@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

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 (192) hide show
  1. package/dist/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.d.ts +1 -1
  2. package/dist/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.d.ts.map +1 -1
  3. package/dist/BackendDrivers/BackendDriver.d.ts +29 -4
  4. package/dist/BackendDrivers/BackendDriver.d.ts.map +1 -1
  5. package/dist/BackendDrivers/CollaborationServerDriver.d.ts +3 -1
  6. package/dist/BackendDrivers/CollaborationServerDriver.d.ts.map +1 -1
  7. package/dist/BackendDrivers/LocalDriver/LocalDriver.d.ts +22 -0
  8. package/dist/BackendDrivers/LocalDriver/LocalDriver.d.ts.map +1 -0
  9. package/dist/BackendDrivers/LocalDriver/db.d.ts +4 -0
  10. package/dist/BackendDrivers/LocalDriver/db.d.ts.map +1 -0
  11. package/dist/BackendDrivers/index.d.ts +1 -2
  12. package/dist/BackendDrivers/index.d.ts.map +1 -1
  13. package/dist/ChangeManager.d.ts +3 -3
  14. package/dist/ChangeManager.d.ts.map +1 -1
  15. package/dist/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.d.ts +0 -6
  16. package/dist/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.d.ts.map +1 -1
  17. package/dist/FeatureDetailsWidget/TranscriptWidgetEditLocation.d.ts.map +1 -1
  18. package/dist/FeatureDetailsWidget/model.d.ts +0 -2
  19. package/dist/FeatureDetailsWidget/model.d.ts.map +1 -1
  20. package/dist/LinearApolloDisplay/components/CheckResultWarnings.d.ts.map +1 -1
  21. package/dist/LinearApolloDisplay/components/LinearApolloDisplay.d.ts.map +1 -1
  22. package/dist/LinearApolloDisplay/components/OverlayCanvas.d.ts +7 -0
  23. package/dist/LinearApolloDisplay/components/OverlayCanvas.d.ts.map +1 -0
  24. package/dist/LinearApolloDisplay/components/Tooltip.d.ts +10 -0
  25. package/dist/LinearApolloDisplay/components/Tooltip.d.ts.map +1 -0
  26. package/dist/LinearApolloDisplay/glyphs/BoxGlyph.d.ts +0 -1
  27. package/dist/LinearApolloDisplay/glyphs/BoxGlyph.d.ts.map +1 -1
  28. package/dist/LinearApolloDisplay/glyphs/CDSGlyph.d.ts +3 -0
  29. package/dist/LinearApolloDisplay/glyphs/CDSGlyph.d.ts.map +1 -0
  30. package/dist/LinearApolloDisplay/glyphs/ExonGlyph.d.ts +3 -0
  31. package/dist/LinearApolloDisplay/glyphs/ExonGlyph.d.ts.map +1 -0
  32. package/dist/LinearApolloDisplay/glyphs/GeneGlyph.d.ts.map +1 -1
  33. package/dist/LinearApolloDisplay/glyphs/GenericChildGlyph.d.ts.map +1 -1
  34. package/dist/LinearApolloDisplay/glyphs/Glyph.d.ts +26 -20
  35. package/dist/LinearApolloDisplay/glyphs/Glyph.d.ts.map +1 -1
  36. package/dist/LinearApolloDisplay/glyphs/TranscriptGlyph.d.ts +3 -0
  37. package/dist/LinearApolloDisplay/glyphs/TranscriptGlyph.d.ts.map +1 -0
  38. package/dist/LinearApolloDisplay/glyphs/util.d.ts +13 -0
  39. package/dist/LinearApolloDisplay/glyphs/util.d.ts.map +1 -1
  40. package/dist/LinearApolloDisplay/stateModel/base.d.ts +17 -0
  41. package/dist/LinearApolloDisplay/stateModel/base.d.ts.map +1 -1
  42. package/dist/LinearApolloDisplay/stateModel/index.d.ts +35 -17
  43. package/dist/LinearApolloDisplay/stateModel/index.d.ts.map +1 -1
  44. package/dist/LinearApolloDisplay/stateModel/layouts.d.ts +29 -7
  45. package/dist/LinearApolloDisplay/stateModel/layouts.d.ts.map +1 -1
  46. package/dist/LinearApolloDisplay/stateModel/mouseEvents.d.ts +69 -23
  47. package/dist/LinearApolloDisplay/stateModel/mouseEvents.d.ts.map +1 -1
  48. package/dist/LinearApolloDisplay/stateModel/rendering.d.ts +26 -9
  49. package/dist/LinearApolloDisplay/stateModel/rendering.d.ts.map +1 -1
  50. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/base.d.ts +6 -0
  51. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/base.d.ts.map +1 -1
  52. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/index.d.ts +6 -0
  53. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/index.d.ts.map +1 -1
  54. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/rendering.d.ts +6 -0
  55. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/rendering.d.ts.map +1 -1
  56. package/dist/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.d.ts.map +1 -1
  57. package/dist/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.d.ts.map +1 -1
  58. package/dist/LinearApolloSixFrameDisplay/glyphs/Glyph.d.ts +1 -1
  59. package/dist/LinearApolloSixFrameDisplay/glyphs/Glyph.d.ts.map +1 -1
  60. package/dist/LinearApolloSixFrameDisplay/stateModel/layouts.d.ts.map +1 -1
  61. package/dist/LinearApolloSixFrameDisplay/stateModel/rendering.d.ts.map +1 -1
  62. package/dist/OntologyManager/OntologyStore/fulltext.d.ts +1 -1
  63. package/dist/OntologyManager/OntologyStore/fulltext.d.ts.map +1 -1
  64. package/dist/OntologyManager/OntologyStore/index.d.ts +2 -2
  65. package/dist/OntologyManager/OntologyStore/index.d.ts.map +1 -1
  66. package/dist/OntologyManager/OntologyStore/indexeddb-storage.d.ts +1 -1
  67. package/dist/OntologyManager/OntologyStore/indexeddb-storage.d.ts.map +1 -1
  68. package/dist/OntologyManager/OntologyStore/types.d.ts +18 -0
  69. package/dist/OntologyManager/OntologyStore/types.d.ts.map +1 -0
  70. package/dist/TabularEditor/HybridGrid/featureContextMenuItems.d.ts.map +1 -1
  71. package/dist/components/AddChildFeature.d.ts.map +1 -1
  72. package/dist/components/ColorFeature.d.ts +13 -0
  73. package/dist/components/ColorFeature.d.ts.map +1 -0
  74. package/dist/components/CreateApolloAnnotation.d.ts.map +1 -1
  75. package/dist/components/DownloadGFF3.d.ts +4 -1
  76. package/dist/components/DownloadGFF3.d.ts.map +1 -1
  77. package/dist/components/DuplicateTranscript.d.ts.map +1 -1
  78. package/dist/components/ViewChangeLog.d.ts +2 -1
  79. package/dist/components/ViewChangeLog.d.ts.map +1 -1
  80. package/dist/components/ViewCheckResults.d.ts +2 -1
  81. package/dist/components/ViewCheckResults.d.ts.map +1 -1
  82. package/dist/components/index.d.ts +1 -1
  83. package/dist/components/index.d.ts.map +1 -1
  84. package/dist/config.d.ts +4 -0
  85. package/dist/config.d.ts.map +1 -0
  86. package/dist/extensions/annotationFromJBrowseFeature.d.ts.map +1 -1
  87. package/dist/extensions/annotationFromPileup.d.ts.map +1 -1
  88. package/dist/index.d.ts +11 -0
  89. package/dist/index.d.ts.map +1 -0
  90. package/dist/index.esm.js +6325 -5997
  91. package/dist/index.esm.js.map +1 -1
  92. package/dist/jbrowse-plugin-apollo.cjs.development.js +5869 -5541
  93. package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -1
  94. package/dist/jbrowse-plugin-apollo.cjs.production.min.js +1 -1
  95. package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -1
  96. package/dist/jbrowse-plugin-apollo.umd.development.js +16782 -25897
  97. package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -1
  98. package/dist/jbrowse-plugin-apollo.umd.production.min.js +1 -1
  99. package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -1
  100. package/dist/makeDisplayComponent.d.ts.map +1 -1
  101. package/dist/menus/Icons.d.ts +3 -0
  102. package/dist/menus/Icons.d.ts.map +1 -0
  103. package/dist/menus/topLevelMenu.d.ts.map +1 -1
  104. package/dist/session/changeHandlers.d.ts +9 -0
  105. package/dist/session/changeHandlers.d.ts.map +1 -0
  106. package/dist/util/annotationFeatureUtils.d.ts +2 -1
  107. package/dist/util/annotationFeatureUtils.d.ts.map +1 -1
  108. package/dist/util/glyphUtils.d.ts +3 -3
  109. package/dist/util/glyphUtils.d.ts.map +1 -1
  110. package/dist/util/index.d.ts +0 -1
  111. package/dist/util/index.d.ts.map +1 -1
  112. package/package.json +4 -4
  113. package/src/ApolloInternetAccount/model.ts +68 -4
  114. package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +6 -3
  115. package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +1 -1
  116. package/src/BackendDrivers/BackendDriver.ts +36 -3
  117. package/src/BackendDrivers/CollaborationServerDriver.ts +78 -23
  118. package/src/BackendDrivers/LocalDriver/LocalDriver.ts +367 -0
  119. package/src/BackendDrivers/LocalDriver/db.ts +37 -0
  120. package/src/BackendDrivers/index.ts +1 -2
  121. package/src/ChangeManager.ts +27 -25
  122. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +1 -1
  123. package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +69 -53
  124. package/src/LinearApolloDisplay/components/CheckResultWarnings.tsx +1 -5
  125. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +95 -115
  126. package/src/LinearApolloDisplay/components/OverlayCanvas.tsx +76 -0
  127. package/src/LinearApolloDisplay/components/Tooltip.tsx +42 -0
  128. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +60 -302
  129. package/src/LinearApolloDisplay/glyphs/CDSGlyph.ts +145 -0
  130. package/src/LinearApolloDisplay/glyphs/ExonGlyph.ts +212 -0
  131. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +65 -999
  132. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +71 -181
  133. package/src/LinearApolloDisplay/glyphs/Glyph.ts +42 -66
  134. package/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts +291 -0
  135. package/src/LinearApolloDisplay/glyphs/util.ts +87 -0
  136. package/src/LinearApolloDisplay/stateModel/base.ts +83 -0
  137. package/src/LinearApolloDisplay/stateModel/layouts.ts +198 -138
  138. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +252 -158
  139. package/src/LinearApolloDisplay/stateModel/rendering.ts +103 -21
  140. package/src/LinearApolloReferenceSequenceDisplay/drawSequenceOverlay.ts +3 -3
  141. package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts +20 -2
  142. package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +7 -2
  143. package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +8 -13
  144. package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts +1 -1
  145. package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +4 -3
  146. package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +1 -1
  147. package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +2 -1
  148. package/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap +18262 -8519
  149. package/src/OntologyManager/OntologyStore/fulltext.ts +1 -2
  150. package/src/OntologyManager/OntologyStore/index.test.ts +5 -2
  151. package/src/OntologyManager/OntologyStore/index.ts +7 -8
  152. package/src/OntologyManager/OntologyStore/indexeddb-storage.ts +2 -2
  153. package/src/OntologyManager/OntologyStore/types.ts +27 -0
  154. package/src/OntologyManager/index.ts +15 -26
  155. package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +4 -5
  156. package/src/components/AddChildFeature.tsx +15 -8
  157. package/src/components/ColorFeature.tsx +167 -0
  158. package/src/components/CreateApolloAnnotation.tsx +35 -9
  159. package/src/components/DownloadGFF3.tsx +92 -121
  160. package/src/components/DuplicateTranscript.tsx +10 -0
  161. package/src/components/ViewChangeLog.tsx +123 -83
  162. package/src/components/ViewCheckResults.tsx +15 -73
  163. package/src/components/index.ts +1 -1
  164. package/src/config.ts +37 -19
  165. package/src/extensions/annotationFromJBrowseFeature.test.ts +1 -1
  166. package/src/extensions/annotationFromJBrowseFeature.ts +91 -63
  167. package/src/extensions/annotationFromPileup.ts +40 -40
  168. package/src/index.ts +45 -1
  169. package/src/makeDisplayComponent.tsx +10 -3
  170. package/src/menus/Icons.tsx +49 -0
  171. package/src/menus/topLevelMenu.ts +24 -96
  172. package/src/session/ClientDataStore.ts +16 -17
  173. package/src/session/changeHandlers.ts +261 -0
  174. package/src/session/session.ts +77 -46
  175. package/src/util/annotationFeatureUtils.ts +29 -1
  176. package/src/util/glyphUtils.ts +74 -31
  177. package/src/util/index.ts +0 -1
  178. package/dist/BackendDrivers/DesktopFileDriver.d.ts +0 -160
  179. package/dist/BackendDrivers/DesktopFileDriver.d.ts.map +0 -1
  180. package/dist/BackendDrivers/InMemoryFileDriver.d.ts +0 -162
  181. package/dist/BackendDrivers/InMemoryFileDriver.d.ts.map +0 -1
  182. package/dist/LinearApolloDisplay/glyphs/index.d.ts +0 -4
  183. package/dist/LinearApolloDisplay/glyphs/index.d.ts.map +0 -1
  184. package/dist/components/OpenLocalFile.d.ts +0 -15
  185. package/dist/components/OpenLocalFile.d.ts.map +0 -1
  186. package/dist/util/loadAssemblyIntoClient.d.ts +0 -5
  187. package/dist/util/loadAssemblyIntoClient.d.ts.map +0 -1
  188. package/src/BackendDrivers/DesktopFileDriver.ts +0 -184
  189. package/src/BackendDrivers/InMemoryFileDriver.ts +0 -107
  190. package/src/LinearApolloDisplay/glyphs/index.ts +0 -3
  191. package/src/components/OpenLocalFile.tsx +0 -189
  192. package/src/util/loadAssemblyIntoClient.ts +0 -94

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