@apollo-annotation/jbrowse-plugin-apollo 0.3.7 → 0.3.9

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Files changed (86) hide show
  1. package/dist/index.esm.js +11212 -10483
  2. package/dist/index.esm.js.map +1 -1
  3. package/dist/jbrowse-plugin-apollo.cjs.development.js +11251 -10509
  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 +7726 -9014
  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 +18 -18
  12. package/src/ApolloInternetAccount/model.ts +123 -70
  13. package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +4 -4
  14. package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +9 -7
  15. package/src/BackendDrivers/CollaborationServerDriver.ts +72 -20
  16. package/src/BackendDrivers/DesktopFileDriver.ts +2 -2
  17. package/src/ChangeManager.ts +36 -14
  18. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +64 -5
  19. package/src/FeatureDetailsWidget/BasicInformation.tsx +6 -4
  20. package/src/FeatureDetailsWidget/NumberTextField.tsx +5 -2
  21. package/src/FeatureDetailsWidget/TranscriptSequence.tsx +70 -73
  22. package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +72 -234
  23. package/src/LinearApolloDisplay/components/CheckResultWarnings.tsx +92 -0
  24. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +23 -131
  25. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +50 -194
  26. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +279 -217
  27. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +53 -34
  28. package/src/LinearApolloDisplay/glyphs/Glyph.ts +7 -9
  29. package/src/LinearApolloDisplay/glyphs/util.ts +19 -0
  30. package/src/LinearApolloDisplay/stateModel/base.ts +34 -43
  31. package/src/LinearApolloDisplay/stateModel/layouts.ts +3 -2
  32. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +32 -261
  33. package/src/LinearApolloDisplay/stateModel/rendering.ts +43 -343
  34. package/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx +87 -0
  35. package/src/LinearApolloReferenceSequenceDisplay/components/index.ts +1 -0
  36. package/src/LinearApolloReferenceSequenceDisplay/configSchema.ts +7 -0
  37. package/src/LinearApolloReferenceSequenceDisplay/drawSequenceOverlay.ts +181 -0
  38. package/src/LinearApolloReferenceSequenceDisplay/drawSequenceTrack.ts +218 -0
  39. package/src/LinearApolloReferenceSequenceDisplay/index.ts +3 -0
  40. package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts +227 -0
  41. package/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts +25 -0
  42. package/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts +157 -0
  43. package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +101 -38
  44. package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +334 -262
  45. package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts +12 -8
  46. package/src/LinearApolloSixFrameDisplay/stateModel/base.ts +42 -4
  47. package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +4 -8
  48. package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +73 -97
  49. package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +49 -61
  50. package/src/TabularEditor/HybridGrid/Feature.tsx +16 -14
  51. package/src/TabularEditor/HybridGrid/HybridGrid.tsx +7 -5
  52. package/src/components/AddAssembly.tsx +34 -38
  53. package/src/components/AddAssemblyAliases.tsx +1 -1
  54. package/src/components/AddChildFeature.tsx +5 -2
  55. package/src/components/AddFeature.tsx +30 -21
  56. package/src/components/AddRefSeqAliases.tsx +64 -50
  57. package/src/components/CopyFeature.tsx +4 -2
  58. package/src/components/CreateApolloAnnotation.tsx +22 -9
  59. package/src/components/DeleteAssembly.tsx +3 -10
  60. package/src/components/DownloadGFF3.tsx +2 -2
  61. package/src/components/EditZoomThresholdDialog.tsx +69 -0
  62. package/src/components/FilterFeatures.tsx +7 -7
  63. package/src/components/FilterTranscripts.tsx +6 -6
  64. package/src/components/ImportFeatures.tsx +1 -1
  65. package/src/components/ManageChecks.tsx +3 -10
  66. package/src/components/ManageUsers.tsx +23 -22
  67. package/src/components/MergeTranscripts.tsx +12 -15
  68. package/src/components/OntologyTermAutocomplete.tsx +1 -8
  69. package/src/components/OntologyTermMultiSelect.tsx +11 -11
  70. package/src/components/OpenLocalFile.tsx +11 -7
  71. package/src/components/ViewChangeLog.tsx +25 -50
  72. package/src/components/ViewCheckResults.tsx +2 -8
  73. package/src/components/index.ts +1 -0
  74. package/src/config.ts +6 -0
  75. package/src/index.ts +53 -115
  76. package/src/makeDisplayComponent.tsx +9 -14
  77. package/src/menus/index.ts +1 -0
  78. package/src/{ApolloInternetAccount/addMenuItems.ts → menus/topLevelMenu.ts} +56 -47
  79. package/src/menus/topLevelMenuAdmin.ts +154 -0
  80. package/src/session/ClientDataStore.ts +32 -14
  81. package/src/session/session.ts +159 -121
  82. package/src/util/annotationFeatureUtils.ts +15 -21
  83. package/src/util/displayUtils.ts +149 -0
  84. package/src/util/glyphUtils.ts +329 -0
  85. package/src/util/loadAssemblyIntoClient.ts +3 -2
  86. package/src/util/mouseEventsUtils.ts +32 -0

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