@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.7

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Files changed (136) hide show
  1. package/dist/index.esm.js +6964 -4598
  2. package/dist/index.esm.js.map +1 -1
  3. package/dist/jbrowse-plugin-apollo.cjs.development.js +6610 -4261
  4. package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -1
  5. package/dist/jbrowse-plugin-apollo.cjs.production.min.js +1 -1
  6. package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -1
  7. package/dist/jbrowse-plugin-apollo.umd.development.js +11563 -7493
  8. package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -1
  9. package/dist/jbrowse-plugin-apollo.umd.production.min.js +1 -1
  10. package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -1
  11. package/package.json +4 -4
  12. package/src/ApolloInternetAccount/addMenuItems.ts +23 -2
  13. package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +1 -0
  14. package/src/ApolloInternetAccount/components/LoginButtons.tsx +1 -1
  15. package/src/ApolloInternetAccount/components/LoginIcons.tsx +1 -1
  16. package/src/ApolloInternetAccount/configSchema.ts +1 -1
  17. package/src/ApolloInternetAccount/model.ts +11 -10
  18. package/src/ApolloJobModel.ts +1 -1
  19. package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +8 -6
  20. package/src/ApolloRefNameAliasAdapter/index.ts +2 -2
  21. package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +4 -4
  22. package/src/ApolloSequenceAdapter/index.ts +1 -1
  23. package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +8 -7
  24. package/src/ApolloTextSearchAdapter/index.ts +1 -1
  25. package/src/BackendDrivers/BackendDriver.ts +7 -7
  26. package/src/BackendDrivers/CollaborationServerDriver.ts +14 -10
  27. package/src/BackendDrivers/DesktopFileDriver.ts +11 -10
  28. package/src/BackendDrivers/InMemoryFileDriver.ts +10 -6
  29. package/src/ChangeManager.ts +15 -11
  30. package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +8 -7
  31. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +35 -14
  32. package/src/FeatureDetailsWidget/AttributeKey.tsx +50 -0
  33. package/src/FeatureDetailsWidget/AttributeKeySelector.tsx +104 -0
  34. package/src/FeatureDetailsWidget/Attributes.tsx +215 -367
  35. package/src/FeatureDetailsWidget/BasicInformation.tsx +6 -5
  36. package/src/FeatureDetailsWidget/DefaultAttributeEditor.tsx +104 -0
  37. package/src/FeatureDetailsWidget/DefaultAttributeViewer.tsx +22 -0
  38. package/src/FeatureDetailsWidget/FeatureDetailsNavigation.tsx +4 -4
  39. package/src/FeatureDetailsWidget/NumberTextField.tsx +1 -1
  40. package/src/FeatureDetailsWidget/Sequence.tsx +2 -2
  41. package/src/FeatureDetailsWidget/StringTextField.tsx +1 -1
  42. package/src/FeatureDetailsWidget/TranscriptSequence.tsx +15 -23
  43. package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +950 -196
  44. package/src/FeatureDetailsWidget/TranscriptWidgetSummary.tsx +8 -4
  45. package/src/FeatureDetailsWidget/model.ts +8 -3
  46. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +7 -7
  47. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +59 -72
  48. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +253 -60
  49. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +52 -6
  50. package/src/LinearApolloDisplay/glyphs/Glyph.ts +16 -8
  51. package/src/LinearApolloDisplay/stateModel/base.ts +81 -10
  52. package/src/LinearApolloDisplay/stateModel/index.ts +4 -3
  53. package/src/LinearApolloDisplay/stateModel/layouts.ts +8 -39
  54. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +63 -46
  55. package/src/LinearApolloDisplay/stateModel/rendering.ts +60 -31
  56. package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +226 -0
  57. package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx +32 -0
  58. package/src/LinearApolloSixFrameDisplay/components/index.ts +2 -0
  59. package/src/LinearApolloSixFrameDisplay/configSchema.ts +7 -0
  60. package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +940 -0
  61. package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts +63 -0
  62. package/src/LinearApolloSixFrameDisplay/glyphs/index.ts +1 -0
  63. package/src/LinearApolloSixFrameDisplay/index.ts +2 -0
  64. package/src/LinearApolloSixFrameDisplay/stateModel/base.ts +302 -0
  65. package/src/LinearApolloSixFrameDisplay/stateModel/index.ts +27 -0
  66. package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +252 -0
  67. package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +368 -0
  68. package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +201 -0
  69. package/src/LinearApolloSixFrameDisplay/types.ts +1 -0
  70. package/src/OntologyManager/OntologyStore/fulltext.test.ts +1 -1
  71. package/src/OntologyManager/OntologyStore/fulltext.ts +8 -3
  72. package/src/OntologyManager/OntologyStore/index.test.ts +3 -1
  73. package/src/OntologyManager/OntologyStore/index.ts +19 -14
  74. package/src/OntologyManager/OntologyStore/indexeddb-schema.ts +6 -5
  75. package/src/OntologyManager/OntologyStore/indexeddb-storage.ts +11 -5
  76. package/src/OntologyManager/index.ts +12 -7
  77. package/src/OntologyManager/util.ts +3 -2
  78. package/src/TabularEditor/HybridGrid/ChangeHandling.ts +2 -2
  79. package/src/TabularEditor/HybridGrid/Feature.tsx +13 -7
  80. package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +1 -1
  81. package/src/TabularEditor/HybridGrid/HybridGrid.tsx +3 -2
  82. package/src/TabularEditor/HybridGrid/ToolBar.tsx +1 -1
  83. package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +114 -22
  84. package/src/TabularEditor/TabularEditorPane.tsx +1 -1
  85. package/src/TabularEditor/model.ts +2 -2
  86. package/src/TabularEditor/types.ts +5 -2
  87. package/src/components/AddAssembly.tsx +182 -179
  88. package/src/components/AddAssemblyAliases.tsx +114 -0
  89. package/src/components/AddChildFeature.tsx +8 -10
  90. package/src/components/AddFeature.tsx +216 -44
  91. package/src/components/AddRefSeqAliases.tsx +14 -12
  92. package/src/components/CopyFeature.tsx +10 -11
  93. package/src/components/CreateApolloAnnotation.tsx +342 -158
  94. package/src/components/DeleteAssembly.tsx +9 -8
  95. package/src/components/DeleteFeature.tsx +362 -14
  96. package/src/components/Dialog.tsx +1 -1
  97. package/src/components/DownloadGFF3.tsx +31 -11
  98. package/src/components/FilterFeatures.tsx +6 -4
  99. package/src/components/FilterTranscripts.tsx +86 -0
  100. package/src/components/ImportFeatures.tsx +7 -6
  101. package/src/components/LogOut.tsx +5 -4
  102. package/src/components/ManageChecks.tsx +9 -8
  103. package/src/components/ManageUsers.tsx +11 -10
  104. package/src/components/MergeExons.tsx +193 -0
  105. package/src/components/MergeTranscripts.tsx +185 -0
  106. package/src/components/OntologyTermAutocomplete.tsx +5 -5
  107. package/src/components/OntologyTermMultiSelect.tsx +6 -6
  108. package/src/components/OpenLocalFile.tsx +4 -3
  109. package/src/components/SplitExon.tsx +134 -0
  110. package/src/components/ViewChangeLog.tsx +7 -6
  111. package/src/components/ViewCheckResults.tsx +8 -7
  112. package/src/components/index.ts +3 -0
  113. package/src/config.ts +5 -0
  114. package/src/extensions/annotationFromJBrowseFeature.test.ts +1 -0
  115. package/src/extensions/annotationFromJBrowseFeature.ts +13 -10
  116. package/src/extensions/annotationFromPileup.ts +104 -94
  117. package/src/index.ts +33 -50
  118. package/src/makeDisplayComponent.tsx +90 -37
  119. package/src/session/ClientDataStore.ts +21 -17
  120. package/src/session/session.ts +46 -39
  121. package/src/types.ts +4 -4
  122. package/src/util/annotationFeatureUtils.ts +66 -1
  123. package/src/util/copyToClipboard.ts +21 -0
  124. package/src/util/glyphUtils.ts +49 -0
  125. package/src/util/index.ts +5 -3
  126. package/src/util/loadAssemblyIntoClient.ts +10 -3
  127. package/src/util/mouseEventsUtils.ts +113 -0
  128. package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx +0 -13
  129. package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +0 -707
  130. package/src/ApolloSixFrameRenderer/configSchema.ts +0 -7
  131. package/src/ApolloSixFrameRenderer/index.ts +0 -3
  132. package/src/SixFrameFeatureDisplay/components/TrackLines.tsx +0 -19
  133. package/src/SixFrameFeatureDisplay/components/index.ts +0 -1
  134. package/src/SixFrameFeatureDisplay/configSchema.ts +0 -21
  135. package/src/SixFrameFeatureDisplay/index.ts +0 -2
  136. package/src/SixFrameFeatureDisplay/stateModel.ts +0 -443

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