@apollo-annotation/jbrowse-plugin-apollo 0.3.4 → 0.3.6

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Files changed (131) hide show
  1. package/dist/index.esm.js +5466 -4490
  2. package/dist/index.esm.js.map +1 -1
  3. package/dist/jbrowse-plugin-apollo.cjs.development.js +5283 -4318
  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 +6806 -4088
  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 +5 -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 +17 -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 +5 -5
  30. package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +92 -20
  31. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +170 -27
  32. package/src/FeatureDetailsWidget/AttributeKey.tsx +50 -0
  33. package/src/FeatureDetailsWidget/AttributeKeySelector.tsx +104 -0
  34. package/src/FeatureDetailsWidget/Attributes.tsx +213 -320
  35. package/src/FeatureDetailsWidget/BasicInformation.tsx +8 -9
  36. package/src/FeatureDetailsWidget/DefaultAttributeEditor.tsx +104 -0
  37. package/src/FeatureDetailsWidget/DefaultAttributeViewer.tsx +22 -0
  38. package/src/FeatureDetailsWidget/FeatureDetailsNavigation.tsx +10 -8
  39. package/src/FeatureDetailsWidget/NumberTextField.tsx +1 -1
  40. package/src/FeatureDetailsWidget/Sequence.tsx +18 -35
  41. package/src/FeatureDetailsWidget/StringTextField.tsx +1 -1
  42. package/src/FeatureDetailsWidget/TranscriptSequence.tsx +140 -95
  43. package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +600 -0
  44. package/src/FeatureDetailsWidget/TranscriptWidgetSummary.tsx +54 -0
  45. package/src/FeatureDetailsWidget/model.ts +8 -3
  46. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +19 -12
  47. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +19 -41
  48. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +44 -22
  49. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +6 -5
  50. package/src/LinearApolloDisplay/glyphs/Glyph.ts +7 -7
  51. package/src/LinearApolloDisplay/stateModel/base.ts +52 -10
  52. package/src/LinearApolloDisplay/stateModel/index.ts +4 -3
  53. package/src/LinearApolloDisplay/stateModel/layouts.ts +8 -34
  54. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +13 -12
  55. package/src/LinearApolloDisplay/stateModel/rendering.ts +63 -31
  56. package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +221 -0
  57. package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx +40 -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 +821 -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 +261 -0
  65. package/src/LinearApolloSixFrameDisplay/stateModel/index.ts +27 -0
  66. package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +236 -0
  67. package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +349 -0
  68. package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +199 -0
  69. package/src/LinearApolloSixFrameDisplay/types.ts +1 -0
  70. package/src/OntologyManager/OntologyStore/fulltext-stopwords.ts +10 -1
  71. package/src/OntologyManager/OntologyStore/fulltext.test.ts +1 -1
  72. package/src/OntologyManager/OntologyStore/fulltext.ts +8 -3
  73. package/src/OntologyManager/OntologyStore/index.test.ts +4 -1
  74. package/src/OntologyManager/OntologyStore/index.ts +19 -14
  75. package/src/OntologyManager/OntologyStore/indexeddb-schema.ts +6 -5
  76. package/src/OntologyManager/OntologyStore/indexeddb-storage.ts +11 -5
  77. package/src/OntologyManager/index.ts +10 -6
  78. package/src/OntologyManager/util.ts +3 -2
  79. package/src/TabularEditor/HybridGrid/ChangeHandling.ts +2 -2
  80. package/src/TabularEditor/HybridGrid/Feature.tsx +9 -8
  81. package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +1 -1
  82. package/src/TabularEditor/HybridGrid/HybridGrid.tsx +3 -2
  83. package/src/TabularEditor/HybridGrid/NumberCell.tsx +8 -1
  84. package/src/TabularEditor/HybridGrid/ToolBar.tsx +15 -13
  85. package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +9 -33
  86. package/src/TabularEditor/TabularEditorPane.tsx +1 -1
  87. package/src/TabularEditor/model.ts +2 -2
  88. package/src/TabularEditor/types.ts +5 -2
  89. package/src/components/AddAssembly.tsx +611 -291
  90. package/src/components/AddChildFeature.tsx +6 -5
  91. package/src/components/AddFeature.tsx +211 -38
  92. package/src/components/AddRefSeqAliases.tsx +14 -12
  93. package/src/components/CopyFeature.tsx +8 -7
  94. package/src/components/CreateApolloAnnotation.tsx +154 -46
  95. package/src/components/DeleteAssembly.tsx +9 -8
  96. package/src/components/DeleteFeature.tsx +5 -4
  97. package/src/components/Dialog.tsx +1 -1
  98. package/src/components/DownloadGFF3.tsx +11 -10
  99. package/src/components/FilterFeatures.tsx +6 -4
  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/OntologyTermAutocomplete.tsx +5 -5
  105. package/src/components/OntologyTermMultiSelect.tsx +9 -6
  106. package/src/components/OpenLocalFile.tsx +4 -3
  107. package/src/components/ViewChangeLog.tsx +7 -6
  108. package/src/components/ViewCheckResults.tsx +8 -7
  109. package/src/components/index.ts +0 -1
  110. package/src/extensions/annotationFromJBrowseFeature.test.ts +1 -0
  111. package/src/extensions/annotationFromJBrowseFeature.ts +14 -12
  112. package/src/extensions/annotationFromPileup.ts +6 -6
  113. package/src/index.ts +33 -50
  114. package/src/makeDisplayComponent.tsx +93 -41
  115. package/src/session/ClientDataStore.ts +21 -17
  116. package/src/session/session.ts +20 -26
  117. package/src/types.ts +4 -4
  118. package/src/util/annotationFeatureUtils.ts +53 -0
  119. package/src/util/index.ts +4 -3
  120. package/src/util/loadAssemblyIntoClient.ts +10 -3
  121. package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx +0 -13
  122. package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +0 -707
  123. package/src/ApolloSixFrameRenderer/configSchema.ts +0 -7
  124. package/src/ApolloSixFrameRenderer/index.ts +0 -3
  125. package/src/FeatureDetailsWidget/TranscriptBasic.tsx +0 -200
  126. package/src/SixFrameFeatureDisplay/components/TrackLines.tsx +0 -19
  127. package/src/SixFrameFeatureDisplay/components/index.ts +0 -1
  128. package/src/SixFrameFeatureDisplay/configSchema.ts +0 -21
  129. package/src/SixFrameFeatureDisplay/index.ts +0 -2
  130. package/src/SixFrameFeatureDisplay/stateModel.ts +0 -439
  131. package/src/components/ModifyFeatureAttribute.tsx +0 -460

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