@apollo-annotation/jbrowse-plugin-apollo 1.0.0 → 1.1.0

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Files changed (172) hide show
  1. package/dist/ApolloInternetAccount/components/AuthTypeSelector.d.ts +8 -2
  2. package/dist/ApolloInternetAccount/components/AuthTypeSelector.d.ts.map +1 -1
  3. package/dist/ApolloInternetAccount/components/LoginButtons.d.ts +8 -3
  4. package/dist/ApolloInternetAccount/components/LoginButtons.d.ts.map +1 -1
  5. package/dist/ApolloInternetAccount/configSchema.d.ts +44 -0
  6. package/dist/ApolloInternetAccount/configSchema.d.ts.map +1 -0
  7. package/dist/ApolloInternetAccount/model.d.ts +174 -0
  8. package/dist/ApolloInternetAccount/model.d.ts.map +1 -0
  9. package/dist/ApolloJobModel.d.ts.map +1 -1
  10. package/dist/ApolloRefNameAliasAdapter/configSchema.d.ts +8 -0
  11. package/dist/ApolloRefNameAliasAdapter/configSchema.d.ts.map +1 -0
  12. package/dist/ApolloSequenceAdapter/configSchema.d.ts +8 -0
  13. package/dist/ApolloSequenceAdapter/configSchema.d.ts.map +1 -0
  14. package/dist/ApolloTextSearchAdapter/configSchema.d.ts +20 -0
  15. package/dist/ApolloTextSearchAdapter/configSchema.d.ts.map +1 -0
  16. package/dist/BackendDrivers/CollaborationServerDriver.d.ts +1 -1
  17. package/dist/BackendDrivers/CollaborationServerDriver.d.ts.map +1 -1
  18. package/dist/BackendDrivers/LocalDriver/LocalDriver.d.ts.map +1 -1
  19. package/dist/FeatureDetailsWidget/ApolloFeatureDetailsWidget.d.ts.map +1 -1
  20. package/dist/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.d.ts.map +1 -1
  21. package/dist/FeatureDetailsWidget/Attributes.d.ts.map +1 -1
  22. package/dist/FeatureDetailsWidget/DefaultAttributeEditor.d.ts.map +1 -1
  23. package/dist/FeatureDetailsWidget/DefaultAttributeViewer.d.ts.map +1 -1
  24. package/dist/FeatureDetailsWidget/NumberTextField.d.ts.map +1 -1
  25. package/dist/FeatureDetailsWidget/StringTextField.d.ts.map +1 -1
  26. package/dist/FeatureDetailsWidget/TranscriptSequence.d.ts.map +1 -1
  27. package/dist/FeatureDetailsWidget/TranscriptWidgetEditLocation.d.ts.map +1 -1
  28. package/dist/FeatureDetailsWidget/Translation.d.ts +14 -0
  29. package/dist/FeatureDetailsWidget/Translation.d.ts.map +1 -0
  30. package/dist/LinearApolloDisplay/components/CheckResultWarnings.d.ts.map +1 -1
  31. package/dist/LinearApolloDisplay/configSchema.d.ts +2 -0
  32. package/dist/LinearApolloDisplay/configSchema.d.ts.map +1 -0
  33. package/dist/LinearApolloDisplay/glyphs/ExonGlyph.d.ts.map +1 -1
  34. package/dist/LinearApolloDisplay/glyphs/GeneGlyph.d.ts.map +1 -1
  35. package/dist/LinearApolloDisplay/glyphs/TranscriptGlyph.d.ts.map +1 -1
  36. package/dist/LinearApolloDisplay/stateModel/base.d.ts +1 -18
  37. package/dist/LinearApolloDisplay/stateModel/base.d.ts.map +1 -1
  38. package/dist/LinearApolloDisplay/stateModel/index.d.ts +1 -17
  39. package/dist/LinearApolloDisplay/stateModel/index.d.ts.map +1 -1
  40. package/dist/LinearApolloDisplay/stateModel/layouts.d.ts +2 -19
  41. package/dist/LinearApolloDisplay/stateModel/layouts.d.ts.map +1 -1
  42. package/dist/LinearApolloDisplay/stateModel/mouseEvents.d.ts +2 -34
  43. package/dist/LinearApolloDisplay/stateModel/mouseEvents.d.ts.map +1 -1
  44. package/dist/LinearApolloDisplay/stateModel/rendering.d.ts +2 -19
  45. package/dist/LinearApolloDisplay/stateModel/rendering.d.ts.map +1 -1
  46. package/dist/LinearApolloReferenceSequenceDisplay/configSchema.d.ts +2 -0
  47. package/dist/LinearApolloReferenceSequenceDisplay/configSchema.d.ts.map +1 -0
  48. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/base.d.ts +1 -1
  49. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/base.d.ts.map +1 -1
  50. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/index.d.ts +1 -1
  51. package/dist/LinearApolloReferenceSequenceDisplay/stateModel/rendering.d.ts +1 -1
  52. package/dist/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.d.ts.map +1 -1
  53. package/dist/LinearApolloSixFrameDisplay/configSchema.d.ts +2 -0
  54. package/dist/LinearApolloSixFrameDisplay/configSchema.d.ts.map +1 -0
  55. package/dist/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.d.ts.map +1 -1
  56. package/dist/LinearApolloSixFrameDisplay/stateModel/base.d.ts +1 -1
  57. package/dist/LinearApolloSixFrameDisplay/stateModel/base.d.ts.map +1 -1
  58. package/dist/LinearApolloSixFrameDisplay/stateModel/index.d.ts +1 -1
  59. package/dist/LinearApolloSixFrameDisplay/stateModel/index.d.ts.map +1 -1
  60. package/dist/LinearApolloSixFrameDisplay/stateModel/layouts.d.ts +2 -3
  61. package/dist/LinearApolloSixFrameDisplay/stateModel/layouts.d.ts.map +1 -1
  62. package/dist/LinearApolloSixFrameDisplay/stateModel/mouseEvents.d.ts +2 -2
  63. package/dist/LinearApolloSixFrameDisplay/stateModel/mouseEvents.d.ts.map +1 -1
  64. package/dist/LinearApolloSixFrameDisplay/stateModel/rendering.d.ts +2 -3
  65. package/dist/LinearApolloSixFrameDisplay/stateModel/rendering.d.ts.map +1 -1
  66. package/dist/OntologyManager/OntologyStore/fulltext.d.ts.map +1 -1
  67. package/dist/OntologyManager/index.d.ts +734 -0
  68. package/dist/OntologyManager/index.d.ts.map +1 -0
  69. package/dist/TabularEditor/HybridGrid/NumberCell.d.ts.map +1 -1
  70. package/dist/components/AddCodingSequence.d.ts +14 -0
  71. package/dist/components/AddCodingSequence.d.ts.map +1 -0
  72. package/dist/components/AddRefSeqAliases.d.ts.map +1 -1
  73. package/dist/components/CopyFeature.d.ts.map +1 -1
  74. package/dist/components/CreateApolloAnnotation.d.ts.map +1 -1
  75. package/dist/components/DeleteFeature.d.ts.map +1 -1
  76. package/dist/components/DownloadGFF3.d.ts.map +1 -1
  77. package/dist/components/DuplicateFeatureDialog.d.ts +12 -0
  78. package/dist/components/DuplicateFeatureDialog.d.ts.map +1 -0
  79. package/dist/components/ImportAnnotations.d.ts +9 -0
  80. package/dist/components/ImportAnnotations.d.ts.map +1 -0
  81. package/dist/components/ManageUsers.d.ts.map +1 -1
  82. package/dist/components/OntologyTermMultiSelect.d.ts.map +1 -1
  83. package/dist/components/ViewChangeLog.d.ts.map +1 -1
  84. package/dist/components/index.d.ts +2 -0
  85. package/dist/components/index.d.ts.map +1 -1
  86. package/dist/extensions/annotationFromPileup.d.ts.map +1 -1
  87. package/dist/index.d.ts.map +1 -1
  88. package/dist/index.esm.js +830 -434
  89. package/dist/index.esm.js.map +1 -1
  90. package/dist/jbrowse-plugin-apollo.cjs.development.js +825 -429
  91. package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -1
  92. package/dist/jbrowse-plugin-apollo.cjs.production.min.js +1 -1
  93. package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -1
  94. package/dist/jbrowse-plugin-apollo.umd.development.js +863 -468
  95. package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -1
  96. package/dist/jbrowse-plugin-apollo.umd.production.min.js +1 -1
  97. package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -1
  98. package/dist/session/ClientDataStore.d.ts +2194 -0
  99. package/dist/session/ClientDataStore.d.ts.map +1 -0
  100. package/dist/session/handleApolloFeaturesUrlParam.d.ts +8 -0
  101. package/dist/session/handleApolloFeaturesUrlParam.d.ts.map +1 -0
  102. package/dist/session/session.d.ts +6788 -0
  103. package/dist/session/session.d.ts.map +1 -0
  104. package/dist/util/displayUtils.d.ts +36 -0
  105. package/dist/util/displayUtils.d.ts.map +1 -0
  106. package/dist/util/sequenceUtils.d.ts +2 -0
  107. package/dist/util/sequenceUtils.d.ts.map +1 -0
  108. package/package.json +14 -14
  109. package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +73 -38
  110. package/src/ApolloInternetAccount/components/LoginButtons.tsx +31 -10
  111. package/src/ApolloInternetAccount/model.ts +8 -5
  112. package/src/ApolloJobModel.ts +3 -8
  113. package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +1 -1
  114. package/src/BackendDrivers/CollaborationServerDriver.ts +7 -11
  115. package/src/BackendDrivers/LocalDriver/LocalDriver.ts +13 -4
  116. package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +1 -0
  117. package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +4 -2
  118. package/src/FeatureDetailsWidget/Attributes.tsx +1 -0
  119. package/src/FeatureDetailsWidget/DefaultAttributeEditor.tsx +1 -0
  120. package/src/FeatureDetailsWidget/DefaultAttributeViewer.tsx +1 -0
  121. package/src/FeatureDetailsWidget/NumberTextField.tsx +1 -0
  122. package/src/FeatureDetailsWidget/StringTextField.tsx +1 -0
  123. package/src/FeatureDetailsWidget/TranscriptSequence.tsx +2 -1
  124. package/src/FeatureDetailsWidget/TranscriptWidgetEditLocation.tsx +17 -354
  125. package/src/FeatureDetailsWidget/Translation.tsx +358 -0
  126. package/src/LinearApolloDisplay/components/CheckResultWarnings.tsx +4 -1
  127. package/src/LinearApolloDisplay/glyphs/ExonGlyph.ts +2 -5
  128. package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +4 -6
  129. package/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts +39 -6
  130. package/src/LinearApolloDisplay/stateModel/base.ts +47 -23
  131. package/src/LinearApolloDisplay/stateModel/layouts.ts +7 -5
  132. package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +4 -1
  133. package/src/LinearApolloDisplay/stateModel/rendering.ts +1 -5
  134. package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts +10 -10
  135. package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx +5 -3
  136. package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx +1 -1
  137. package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +2 -3
  138. package/src/LinearApolloSixFrameDisplay/stateModel/base.ts +12 -20
  139. package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +10 -6
  140. package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +38 -45
  141. package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +1 -4
  142. package/src/OntologyManager/OntologyStore/fulltext.ts +0 -2
  143. package/src/OntologyManager/OntologyStore/index.ts +1 -1
  144. package/src/TabularEditor/HybridGrid/ChangeHandling.ts +2 -2
  145. package/src/TabularEditor/HybridGrid/NumberCell.tsx +2 -1
  146. package/src/components/AddAssemblyAliases.tsx +1 -1
  147. package/src/components/AddCodingSequence.tsx +255 -0
  148. package/src/components/AddFeature.tsx +1 -1
  149. package/src/components/AddRefSeqAliases.tsx +3 -2
  150. package/src/components/CopyFeature.tsx +9 -7
  151. package/src/components/CreateApolloAnnotation.tsx +28 -23
  152. package/src/components/DeleteAssembly.tsx +2 -2
  153. package/src/components/DeleteFeature.tsx +1 -4
  154. package/src/components/DownloadGFF3.tsx +4 -3
  155. package/src/components/DuplicateFeatureDialog.tsx +154 -0
  156. package/src/components/DuplicateTranscript.tsx +1 -1
  157. package/src/components/FilterTranscripts.tsx +1 -1
  158. package/src/components/ImportAnnotations.tsx +108 -0
  159. package/src/components/ManageUsers.tsx +1 -2
  160. package/src/components/OntologyTermAutocomplete.tsx +1 -3
  161. package/src/components/OntologyTermMultiSelect.tsx +3 -1
  162. package/src/components/ViewChangeLog.tsx +2 -1
  163. package/src/components/index.ts +2 -0
  164. package/src/extensions/annotationFromPileup.ts +34 -26
  165. package/src/index.ts +9 -8
  166. package/src/session/ClientDataStore.ts +16 -21
  167. package/src/session/handleApolloFeaturesUrlParam.ts +122 -0
  168. package/src/session/session.ts +49 -9
  169. package/src/util/annotationFeatureUtils.ts +1 -1
  170. package/src/util/displayUtils.ts +1 -1
  171. package/src/util/glyphUtils.ts +3 -3
  172. package/src/util/sequenceUtils.ts +29 -0

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