helperComponents/PrintDialog/style.css +4 -0
  210. package/src/helperComponents/PropertiesDialog/ColorPicker.js +30 -0
  211. package/src/helperComponents/PropertiesDialog/CutsiteProperties.js +185 -0
  212. package/src/helperComponents/PropertiesDialog/FeatureProperties.js +6 -0
  213. package/src/helperComponents/PropertiesDialog/GenbankView.js +74 -0
  214. package/src/helperComponents/PropertiesDialog/GeneralProperties.js +140 -0
  215. package/src/helperComponents/PropertiesDialog/GenericAnnotationProperties.js +406 -0
  216. package/src/helperComponents/PropertiesDialog/OrfProperties.js +117 -0
  217. package/src/helperComponents/PropertiesDialog/PartProperties.js +9 -0
  218. package/src/helperComponents/PropertiesDialog/PrimerProperties.js +19 -0
  219. package/src/helperComponents/PropertiesDialog/SingleEnzymeCutsiteInfo.js +131 -0
  220. package/src/helperComponents/PropertiesDialog/TranslationProperties.js +149 -0
  221. package/src/helperComponents/PropertiesDialog/index.js +166 -0
  222. package/src/helperComponents/PropertiesDialog/style.css +68 -0
  223. package/src/helperComponents/PropertiesDialog/typeField.js +24 -0
  224. package/src/helperComponents/PropertiesDialog/utils.js +37 -0
  225. package/src/helperComponents/RemoveDuplicates/index.js +194 -0
  226. package/src/helperComponents/RenameSequenceDialog.js +7 -0
  227. package/src/helperComponents/SelectDialog.js +150 -0
  228. package/src/helperComponents/UncontrolledSliderWithPlusMinusBtns.css +5 -0
  229. package/src/helperComponents/UncontrolledSliderWithPlusMinusBtns.js +134 -0
  230. package/src/helperComponents/VeWarning/index.js +22 -0
  231. package/src/helperComponents/VeWarning/style.css +10 -0
  232. package/src/helperComponents/createSimpleDialog.js +89 -0
  233. package/src/helperComponents/partTagSearch.js +72 -0
  234. package/src/helperComponents/simpleDialog.css +13 -0
  235. package/src/helperComponents/withHover.js +90 -0
  236. package/src/index.js +60 -0
  237. package/src/redux/alignments.js +373 -0
  238. package/src/redux/annotationLabelVisibility.js +53 -0
  239. package/src/redux/annotationVisibility.js +196 -0
  240. package/src/redux/annotationsToSupport.js +104 -0
  241. package/src/redux/caretPosition.js +27 -0
  242. package/src/redux/charWidth.js +22 -0
  243. package/src/redux/copyOptions.js +34 -0
  244. package/src/redux/createYourOwnEnzyme.js +39 -0
  245. package/src/redux/deletionLayers.js +36 -0
  246. package/src/redux/digestTool.js +34 -0
  247. package/src/redux/featureLengthsToHide.js +27 -0
  248. package/src/redux/findTool.js +79 -0
  249. package/src/redux/frameTranslations.js +52 -0
  250. package/src/redux/hoveredAnnotation.js +24 -0
  251. package/src/redux/index.js +196 -0
  252. package/src/redux/labelLineIntensity.js +25 -0
  253. package/src/redux/labelSize.js +23 -0
  254. package/src/redux/lastSavedId.js +20 -0
  255. package/src/redux/middleware.js +112 -0
  256. package/src/redux/minimumOrfSize.js +24 -0
  257. package/src/redux/modalActions.js +3 -0
  258. package/src/redux/panelsShown.js +273 -0
  259. package/src/redux/partLengthsToHide.js +23 -0
  260. package/src/redux/primerLengthsToHide.js +27 -0
  261. package/src/redux/propertiesTool.js +40 -0
  262. package/src/redux/readOnly.js +28 -0
  263. package/src/redux/replacementLayers.js +36 -0
  264. package/src/redux/restrictionEnzymes.js +52 -0
  265. package/src/redux/selectedAnnotations.js +89 -0
  266. package/src/redux/selectedPartTags.js +21 -0
  267. package/src/redux/selectionLayer.js +46 -0
  268. package/src/redux/sequenceData/circular.js +19 -0
  269. package/src/redux/sequenceData/description.js +21 -0
  270. package/src/redux/sequenceData/features.js +19 -0
  271. package/src/redux/sequenceData/index.js +81 -0
  272. package/src/redux/sequenceData/lineageLines.js +11 -0
  273. package/src/redux/sequenceData/materiallyAvailable.js +19 -0
  274. package/src/redux/sequenceData/name.js +19 -0
  275. package/src/redux/sequenceData/parts.js +19 -0
  276. package/src/redux/sequenceData/primers.js +19 -0
  277. package/src/redux/sequenceData/sequence.js +12 -0
  278. package/src/redux/sequenceData/sharedActionCreators.js +0 -0
  279. package/src/redux/sequenceData/translations.js +20 -0
  280. package/src/redux/sequenceData/upsertDeleteActionGenerator.js +31 -0
  281. package/src/redux/sequenceDataHistory.js +43 -0
  282. package/src/redux/showGCContent.js +23 -0
  283. package/src/redux/toolBar.js +25 -0
  284. package/src/redux/uppercaseSequenceMapFont.js +25 -0
  285. package/src/redux/useAdditionalOrfStartCodons.js +24 -0
  286. package/src/redux/utils/addDashesForMatchStartAndEndForTracks/index.js +71 -0
  287. package/src/redux/utils/addMetaToActionCreators.js +12 -0
  288. package/src/redux/utils/createMergedDefaultStateReducer.js +30 -0
  289. package/src/redux/utils/createMetaAction.js +12 -0
  290. package/src/redux/versionHistory.js +27 -0
  291. package/src/selectors/annotationLabelVisibility.js +2 -0
  292. package/src/selectors/annotationSearchSelector.js +24 -0
  293. package/src/selectors/cdsFeaturesSelector.js +9 -0
  294. package/src/selectors/circularSelector.js +4 -0
  295. package/src/selectors/cutsiteLabelColorSelector.js +6 -0
  296. package/src/selectors/cutsitesByRangeSelector.js +5 -0
  297. package/src/selectors/cutsitesSelector.js +61 -0
  298. package/src/selectors/editorSelector.js +2 -0
  299. package/src/selectors/featuresSelector.js +8 -0
  300. package/src/selectors/filteredCutsitesSelector.js +137 -0
  301. package/src/selectors/filteredFeaturesSelector.js +32 -0
  302. package/src/selectors/filteredPartsSelector.js +57 -0
  303. package/src/selectors/filteredPrimersSelector.js +27 -0
  304. package/src/selectors/filteredRestrictionEnzymesSelector.js +1 -0
  305. package/src/selectors/getAdditionalEnzymesSelector.js +46 -0
  306. package/src/selectors/index.js +41 -0
  307. package/src/selectors/isEnzymeFilterAndSelector.js +1 -0
  308. package/src/selectors/minimumOrfSizeSelector.js +2 -0
  309. package/src/selectors/orfsSelector.js +15 -0
  310. package/src/selectors/partsSelector.js +8 -0
  311. package/src/selectors/primersSelector.js +8 -0
  312. package/src/selectors/restrictionEnzymesSelector.js +34 -0
  313. package/src/selectors/searchLayersSelector.js +71 -0
  314. package/src/selectors/selectedAnnotationsSelector.js +1 -0
  315. package/src/selectors/selectedCutsitesSelector.js +21 -0
  316. package/src/selectors/sequenceDataSelector.js +2 -0
  317. package/src/selectors/sequenceLengthSelector.js +5 -0
  318. package/src/selectors/sequenceSelector.js +4 -0
  319. package/src/selectors/tagsToBoldSelector.js +2 -0
  320. package/src/selectors/translationSearchMatchesSelector.js +14 -0
  321. package/src/selectors/translationsRawSelector.js +8 -0
  322. package/src/selectors/translationsSelector.js +137 -0
  323. package/src/style.css +82 -0
  324. package/src/updateEditor.js +198 -0
  325. package/src/utils/PassThrough.js +3 -0
  326. package/src/utils/addWrappedAddons.js +20 -0
  327. package/src/utils/annotationTypes.js +37 -0
  328. package/src/utils/arrayUtils.js +19 -0
  329. package/src/utils/calculateTickMarkPositionsForGivenRange.js +47 -0
  330. package/src/utils/cleanSequenceData_DEPRECATED/arrayToObjWithIds.js +17 -0
  331. package/src/utils/combineReducersDontIgnoreKeys.js +12 -0
  332. package/src/utils/commandUtils.js +18 -0
  333. package/src/utils/editorUtils.js +223 -0
  334. package/src/utils/getAnnotationClassnames.js +12 -0
  335. package/src/utils/getAnnotationNameAndStartStopString.js +61 -0
  336. package/src/utils/getVisibleStartEnd.js +7 -0
  337. package/src/utils/massageTickSpacing.js +19 -0
  338. package/src/utils/onlyUpdateForKeysDeep.js +31 -0
  339. package/src/utils/prepareRowData.js +64 -0
  340. package/src/utils/proteinUtils.js +3 -0
  341. package/src/utils/pureNoFunc.js +18 -0
  342. package/src/utils/selectionLayer.js +25 -0
  343. package/src/utils/shouldRerender.js +27 -0
  344. package/src/utils/showFileDialog.js +26 -0
  345. package/src/utils/updateLabelsForInViewFeatures.js +55 -0
  346. package/src/utils/updateLabelsForInViewFeaturesCircView.js +41 -0
  347. package/src/utils/useAAColorType.js +8 -0
  348. package/src/utils/useAnnotationLimits.js +42 -0
  349. package/src/utils/useChromatogramPrefs.js +31 -0
  350. package/src/utils/useLadders.js +6 -0
  351. package/src/utils/useMeltingTemp.js +7 -0
  352. package/src/utils/useTmType.js +10 -0
  353. package/src/withEditorInteractions/Keyboard.js +86 -0
  354. package/src/withEditorInteractions/clickAndDragUtils.js +576 -0
  355. package/src/withEditorInteractions/createSequenceInputPopup.js +296 -0
  356. package/src/withEditorInteractions/createSequenceInputPopupStyle.css +85 -0
  357. package/src/withEditorInteractions/getBpsPerRow.js +19 -0
  358. package/src/withEditorInteractions/index.js +1252 -0
  359. package/src/withEditorInteractions/isElementInViewport.js +29 -0
  360. package/src/withEditorInteractions/moveCaret.js +58 -0
  361. package/src/withEditorProps/index.js +1010 -0
  362. package/index.mjs +0 -193228

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