@apollo-annotation/jbrowse-plugin-apollo 0.1.0

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Files changed (116) hide show
  1. package/README.md +76 -0
  2. package/dist/index.esm.js +10248 -0
  3. package/dist/index.esm.js.map +1 -0
  4. package/dist/index.js +7 -0
  5. package/dist/jbrowse-plugin-apollo.cjs.development.js +10298 -0
  6. package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -0
  7. package/dist/jbrowse-plugin-apollo.cjs.production.min.js +2 -0
  8. package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -0
  9. package/dist/jbrowse-plugin-apollo.umd.development.js +46957 -0
  10. package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -0
  11. package/dist/jbrowse-plugin-apollo.umd.production.min.js +2 -0
  12. package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -0
  13. package/package.json +130 -0
  14. package/src/ApolloInternetAccount/addMenuItems.ts +94 -0
  15. package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +121 -0
  16. package/src/ApolloInternetAccount/components/LoginButtons.tsx +62 -0
  17. package/src/ApolloInternetAccount/components/LoginIcons.tsx +74 -0
  18. package/src/ApolloInternetAccount/configSchema.ts +26 -0
  19. package/src/ApolloInternetAccount/index.ts +2 -0
  20. package/src/ApolloInternetAccount/model.ts +448 -0
  21. package/src/ApolloJobModel.ts +117 -0
  22. package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +186 -0
  23. package/src/ApolloSequenceAdapter/configSchema.ts +12 -0
  24. package/src/ApolloSequenceAdapter/index.ts +21 -0
  25. package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx +12 -0
  26. package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +692 -0
  27. package/src/ApolloSixFrameRenderer/configSchema.ts +7 -0
  28. package/src/ApolloSixFrameRenderer/index.ts +3 -0
  29. package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +64 -0
  30. package/src/ApolloTextSearchAdapter/configSchema.ts +24 -0
  31. package/src/ApolloTextSearchAdapter/index.ts +18 -0
  32. package/src/BackendDrivers/BackendDriver.ts +31 -0
  33. package/src/BackendDrivers/CollaborationServerDriver.ts +318 -0
  34. package/src/BackendDrivers/DesktopFileDriver.ts +170 -0
  35. package/src/BackendDrivers/InMemoryFileDriver.ts +76 -0
  36. package/src/BackendDrivers/index.ts +4 -0
  37. package/src/ChangeManager.ts +148 -0
  38. package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +248 -0
  39. package/src/LinearApolloDisplay/components/index.ts +1 -0
  40. package/src/LinearApolloDisplay/configSchema.ts +16 -0
  41. package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +422 -0
  42. package/src/LinearApolloDisplay/glyphs/CanonicalGeneGlyph.ts +1191 -0
  43. package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +151 -0
  44. package/src/LinearApolloDisplay/glyphs/Glyph.ts +382 -0
  45. package/src/LinearApolloDisplay/glyphs/ImplicitExonGeneGlyph.ts +697 -0
  46. package/src/LinearApolloDisplay/glyphs/index.ts +4 -0
  47. package/src/LinearApolloDisplay/index.ts +2 -0
  48. package/src/LinearApolloDisplay/stateModel/base.ts +146 -0
  49. package/src/LinearApolloDisplay/stateModel/getGlyph.ts +39 -0
  50. package/src/LinearApolloDisplay/stateModel/glyphs.ts +45 -0
  51. package/src/LinearApolloDisplay/stateModel/index.ts +20 -0
  52. package/src/LinearApolloDisplay/stateModel/layouts.ts +230 -0
  53. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +513 -0
  54. package/src/LinearApolloDisplay/stateModel/rendering.ts +441 -0
  55. package/src/LinearApolloDisplay/stateModel/trackHeightMixin.ts +43 -0
  56. package/src/LinearApolloDisplay/types.ts +1 -0
  57. package/src/OntologyManager/OntologyStore/__snapshots__/fulltext.test.ts.snap +208 -0
  58. package/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap +18846 -0
  59. package/src/OntologyManager/OntologyStore/fulltext-stopwords.ts +137 -0
  60. package/src/OntologyManager/OntologyStore/fulltext.test.ts +94 -0
  61. package/src/OntologyManager/OntologyStore/fulltext.ts +264 -0
  62. package/src/OntologyManager/OntologyStore/index.test.ts +130 -0
  63. package/src/OntologyManager/OntologyStore/index.ts +526 -0
  64. package/src/OntologyManager/OntologyStore/indexeddb-schema.ts +89 -0
  65. package/src/OntologyManager/OntologyStore/indexeddb-storage.ts +180 -0
  66. package/src/OntologyManager/OntologyStore/obo-graph-json-schema.ts +110 -0
  67. package/src/OntologyManager/OntologyStore/prefixes.ts +35 -0
  68. package/src/OntologyManager/index.ts +173 -0
  69. package/src/SixFrameFeatureDisplay/components/TrackLines.tsx +19 -0
  70. package/src/SixFrameFeatureDisplay/components/index.ts +1 -0
  71. package/src/SixFrameFeatureDisplay/configSchema.ts +21 -0
  72. package/src/SixFrameFeatureDisplay/index.ts +2 -0
  73. package/src/SixFrameFeatureDisplay/stateModel.ts +413 -0
  74. package/src/TabularEditor/HybridGrid/ChangeHandling.ts +88 -0
  75. package/src/TabularEditor/HybridGrid/Feature.tsx +346 -0
  76. package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +34 -0
  77. package/src/TabularEditor/HybridGrid/Highlight.tsx +40 -0
  78. package/src/TabularEditor/HybridGrid/HybridGrid.tsx +138 -0
  79. package/src/TabularEditor/HybridGrid/NumberCell.tsx +77 -0
  80. package/src/TabularEditor/HybridGrid/ToolBar.tsx +59 -0
  81. package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +119 -0
  82. package/src/TabularEditor/HybridGrid/index.ts +1 -0
  83. package/src/TabularEditor/TabularEditorPane.tsx +34 -0
  84. package/src/TabularEditor/index.ts +3 -0
  85. package/src/TabularEditor/model.ts +44 -0
  86. package/src/TabularEditor/types.ts +3 -0
  87. package/src/components/AddAssembly.tsx +464 -0
  88. package/src/components/AddChildFeature.tsx +247 -0
  89. package/src/components/AddFeature.tsx +252 -0
  90. package/src/components/CopyFeature.tsx +328 -0
  91. package/src/components/DeleteAssembly.tsx +185 -0
  92. package/src/components/DeleteFeature.tsx +90 -0
  93. package/src/components/Dialog.tsx +47 -0
  94. package/src/components/DownloadGFF3.tsx +213 -0
  95. package/src/components/ImportFeatures.tsx +295 -0
  96. package/src/components/ManageChecks.tsx +280 -0
  97. package/src/components/ManageUsers.tsx +218 -0
  98. package/src/components/ModifyFeatureAttribute.tsx +457 -0
  99. package/src/components/OntologyTermAutocomplete.tsx +240 -0
  100. package/src/components/OntologyTermMultiSelect.tsx +349 -0
  101. package/src/components/OpenLocalFile.tsx +178 -0
  102. package/src/components/ViewChangeLog.tsx +208 -0
  103. package/src/components/ViewCheckResults.tsx +151 -0
  104. package/src/components/index.ts +12 -0
  105. package/src/config.ts +10 -0
  106. package/src/declare.d.ts +3 -0
  107. package/src/extensions/annotationFromPileup.ts +208 -0
  108. package/src/extensions/index.ts +1 -0
  109. package/src/index.ts +394 -0
  110. package/src/makeDisplayComponent.tsx +244 -0
  111. package/src/session/ClientDataStore.ts +282 -0
  112. package/src/session/index.ts +1 -0
  113. package/src/session/session.ts +373 -0
  114. package/src/types.ts +10 -0
  115. package/src/util/index.ts +31 -0
  116. package/src/util/loadAssemblyIntoClient.ts +291 -0

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