@apollo-annotation/jbrowse-plugin-apollo 0.1.18 → 0.1.20

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Files changed (85) hide show
  1. package/dist/index.esm.js +3189 -3575
  2. package/dist/index.esm.js.map +1 -1
  3. package/dist/jbrowse-plugin-apollo.cjs.development.js +3185 -3570
  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 +14884 -15905
  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 +33 -33
  12. package/src/ApolloInternetAccount/addMenuItems.ts +18 -0
  13. package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +1 -0
  14. package/src/ApolloInternetAccount/configSchema.ts +5 -2
  15. package/src/ApolloInternetAccount/model.ts +14 -5
  16. package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +94 -0
  17. package/src/ApolloRefNameAliasAdapter/configSchema.ts +12 -0
  18. package/src/ApolloRefNameAliasAdapter/index.ts +21 -0
  19. package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +1 -0
  20. package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +10 -10
  21. package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +35 -32
  22. package/src/BackendDrivers/BackendDriver.ts +8 -0
  23. package/src/BackendDrivers/CollaborationServerDriver.ts +49 -1
  24. package/src/BackendDrivers/DesktopFileDriver.ts +14 -1
  25. package/src/BackendDrivers/InMemoryFileDriver.ts +17 -1
  26. package/src/ChangeManager.ts +1 -1
  27. package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +5 -25
  28. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +82 -0
  29. package/src/FeatureDetailsWidget/Attributes.tsx +11 -3
  30. package/src/FeatureDetailsWidget/BasicInformation.tsx +38 -30
  31. package/src/FeatureDetailsWidget/Sequence.tsx +7 -7
  32. package/src/FeatureDetailsWidget/TranscriptBasic.tsx +446 -0
  33. package/src/FeatureDetailsWidget/TranscriptSequence.tsx +365 -0
  34. package/src/FeatureDetailsWidget/index.ts +2 -0
  35. package/src/FeatureDetailsWidget/model.ts +77 -9
  36. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +0 -2
  37. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +453 -380
  38. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +520 -0
  39. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +138 -134
  40. package/src/LinearApolloDisplay/glyphs/Glyph.ts +38 -370
  41. package/src/LinearApolloDisplay/glyphs/index.ts +1 -2
  42. package/src/LinearApolloDisplay/stateModel/base.ts +3 -6
  43. package/src/LinearApolloDisplay/stateModel/getGlyph.ts +30 -30
  44. package/src/LinearApolloDisplay/stateModel/index.ts +5 -1
  45. package/src/LinearApolloDisplay/stateModel/layouts.ts +32 -24
  46. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +206 -217
  47. package/src/LinearApolloDisplay/stateModel/rendering.ts +43 -67
  48. package/src/OntologyManager/OntologyStore/fulltext.ts +1 -1
  49. package/src/OntologyManager/OntologyStore/index.ts +2 -1
  50. package/src/OntologyManager/index.ts +6 -2
  51. package/src/OntologyManager/util.ts +2 -2
  52. package/src/SixFrameFeatureDisplay/stateModel.ts +15 -10
  53. package/src/TabularEditor/HybridGrid/ChangeHandling.ts +21 -46
  54. package/src/TabularEditor/HybridGrid/Feature.tsx +31 -82
  55. package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +3 -2
  56. package/src/TabularEditor/HybridGrid/HybridGrid.tsx +2 -3
  57. package/src/TabularEditor/HybridGrid/NumberCell.tsx +1 -0
  58. package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +46 -5
  59. package/src/TabularEditor/model.ts +5 -3
  60. package/src/components/AddAssembly.tsx +15 -9
  61. package/src/components/AddChildFeature.tsx +7 -73
  62. package/src/components/AddFeature.tsx +2 -57
  63. package/src/components/AddRefSeqAliases.tsx +285 -0
  64. package/src/components/CopyFeature.tsx +16 -33
  65. package/src/components/DeleteFeature.tsx +4 -6
  66. package/src/components/ImportFeatures.tsx +6 -3
  67. package/src/components/LogOut.tsx +105 -0
  68. package/src/components/ManageChecks.tsx +1 -0
  69. package/src/components/ManageUsers.tsx +21 -1
  70. package/src/components/ModifyFeatureAttribute.tsx +2 -2
  71. package/src/components/OntologyTermAutocomplete.tsx +0 -2
  72. package/src/components/OntologyTermMultiSelect.tsx +1 -0
  73. package/src/components/OpenLocalFile.tsx +6 -5
  74. package/src/components/ViewChangeLog.tsx +1 -0
  75. package/src/components/ViewCheckResults.tsx +1 -0
  76. package/src/components/index.ts +4 -0
  77. package/src/extensions/annotationFromPileup.ts +10 -16
  78. package/src/index.ts +57 -3
  79. package/src/session/ClientDataStore.ts +49 -46
  80. package/src/session/session.ts +186 -114
  81. package/src/util/loadAssemblyIntoClient.ts +4 -210
  82. package/src/FeatureDetailsWidget/RelatedFeature.tsx +0 -97
  83. package/src/LinearApolloDisplay/glyphs/CanonicalGeneGlyph.ts +0 -1204
  84. package/src/LinearApolloDisplay/glyphs/ImplicitExonGeneGlyph.ts +0 -716
  85. package/src/LinearApolloDisplay/stateModel/glyphs.ts +0 -47

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