@apollo-annotation/jbrowse-plugin-apollo 0.3.6 → 0.3.8

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Files changed (84) hide show
  1. package/dist/index.esm.js +4603 -2045
  2. package/dist/index.esm.js.map +1 -1
  3. package/dist/jbrowse-plugin-apollo.cjs.development.js +4611 -2039
  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 +9387 -4016
  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 +15 -15
  12. package/src/ApolloInternetAccount/model.ts +48 -13
  13. package/src/BackendDrivers/CollaborationServerDriver.ts +23 -2
  14. package/src/ChangeManager.ts +42 -18
  15. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +64 -5
  16. package/src/FeatureDetailsWidget/Attributes.tsx +8 -3
  17. package/src/FeatureDetailsWidget/TranscriptSequence.tsx +70 -81
  18. package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +946 -190
  19. package/src/FeatureDetailsWidget/TranscriptWidgetSummary.tsx +4 -0
  20. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +61 -73
  21. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +55 -211
  22. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +562 -108
  23. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +78 -14
  24. package/src/LinearApolloDisplay/glyphs/Glyph.ts +15 -9
  25. package/src/LinearApolloDisplay/stateModel/base.ts +63 -43
  26. package/src/LinearApolloDisplay/stateModel/layouts.ts +3 -2
  27. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +79 -292
  28. package/src/LinearApolloDisplay/stateModel/rendering.ts +45 -344
  29. package/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx +87 -0
  30. package/src/LinearApolloReferenceSequenceDisplay/components/index.ts +1 -0
  31. package/src/LinearApolloReferenceSequenceDisplay/configSchema.ts +7 -0
  32. package/src/LinearApolloReferenceSequenceDisplay/index.ts +3 -0
  33. package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts +227 -0
  34. package/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts +25 -0
  35. package/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts +481 -0
  36. package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +102 -40
  37. package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx +12 -20
  38. package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +382 -243
  39. package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts +12 -8
  40. package/src/LinearApolloSixFrameDisplay/stateModel/base.ts +83 -4
  41. package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +23 -11
  42. package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +118 -123
  43. package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +53 -63
  44. package/src/OntologyManager/index.ts +4 -1
  45. package/src/TabularEditor/HybridGrid/Feature.tsx +20 -14
  46. package/src/TabularEditor/HybridGrid/HybridGrid.tsx +7 -5
  47. package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +108 -16
  48. package/src/components/AddAssembly.tsx +1 -1
  49. package/src/components/AddAssemblyAliases.tsx +114 -0
  50. package/src/components/AddChildFeature.tsx +7 -7
  51. package/src/components/AddFeature.tsx +20 -15
  52. package/src/components/AddRefSeqAliases.tsx +9 -9
  53. package/src/components/CopyFeature.tsx +4 -4
  54. package/src/components/CreateApolloAnnotation.tsx +335 -151
  55. package/src/components/DeleteAssembly.tsx +1 -1
  56. package/src/components/DeleteFeature.tsx +358 -11
  57. package/src/components/DownloadGFF3.tsx +20 -1
  58. package/src/components/EditZoomThresholdDialog.tsx +69 -0
  59. package/src/components/FilterFeatures.tsx +7 -7
  60. package/src/components/FilterTranscripts.tsx +86 -0
  61. package/src/components/ImportFeatures.tsx +1 -1
  62. package/src/components/ManageChecks.tsx +1 -1
  63. package/src/components/MergeExons.tsx +193 -0
  64. package/src/components/MergeTranscripts.tsx +182 -0
  65. package/src/components/OntologyTermMultiSelect.tsx +11 -11
  66. package/src/components/OpenLocalFile.tsx +11 -7
  67. package/src/components/SplitExon.tsx +134 -0
  68. package/src/components/ViewCheckResults.tsx +1 -1
  69. package/src/components/index.ts +4 -0
  70. package/src/config.ts +11 -0
  71. package/src/extensions/annotationFromJBrowseFeature.ts +2 -0
  72. package/src/extensions/annotationFromPileup.ts +99 -89
  73. package/src/index.ts +42 -105
  74. package/src/makeDisplayComponent.tsx +0 -1
  75. package/src/menus/index.ts +1 -0
  76. package/src/{ApolloInternetAccount/addMenuItems.ts → menus/topLevelMenu.ts} +60 -33
  77. package/src/menus/topLevelMenuAdmin.ts +154 -0
  78. package/src/session/session.ts +163 -104
  79. package/src/util/annotationFeatureUtils.ts +59 -0
  80. package/src/util/copyToClipboard.ts +21 -0
  81. package/src/util/displayUtils.ts +149 -0
  82. package/src/util/glyphUtils.ts +201 -0
  83. package/src/util/index.ts +2 -0
  84. package/src/util/mouseEventsUtils.ts +145 -0

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