@rcsb/rcsb-saguaro-app 6.3.7-dev-js-seqcoord.14 → 6.3.7-react-downgrade.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (566) hide show
  1. package/build/39795c0b4513de014cf8.woff +0 -0
  2. package/build/app.js +1 -1
  3. package/build/app.js.LICENSE.txt +8 -18
  4. package/build/b7bcc075b395c14ce8c2.woff2 +0 -0
  5. package/build/constants.js +1 -1
  6. package/build/plot.js +1 -1
  7. package/build/plot.js.LICENSE.txt +23 -18
  8. package/build/worker.js +1 -1
  9. package/lib/ExternalResources/NcbiData/NcbiGenomeSequenceData.js +0 -1
  10. package/lib/ExternalResources/NcbiData/NcbiSummary.js +0 -1
  11. package/lib/RcsbAnnotationConfig/AnnotationConfigInterface.js +0 -1
  12. package/lib/RcsbAnnotationConfig/RcsbAnnotationConfig.d.ts +2 -2
  13. package/lib/RcsbAnnotationConfig/RcsbAnnotationConfig.js +0 -1
  14. package/lib/RcsbAnnotationConfig/RcsbAnnotationConstants.js +0 -1
  15. package/lib/RcsbAnnotationConfig/RcsbDistributionConfig.js +0 -1
  16. package/lib/RcsbChartWeb/AbsractChartComponent.js +0 -1
  17. package/lib/RcsbChartWeb/BarChartComponent.js +0 -1
  18. package/lib/RcsbChartWeb/HistogramChartComponent.d.ts +1 -2
  19. package/lib/RcsbChartWeb/HistogramChartComponent.js +0 -1
  20. package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.d.ts +4 -4
  21. package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js +8 -9
  22. package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.d.ts +4 -4
  23. package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.js +0 -1
  24. package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.d.ts +4 -4
  25. package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js +9 -17
  26. package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.d.ts +10 -11
  27. package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.js +0 -1
  28. package/lib/RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector.js +0 -1
  29. package/lib/RcsbCollectTools/DataCollectors/DataCollectorInterface.js +0 -1
  30. package/lib/RcsbCollectTools/DataCollectors/EntryAssembliesCollector.js +0 -1
  31. package/lib/RcsbCollectTools/DataCollectors/GroupMemberCollector.js +0 -1
  32. package/lib/RcsbCollectTools/DataCollectors/GroupPropertyCollector.js +0 -1
  33. package/lib/RcsbCollectTools/DataCollectors/InterfaceInstanceCollector.js +0 -1
  34. package/lib/RcsbCollectTools/DataCollectors/MultipleEntityInstancesCollector.js +0 -1
  35. package/lib/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.js +0 -1
  36. package/lib/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector.js +0 -1
  37. package/lib/RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector.js +0 -1
  38. package/lib/RcsbCollectTools/DataCollectors/PolymerEntityChromosomeCollector.js +1 -2
  39. package/lib/RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector.js +0 -1
  40. package/lib/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts +7 -7
  41. package/lib/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.js +0 -1
  42. package/lib/RcsbCollectTools/FeatureTools/FeatureTools.js +0 -1
  43. package/lib/RcsbExport/FeatureType.d.ts +4 -4
  44. package/lib/RcsbExport/FeatureType.js +2 -3
  45. package/lib/RcsbExport/RcsbFvUI.js +0 -1
  46. package/lib/RcsbFvExamples/ChromosomeFv.js +0 -1
  47. package/lib/RcsbFvExamples/EntitySummaryFv.js +0 -1
  48. package/lib/RcsbFvExamples/ExternalDataProvider.js +4 -5
  49. package/lib/RcsbFvExamples/GroupHistogram.js +0 -1
  50. package/lib/RcsbFvExamples/InstanceFv.js +0 -1
  51. package/lib/RcsbFvExamples/InstanceSequenceFv.js +2 -3
  52. package/lib/RcsbFvExamples/ResidueDistribution.js +0 -1
  53. package/lib/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js +2 -3
  54. package/lib/RcsbFvExamples/SequenceIdentityGroupFv.js +0 -1
  55. package/lib/RcsbFvExamples/SingleEntitySummaryFv.js +0 -1
  56. package/lib/RcsbFvExamples/TestCollectors.js +0 -1
  57. package/lib/RcsbFvExamples/UniprotAlignmentFv.js +0 -1
  58. package/lib/RcsbFvExamples/UniprotEntityInstanceFv.js +0 -1
  59. package/lib/RcsbFvExamples/UniprotFv.js +0 -1
  60. package/lib/RcsbFvExamples/UniprotGroupFv.js +5 -7
  61. package/lib/RcsbFvExamples/utils/events.js +0 -1
  62. package/lib/RcsbFvUI/AbstractMenuItemComponent.js +0 -1
  63. package/lib/RcsbFvUI/Components/FilterItemComponent.d.ts +1 -2
  64. package/lib/RcsbFvUI/Components/FilterItemComponent.js +0 -1
  65. package/lib/RcsbFvUI/Components/ItemComponent.js +0 -1
  66. package/lib/RcsbFvUI/Components/PaginationItemComponent.d.ts +2 -3
  67. package/lib/RcsbFvUI/Components/PaginationItemComponent.js +1 -2
  68. package/lib/RcsbFvUI/GroupPfvUI.js +0 -1
  69. package/lib/RcsbFvUI/Helper/ActionMethods.js +0 -1
  70. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvAssemblyBuilder.js +0 -1
  71. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvChromosomeBuilder.js +0 -1
  72. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvContextManager.js +0 -1
  73. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder.js +0 -1
  74. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvDataProviderBuilder.js +0 -1
  75. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvEntityBuilder.js +5 -6
  76. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js +4 -5
  77. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupBuilder.js +0 -1
  78. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.d.ts +1 -2
  79. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.js +0 -1
  80. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvPairwiseAligmentBuilder.js +0 -1
  81. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js +4 -5
  82. package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder.js +0 -1
  83. package/lib/RcsbFvWeb/RcsbFvBuilder.js +0 -1
  84. package/lib/RcsbFvWeb/RcsbFvComponents/ComponentsManager.d.ts +1 -2
  85. package/lib/RcsbFvWeb/RcsbFvComponents/ComponentsManager.js +0 -1
  86. package/lib/RcsbFvWeb/RcsbFvComponents/LoaderSpinner.d.ts +2 -2
  87. package/lib/RcsbFvWeb/RcsbFvComponents/LoaderSpinner.js +0 -1
  88. package/lib/RcsbFvWeb/RcsbFvComponents/MountableComponent.js +0 -1
  89. package/lib/RcsbFvWeb/RcsbFvComponents/RcsbTabs.d.ts +3 -3
  90. package/lib/RcsbFvWeb/RcsbFvComponents/RcsbTabs.js +0 -1
  91. package/lib/RcsbFvWeb/RcsbFvComponents/SelectButton.d.ts +3 -3
  92. package/lib/RcsbFvWeb/RcsbFvComponents/SelectButton.js +3 -6
  93. package/lib/RcsbFvWeb/RcsbFvComponents/SelectButtonManager.js +0 -1
  94. package/lib/RcsbFvWeb/RcsbFvComponents/SelectButtonTitle.d.ts +2 -2
  95. package/lib/RcsbFvWeb/RcsbFvComponents/SelectButtonTitle.js +0 -1
  96. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory.d.ts +6 -6
  97. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory.js +2 -3
  98. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory.d.ts +4 -4
  99. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory.js +0 -1
  100. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockFactoryInterface.js +0 -1
  101. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager.d.ts +3 -3
  102. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager.js +0 -1
  103. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager.d.ts +2 -2
  104. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager.js +2 -3
  105. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/BlockManagerInterface.js +0 -1
  106. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.d.ts +3 -3
  107. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.js +0 -1
  108. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface.js +0 -1
  109. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.d.ts +5 -5
  110. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.js +0 -1
  111. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory.js +0 -1
  112. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.d.ts +3 -3
  113. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.js +0 -1
  114. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory.d.ts +4 -4
  115. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory.js +0 -1
  116. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory.d.ts +5 -5
  117. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory.js +0 -1
  118. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.d.ts +4 -4
  119. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.js +0 -1
  120. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.d.ts +4 -4
  121. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.js +2 -3
  122. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js +1 -2
  123. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface.js +0 -1
  124. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.d.ts +5 -5
  125. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.js +0 -1
  126. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AnnotationsTrackTitleFactory.js +0 -1
  127. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.d.ts +5 -5
  128. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.js +0 -1
  129. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory.js +0 -1
  130. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.d.ts +5 -5
  131. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.js +0 -1
  132. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.js +0 -1
  133. package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.js +0 -1
  134. package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.d.ts +2 -2
  135. package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.js +11 -12
  136. package/lib/RcsbFvWeb/RcsbFvGroup/GroupTabs/GroupPfvApp.js +23 -30
  137. package/lib/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.js +0 -1
  138. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts +6 -6
  139. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js +0 -1
  140. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js +8 -9
  141. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.js +0 -1
  142. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js +3 -4
  143. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.js +45 -31
  144. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.js +5 -7
  145. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.js +2 -3
  146. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.d.ts +3 -3
  147. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.js +11 -14
  148. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts +9 -10
  149. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.js +0 -1
  150. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvPairwiseAlignment.js +0 -1
  151. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js +2 -5
  152. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js +6 -7
  153. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js +6 -7
  154. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js +4 -5
  155. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js +4 -5
  156. package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.js +1 -2
  157. package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.d.ts +2 -2
  158. package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.js +0 -1
  159. package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorWorker.worker.js +0 -1
  160. package/lib/RcsbGraphQL/RcsbClient.d.ts +5 -7
  161. package/lib/RcsbGraphQL/RcsbClient.js +1 -8
  162. package/lib/RcsbGraphQL/RcsbCoreQueryInterface.js +0 -1
  163. package/lib/RcsbGraphQL/RcsbQueryAlignment.d.ts +7 -7
  164. package/lib/RcsbGraphQL/RcsbQueryAlignment.js +2 -3
  165. package/lib/RcsbGraphQL/RcsbQueryAnnotations.d.ts +5 -10
  166. package/lib/RcsbGraphQL/RcsbQueryAnnotations.js +7 -20
  167. package/lib/RcsbGraphQL/RcsbQueryAssemblyInterfaces.js +0 -1
  168. package/lib/RcsbGraphQL/RcsbQueryEntryInstances.js +0 -1
  169. package/lib/RcsbGraphQL/RcsbQueryGroup.js +0 -1
  170. package/lib/RcsbGraphQL/RcsbQueryInterfaceInstances.js +0 -1
  171. package/lib/RcsbGraphQL/RcsbQueryMultipleEntityInstances.js +0 -1
  172. package/lib/RcsbGraphQL/RcsbQueryMultipleEntriesProperties.js +0 -1
  173. package/lib/RcsbGraphQL/RcsbQueryMultipleInstanceSequences.js +0 -1
  174. package/lib/RcsbGroupWeb/RcsbGroupBuilder.js +0 -1
  175. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartAdditionalProperties.js +0 -1
  176. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartEvents.js +0 -1
  177. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartLayout.d.ts +2 -2
  178. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartLayout.js +0 -1
  179. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartTools.js +0 -1
  180. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.d.ts +2 -2
  181. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.js +0 -1
  182. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbStatsChartComponent.d.ts +2 -2
  183. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbStatsChartComponent.js +0 -1
  184. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupContent/RcsbGroupContentComponent.js +0 -1
  185. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupDisplay.js +0 -1
  186. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/Components/Slider.d.ts +2 -2
  187. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/Components/Slider.js +0 -1
  188. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js +1 -2
  189. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.d.ts +2 -2
  190. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.js +0 -1
  191. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/RcsbGroupMembersComponent.d.ts +2 -2
  192. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/RcsbGroupMembersComponent.js +0 -1
  193. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.d.ts +1 -2
  194. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.js +0 -1
  195. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/SearchQueryContextManager.js +0 -1
  196. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.d.ts +2 -2
  197. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.js +0 -1
  198. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory.js +0 -1
  199. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/MultipleTrackDistributionFactory.js +0 -1
  200. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/NumericalTrackDistributionFactory.js +0 -1
  201. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory.js +0 -1
  202. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryInterface.js +0 -1
  203. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory.js +0 -1
  204. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/Helper.js +0 -1
  205. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.js +2 -3
  206. package/lib/RcsbQueries/Borrego/.graphqlconfig +15 -0
  207. package/lib/RcsbQueries/Borrego/QueryAlignments.graphql +3 -3
  208. package/lib/RcsbQueries/Borrego/QueryAnnotations.graphql +1 -7
  209. package/lib/RcsbQueries/Borrego/QueryGroupAlignments.graphql +29 -24
  210. package/lib/RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql +28 -22
  211. package/lib/RcsbQueries/Borrego/QueryGroupAnnotations.graphql +2 -6
  212. package/lib/RcsbQueries/Borrego/schema.graphql +163 -376
  213. package/lib/RcsbQueries/QueryCheck.js +0 -1
  214. package/lib/RcsbRequest/RcsbRequestClient.js +0 -1
  215. package/lib/RcsbRequest/RcsbRequestContextManager.d.ts +3 -3
  216. package/lib/RcsbRequest/RcsbRequestContextManager.js +0 -1
  217. package/lib/RcsbRequest/RcsbRequestTools.js +12 -15
  218. package/lib/RcsbSeacrh/FacetStore/DepositionGroupFacetStore.js +0 -1
  219. package/lib/RcsbSeacrh/FacetStore/EntityGranularitySearchFacetStore.js +0 -1
  220. package/lib/RcsbSeacrh/FacetStore/FacetMemberInterface.js +0 -1
  221. package/lib/RcsbSeacrh/FacetStore/FacetStoreInterface.js +0 -1
  222. package/lib/RcsbSeacrh/FacetStore/SequenceGroupFacetStore.js +0 -1
  223. package/lib/RcsbSeacrh/FacetStore/SingleFacets.js +0 -1
  224. package/lib/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.js +0 -1
  225. package/lib/RcsbSeacrh/FacetTools.js +0 -1
  226. package/lib/RcsbSeacrh/SearchQueryTools.js +0 -1
  227. package/lib/RcsbSeacrh/SearchRequestProperty.js +0 -1
  228. package/lib/RcsbServerConfig/ServerConfig.js +0 -1
  229. package/lib/RcsbServerConfig/codegen.borrego.json +1 -1
  230. package/lib/RcsbUtils/Groups/GroupGapLessTransformer.d.ts +3 -3
  231. package/lib/RcsbUtils/Groups/GroupGapLessTransformer.js +21 -11
  232. package/lib/RcsbUtils/Groups/GroupPropertiesProvider.js +0 -1
  233. package/lib/RcsbUtils/Groups/GroupProvenanceToAggregationType.js +0 -1
  234. package/lib/RcsbUtils/Helpers/Assertions.js +0 -1
  235. package/lib/RcsbUtils/Helpers/DataContainer.js +0 -1
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  466. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js.map +0 -1
  467. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js.map +0 -1
  468. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.js.map +0 -1
  469. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js.map +0 -1
  470. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.js.map +0 -1
  471. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.js.map +0 -1
  472. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.js.map +0 -1
  473. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.js.map +0 -1
  474. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.js.map +0 -1
  475. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvPairwiseAlignment.js.map +0 -1
  476. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js.map +0 -1
  477. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js.map +0 -1
  478. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js.map +0 -1
  479. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js.map +0 -1
  480. package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js.map +0 -1
  481. package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.js.map +0 -1
  482. package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.js.map +0 -1
  483. package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorWorker.worker.js.map +0 -1
  484. package/lib/RcsbGraphQL/RcsbClient.js.map +0 -1
  485. package/lib/RcsbGraphQL/RcsbCoreQueryInterface.js.map +0 -1
  486. package/lib/RcsbGraphQL/RcsbQueryAlignment.js.map +0 -1
  487. package/lib/RcsbGraphQL/RcsbQueryAnnotations.js.map +0 -1
  488. package/lib/RcsbGraphQL/RcsbQueryAssemblyInterfaces.js.map +0 -1
  489. package/lib/RcsbGraphQL/RcsbQueryEntryInstances.js.map +0 -1
  490. package/lib/RcsbGraphQL/RcsbQueryGroup.js.map +0 -1
  491. package/lib/RcsbGraphQL/RcsbQueryInterfaceInstances.js.map +0 -1
  492. package/lib/RcsbGraphQL/RcsbQueryMultipleEntityInstances.js.map +0 -1
  493. package/lib/RcsbGraphQL/RcsbQueryMultipleEntriesProperties.js.map +0 -1
  494. package/lib/RcsbGraphQL/RcsbQueryMultipleInstanceSequences.js.map +0 -1
  495. package/lib/RcsbGroupWeb/RcsbGroupBuilder.js.map +0 -1
  496. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartAdditionalProperties.js.map +0 -1
  497. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartEvents.js.map +0 -1
  498. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartLayout.js.map +0 -1
  499. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartTools.js.map +0 -1
  500. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.js.map +0 -1
  501. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbStatsChartComponent.js.map +0 -1
  502. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupContent/RcsbGroupContentComponent.js.map +0 -1
  503. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupDisplay.js.map +0 -1
  504. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/Components/Slider.js.map +0 -1
  505. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js.map +0 -1
  506. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.js.map +0 -1
  507. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/RcsbGroupMembersComponent.js.map +0 -1
  508. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/icons/bxs-cube.svg +0 -1
  509. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.js.map +0 -1
  510. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/SearchQueryContextManager.js.map +0 -1
  511. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.js.map +0 -1
  512. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory.js.map +0 -1
  513. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/MultipleTrackDistributionFactory.js.map +0 -1
  514. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/NumericalTrackDistributionFactory.js.map +0 -1
  515. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory.js.map +0 -1
  516. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryInterface.js.map +0 -1
  517. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory.js.map +0 -1
  518. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/Helper.js.map +0 -1
  519. package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.js.map +0 -1
  520. package/lib/RcsbQueries/Borrego/QueryGroupAnnotationsSummary.graphql +0 -35
  521. package/lib/RcsbQueries/Borrego/graphql.config.yml +0 -8
  522. package/lib/RcsbQueries/QueryCheck.js.map +0 -1
  523. package/lib/RcsbRequest/RcsbRequestClient.js.map +0 -1
  524. package/lib/RcsbRequest/RcsbRequestContextManager.js.map +0 -1
  525. package/lib/RcsbRequest/RcsbRequestTools.js.map +0 -1
  526. package/lib/RcsbSeacrh/FacetStore/DepositionGroupFacetStore.js.map +0 -1
  527. package/lib/RcsbSeacrh/FacetStore/EntityGranularitySearchFacetStore.js.map +0 -1
  528. package/lib/RcsbSeacrh/FacetStore/FacetMemberInterface.js.map +0 -1
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  531. package/lib/RcsbSeacrh/FacetStore/SingleFacets.js.map +0 -1
  532. package/lib/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.js.map +0 -1
  533. package/lib/RcsbSeacrh/FacetTools.js.map +0 -1
  534. package/lib/RcsbSeacrh/SearchQueryTools.js.map +0 -1
  535. package/lib/RcsbSeacrh/SearchRequestProperty.js.map +0 -1
  536. package/lib/RcsbServerConfig/ServerConfig.js.map +0 -1
  537. package/lib/RcsbUtils/Groups/GroupGapLessTransformer.js.map +0 -1
  538. package/lib/RcsbUtils/Groups/GroupPropertiesProvider.js.map +0 -1
  539. package/lib/RcsbUtils/Groups/GroupProvenanceToAggregationType.js.map +0 -1
  540. package/lib/RcsbUtils/Helpers/Assertions.js.map +0 -1
  541. package/lib/RcsbUtils/Helpers/DataContainer.js.map +0 -1
  542. package/lib/RcsbUtils/Helpers/ObservableHelper.js.map +0 -1
  543. package/lib/RcsbUtils/Helpers/Operator.js.map +0 -1
  544. package/lib/RcsbUtils/Helpers/SingletonMap.js.map +0 -1
  545. package/lib/RcsbUtils/Helpers/UrlTools.js.map +0 -1
  546. package/lib/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.js.map +0 -1
  547. package/lib/RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder.js.map +0 -1
  548. package/lib/RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite.js.map +0 -1
  549. package/lib/RcsbUtils/TrackGenerators/BurialFraction.js.map +0 -1
  550. package/lib/RcsbUtils/TrackGenerators/BuriedResidues.js.map +0 -1
  551. package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js.map +0 -1
  552. package/lib/RcsbUtils/TrackGenerators/Logo.js.map +0 -1
  553. package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.js.map +0 -1
  554. package/lib/RcsbUtils/Translators/AssemblyInterfacesTranslate.js.map +0 -1
  555. package/lib/RcsbUtils/Translators/EntryAssemblyTranslate.js.map +0 -1
  556. package/lib/RcsbUtils/Translators/InterfaceInstanceTranslate.js.map +0 -1
  557. package/lib/RcsbUtils/Translators/MultipleEntityInstanceTranslate.js.map +0 -1
  558. package/lib/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.js.map +0 -1
  559. package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.js.map +0 -1
  560. package/lib/app.js.map +0 -1
  561. package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/icons/bxs-cube.svg +0 -1
  562. package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAnnotationsSummary.graphql +0 -35
  563. package/lib/commonjs/RcsbQueries/Borrego/graphql.config.yml +0 -8
  564. package/lib/constants.js.map +0 -1
  565. package/lib/plot.js.map +0 -1
  566. package/lib/tsconfig.commonjs.tsbuildinfo +0 -1
@@ -20,20 +20,18 @@ var RcsbRequestTools;
20
20
  if (!Array.isArray(ids))
21
21
  ids = [ids];
22
22
  const missing = ids.filter(id => !map.has(id));
23
- if (missing.length > 0) {
24
- const collectorPromise = collector.collect({ [collectorKey]: missing });
25
- missing.forEach(id => {
26
- map.set(id, new Promise((resolve, reject) => {
27
- collectorPromise.then(t => {
28
- const d = t.find(t => propertyKey(t) == id);
29
- if (d)
30
- resolve(d);
31
- else
32
- reject(`${id} not available`);
33
- });
34
- }));
35
- });
36
- }
23
+ const collectorPromise = collector.collect({ [collectorKey]: missing });
24
+ missing.forEach(id => {
25
+ map.set(id, new Promise((resolve, reject) => {
26
+ collectorPromise.then(t => {
27
+ const d = t.find(t => propertyKey(t) == id);
28
+ if (d)
29
+ resolve(d);
30
+ else
31
+ reject(`${id} not available`);
32
+ });
33
+ }));
34
+ });
37
35
  return Promise.all(ids.map(i => map.get(i)).filter((x) => typeof x !== undefined));
38
36
  });
39
37
  }
@@ -1,4 +1,4 @@
1
1
  {
2
- "schema": "https://sequence-coordinates.rcsb.org/graphql",
2
+ "schema": "https://1d-coordinates.rcsb.org/graphql",
3
3
  "documents": "src/RcsbQueries/Borrego/Query*.graphql"
4
4
  }
@@ -1,8 +1,8 @@
1
- import { SequenceAlignments, SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
1
+ import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
2
  export declare class GroupGapLessTransformer {
3
3
  private readonly gapLessReference;
4
4
  private refLength;
5
5
  private processAlignments;
6
- gapLessAlignments(alignments: SequenceAlignments): void;
7
- gapLessFeatures(annotations: Array<SequenceAnnotations>): void;
6
+ gapLessAlignments(alignments: AlignmentResponse): void;
7
+ gapLessFeatures(annotations: Array<AnnotationFeatures>): void;
8
8
  }
@@ -32,20 +32,31 @@ class GroupGapLessTransformer {
32
32
  this.refLength = newIndex - 1;
33
33
  }
34
34
  gapLessAlignments(alignments) {
35
- var _a, _b;
35
+ var _a, _b, _c, _d;
36
36
  this.processAlignments(alignments);
37
37
  if (this.gapLessReference.length == 0)
38
38
  return;
39
- (_a = alignments.target_alignments) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
40
- var _a;
41
- (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
42
- if (region === null || region === void 0 ? void 0 : region.query_begin)
43
- region.query_begin = this.gapLessReference[region.query_begin];
44
- if (region === null || region === void 0 ? void 0 : region.query_end)
45
- region.query_end = this.gapLessReference[region.query_end];
39
+ if (alignments.target_alignment)
40
+ (_a = alignments.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
41
+ var _a;
42
+ (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
43
+ if (region === null || region === void 0 ? void 0 : region.query_begin)
44
+ region.query_begin = this.gapLessReference[region.query_begin];
45
+ if (region === null || region === void 0 ? void 0 : region.query_end)
46
+ region.query_end = this.gapLessReference[region.query_end];
47
+ });
46
48
  });
47
- });
48
- alignments.alignment_logo = (_b = alignments.alignment_logo) === null || _b === void 0 ? void 0 : _b.filter((al, n) => this.gapLessReference[n + 1] != -1);
49
+ else
50
+ (_c = (_b = alignments.target_alignment_subset) === null || _b === void 0 ? void 0 : _b.edges) === null || _c === void 0 ? void 0 : _c.forEach(edge => {
51
+ var _a, _b;
52
+ (_b = (_a = edge === null || edge === void 0 ? void 0 : edge.node) === null || _a === void 0 ? void 0 : _a.aligned_regions) === null || _b === void 0 ? void 0 : _b.forEach(region => {
53
+ if (region === null || region === void 0 ? void 0 : region.query_begin)
54
+ region.query_begin = this.gapLessReference[region.query_begin];
55
+ if (region === null || region === void 0 ? void 0 : region.query_end)
56
+ region.query_end = this.gapLessReference[region.query_end];
57
+ });
58
+ });
59
+ alignments.alignment_logo = (_d = alignments.alignment_logo) === null || _d === void 0 ? void 0 : _d.filter((al, n) => this.gapLessReference[n + 1] != -1);
49
60
  if (alignments.alignment_length)
50
61
  alignments.alignment_length = this.refLength;
51
62
  }
@@ -1,4 +1,4 @@
1
- import { SequenceAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
1
+ import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
2
  type AlignmentRefType = (number | undefined)[];
3
3
  export declare class AlignmentReference {
4
4
  private readonly alignmentRefMap;
@@ -7,7 +7,7 @@ export declare class AlignmentReference {
7
7
  private readonly memberRefList;
8
8
  constructor(refId: string, targetId: string, alignment: AlignmentRefType, target: AlignmentRefType);
9
9
  addAlignment(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void;
10
- buildAlignments(): SequenceAlignments;
10
+ buildAlignments(): AlignmentResponse;
11
11
  private addRef;
12
12
  private addEnd;
13
13
  private addBeg;
@@ -96,14 +96,14 @@ class AlignmentReference {
96
96
  exports.AlignmentReference = AlignmentReference;
97
97
  function buildAlignments(refId, alignmentRefMap, alignmentMembers) {
98
98
  const out = {};
99
- out.target_alignments = [];
100
- out.target_alignments.push({
99
+ out.target_alignment = [];
100
+ out.target_alignment.push({
101
101
  aligned_regions: buildRegions(alignmentRefMap),
102
102
  target_id: refId
103
103
  });
104
104
  alignmentMembers.forEach(am => {
105
105
  var _a;
106
- (_a = out.target_alignments) === null || _a === void 0 ? void 0 : _a.push({
106
+ (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.push({
107
107
  target_id: am.id,
108
108
  aligned_regions: buildRegions(am.map.map((v, n) => typeof v === "number" ? am.target[v] : undefined))
109
109
  });
@@ -66,33 +66,35 @@ function alignmentGlobalLigandBindingSite() {
66
66
  var _a;
67
67
  if (d)
68
68
  (_a = d.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(p => {
69
- var _a, _b;
70
- if (p === null || p === void 0 ? void 0 : p.beg_seq_id) {
71
- const key = (p.beg_seq_id).toString();
72
- if (!ligandMap.has(key))
73
- ligandMap.set(key, new Set());
74
- else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
75
- (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
76
- else
77
- return;
78
- const bs = bindingSiteMap.get(key);
79
- if (!bs) {
80
- bindingSiteMap.set(key, {
81
- begin: p.beg_seq_id,
82
- type: trackName,
83
- value: 1
84
- });
85
- if (max == 0)
86
- max = 1;
87
- }
88
- else {
89
- if (bs) {
90
- bs.value += 1;
91
- if (bs.value > max)
92
- max = bs.value;
69
+ var _a;
70
+ if (p === null || p === void 0 ? void 0 : p.beg_seq_id)
71
+ (_a = p.values) === null || _a === void 0 ? void 0 : _a.forEach((v, n) => {
72
+ var _a, _b;
73
+ const key = (p.beg_seq_id + n).toString();
74
+ if (!ligandMap.has(key))
75
+ ligandMap.set(key, new Set());
76
+ else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
77
+ (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
78
+ else
79
+ return;
80
+ const bs = bindingSiteMap.get(key);
81
+ if (!bs) {
82
+ bindingSiteMap.set(key, {
83
+ begin: p.beg_seq_id + n,
84
+ type: trackName,
85
+ value: 1
86
+ });
87
+ if (max == 0)
88
+ max = 1;
93
89
  }
94
- }
95
- }
90
+ else {
91
+ if (bs) {
92
+ bs.value += 1;
93
+ if (bs.value > max)
94
+ max = bs.value;
95
+ }
96
+ }
97
+ });
96
98
  });
97
99
  });
98
100
  });
@@ -1,3 +1,3 @@
1
- import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
- export declare function burialFraction(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
3
- export declare function burialFractionFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
1
+ import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
+ export declare function burialFraction(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
3
+ export declare function burialFractionFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
@@ -9,12 +9,12 @@ function burialFraction(annotations) {
9
9
  const burialFractionOut = new Array();
10
10
  const asaUnboundAnn = (0, lodash_1.cloneDeep)(annotations).map(ann => {
11
11
  var _a;
12
- ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.AsaUnbound));
12
+ ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === GqlTypes_1.Type.AsaUnbound));
13
13
  return ann;
14
14
  }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
15
15
  const asaBoundAnn = (0, lodash_1.cloneDeep)(annotations).map(ann => {
16
16
  var _a;
17
- ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.AsaBound));
17
+ ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === GqlTypes_1.Type.AsaBound));
18
18
  return ann;
19
19
  }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
20
20
  asaUnboundAnn.forEach((asaUnbound) => {
@@ -60,7 +60,7 @@ function burialFraction(annotations) {
60
60
  function burialFractionFilter(annotations) {
61
61
  return (0, lodash_1.cloneDeep)(annotations).map(ann => {
62
62
  var _a;
63
- ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== GqlTypes_1.AnnotationReference.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.BurialFraction));
63
+ ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== GqlTypes_1.Source.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.BurialFraction));
64
64
  return ann;
65
65
  }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
66
66
  }
@@ -1,3 +1,3 @@
1
- import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
- export declare function buriedResidues(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
3
- export declare function buriedResiduesFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
1
+ import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
+ export declare function buriedResidues(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
3
+ export declare function buriedResiduesFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
@@ -11,11 +11,11 @@ function buriedResidues(annotations) {
11
11
  let buriedResidues = {};
12
12
  let nBuried = 0;
13
13
  mainloop: for (const ann of annotations) {
14
- if (ann.source === GqlTypes_1.AnnotationReference.PdbInstance) {
14
+ if (ann.source === GqlTypes_1.Source.PdbInstance) {
15
15
  for (const f of (_a = ann.features) !== null && _a !== void 0 ? _a : []) {
16
- if ((f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.Asa) {
16
+ if ((f === null || f === void 0 ? void 0 : f.type) === GqlTypes_1.Type.Asa) {
17
17
  buriedResidues = (0, lodash_1.cloneDeep)(ann);
18
- buriedResidues.source = GqlTypes_1.AnnotationReference.PdbInstance;
18
+ buriedResidues.source = GqlTypes_1.Source.PdbInstance;
19
19
  const feature = (0, lodash_1.cloneDeep)(f);
20
20
  feature.type = FeatureType_1.FeatureType.BuriedResidues;
21
21
  feature.name = "Unbound chain core residues";
@@ -45,7 +45,7 @@ function buriedResidues(annotations) {
45
45
  function buriedResiduesFilter(annotations) {
46
46
  return (0, lodash_1.cloneDeep)(annotations).map(ann => {
47
47
  var _a;
48
- ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== FeatureType_1.FeatureType.Asa));
48
+ ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== GqlTypes_1.Type.Asa));
49
49
  return ann;
50
50
  }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
51
51
  }
@@ -1,4 +1,4 @@
1
- import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
1
+ import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
2
2
  import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
3
3
  import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
4
4
  import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
@@ -6,9 +6,9 @@ export declare function addUnmodeledTrackBuilder(unmodeledTrackBuilder: Unmodele
6
6
  export declare class UnmodeledTrackBuilder {
7
7
  private readonly unmodeledDescription;
8
8
  filterFeatures(data: {
9
- annotations: Array<SequenceAnnotations>;
9
+ annotations: Array<AnnotationFeatures>;
10
10
  rcsbContext?: Partial<PolymerEntityInstanceInterface>;
11
- }): Promise<Array<SequenceAnnotations>>;
11
+ }): Promise<Array<AnnotationFeatures>>;
12
12
  getTooltip(): RcsbFvTooltipInterface;
13
13
  private buildUnobserved;
14
14
  }
@@ -47,10 +47,10 @@ class UnmodeledTrackBuilder {
47
47
  const nInstances = (yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntityProperties((_a = rcsbContext.entityId) !== null && _a !== void 0 ? _a : "none"))[0].instances.length;
48
48
  const featurePositions = Array.from(annotations.filter(ann => {
49
49
  var _a, _b, _c;
50
- return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.FeaturesType.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
50
+ return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.Type.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
51
51
  }).map(ann => {
52
52
  var _a, _b;
53
- return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.FeaturesType.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
53
+ return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.Type.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
54
54
  }).flat().map(feature => {
55
55
  var _a, _b;
56
56
  return (_b = (_a = feature.feature_positions) === null || _a === void 0 ? void 0 : _a.filter((p) => typeof p != "undefined")) !== null && _b !== void 0 ? _b : [];
@@ -62,7 +62,7 @@ class UnmodeledTrackBuilder {
62
62
  };
63
63
  });
64
64
  return [{
65
- source: GqlTypes_1.AnnotationReference.PdbEntity,
65
+ source: GqlTypes_1.Source.PdbEntity,
66
66
  target_id: rcsbContext.entityId,
67
67
  features: [{
68
68
  type: UNMODELED,
@@ -99,7 +99,7 @@ class UnobservedToolTip {
99
99
  function filterUnobserved(annotations) {
100
100
  return annotations.map(ann => {
101
101
  var _a;
102
- return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != GqlTypes_1.FeaturesType.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != GqlTypes_1.FeaturesType.UnobservedAtomXyz) });
102
+ return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != GqlTypes_1.Type.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != GqlTypes_1.Type.UnobservedAtomXyz) });
103
103
  });
104
104
  }
105
105
  const UNMODELED = "UNMODELED";
@@ -1,11 +1,11 @@
1
1
  import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
2
2
  import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
3
- import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
3
+ import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
4
4
  export interface AlignmentContextInterface {
5
5
  queryId: string;
6
6
  targetId: string;
7
7
  from: SequenceReference | undefined;
8
- to: SequenceReference | AnnotationReference | undefined;
8
+ to: SequenceReference | Source | undefined;
9
9
  targetSequenceLength?: number;
10
10
  querySequenceLength?: number;
11
11
  }
@@ -70,7 +70,7 @@ class PolymerEntityInstanceTranslate {
70
70
  const authResIds = this.instanceAuthResIds.get(asymId);
71
71
  if (!authResIds)
72
72
  return out;
73
- if (reference === GqlTypes_1.SequenceReference.PdbInstance || (reference === GqlTypes_1.SequenceReference.PdbEntity && source === GqlTypes_1.AnnotationReference.PdbInstance)) {
73
+ if (reference === GqlTypes_1.SequenceReference.PdbInstance || (reference === GqlTypes_1.SequenceReference.PdbEntity && source === GqlTypes_1.Source.PdbInstance)) {
74
74
  const x = authResIds[e.begin - 1];
75
75
  if (typeof e.end === "number" && authResIds[e.end - 1] != x) {
76
76
  out.beginName = x;
@@ -80,7 +80,7 @@ class PolymerEntityInstanceTranslate {
80
80
  out.beginName = x;
81
81
  }
82
82
  }
83
- else if (source === GqlTypes_1.AnnotationReference.PdbInstance && e.oriBegin) {
83
+ else if (source === GqlTypes_1.Source.PdbInstance && e.oriBegin) {
84
84
  const x = authResIds[e.oriBegin - 1];
85
85
  if (typeof e.oriEnd === "number" && authResIds[e.oriEnd - 1] != x) {
86
86
  out.oriBeginName = x;
package/lib/constants.js CHANGED
@@ -1,2 +1 @@
1
1
  export { SearchFacets } from "./RcsbSeacrh/FacetStore/SingleFacets";
2
- //# sourceMappingURL=constants.js.map
package/lib/plot.js CHANGED
@@ -1,3 +1,2 @@
1
1
  export { buildSearchRequest, buildGroup, buildGroupMembers, buildGroupContent, buildResidueDistribution, searchQueryContextManager } from "./RcsbGroupWeb/RcsbGroupBuilder";
2
2
  export { rcsbRequestCtxManager as RcsbRequestContextManager } from "./RcsbRequest/RcsbRequestContextManager";
3
- //# sourceMappingURL=plot.js.map
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@rcsb/rcsb-saguaro-app",
3
- "version": "6.3.7-dev-js-seqcoord.14",
3
+ "version": "6.3.7-react-downgrade.1",
4
4
  "description": "RCSB 1D Saguaro Web App",
5
5
  "main": "build/app.js",
6
6
  "files": [
@@ -10,7 +10,7 @@
10
10
  "scripts": {
11
11
  "devServer": "webpack-dev-server --config webpack.server.dev.config.js",
12
12
  "buildAll": "npm run buildApp && npm run buildAllDoc",
13
- "buildOnlyApp": "npm run build-tsc && npm run build-commonjs && npm run copyQueries && npm run copyCss && npm run copyIcons && npm run build && npm run copyConfig",
13
+ "buildOnlyApp": "npm run build-tsc && npm run build-commonjs && npm run copyQueries && npm run copyCss && npm run build && npm run copyConfig",
14
14
  "buildApp": "npm run clean && npm run checkQueries && npm run buildOnlyApp",
15
15
  "buildAppDev": "npm run clean && npm run checkQueries && npm run buildDev",
16
16
  "build": "webpack --config ./webpack.config.js",
@@ -20,14 +20,13 @@
20
20
  "copyYosemiteQueries": "ncp src/RcsbQueries/Yosemite lib/RcsbQueries/Yosemite && ncp src/RcsbQueries/Yosemite lib/commonjs/RcsbQueries/Yosemite",
21
21
  "copyConfig": "ncp lib/commonjs/RcsbServerConfig/ServerConfig.js build/config.js",
22
22
  "copyCss": "ncp src/scss lib/scss && ncp src/scss lib/commonjs/scss",
23
- "copyIcons": "ncp src/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/icons lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/icons && ncp src/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/icons lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/icons",
24
23
  "build-tsc": "tsc",
25
24
  "build-commonjs": "tsc --build tsconfig.commonjs.json",
26
25
  "clean": "del-cli lib && del-cli build",
27
26
  "buildDoc": "typedoc --excludeExternals --externalPattern \"**/node_modules/**\" --plugin typedoc-plugin-missing-exports --plugin typedoc-theme-hierarchy --theme hierarchy --entryPointStrategy expand ./src && sed -i '' '/---/d' docs/index.html",
28
27
  "cpExamples": "ncp examples docs/examples",
29
28
  "buildAllDoc": "npm run buildDoc && npm run cpExamples",
30
- "publishApp": "npm publish --tag dev-js-seqcoord",
29
+ "publishApp": "npm publish",
31
30
  "test": "echo \"Error: no test specified\" && exit 1"
32
31
  },
33
32
  "repository": {
@@ -51,58 +50,61 @@
51
50
  },
52
51
  "license": "MIT",
53
52
  "devDependencies": {
54
- "@babel/core": "^7.26.10",
55
- "@babel/preset-env": "^7.26.9",
53
+ "@babel/core": "^7.25.2",
54
+ "@babel/plugin-proposal-class-properties": "^7.18.6",
55
+ "@babel/preset-env": "^7.25.3",
56
56
  "@svgr/webpack": "^8.1.0",
57
- "@types/lodash": "^4.17.16",
57
+ "@types/lodash": "^4.17.7",
58
58
  "@types/lodash.range": "^3.2.9",
59
59
  "@types/object-hash": "^3.0.6",
60
- "@types/react": "^19.0.12",
61
- "@types/react-dom": "^19.0.4",
60
+ "@types/react": "^18.3.4",
61
+ "@types/react-dom": "^18.3.0",
62
62
  "@types/uniqid": "^5.3.4",
63
- "babel-loader": "^10.0.0",
63
+ "babel-loader": "^9.1.3",
64
64
  "bootstrap": "^5.3.3",
65
65
  "buffer": "^6.0.3",
66
- "crypto-browserify": "^3.12.1",
66
+ "crypto-browserify": "^3.12.0",
67
67
  "css-loader": "^7.1.2",
68
- "del-cli": "^6.0.0",
69
- "html-webpack-plugin": "^5.6.3",
68
+ "del-cli": "^5.1.0",
69
+ "graphql-request": "^6.1.0",
70
+ "html-webpack-plugin": "^5.6.0",
70
71
  "lodash": "^4.17.21",
71
72
  "ncp": "^2.0.0",
72
73
  "object-hash": "^3.0.0",
73
74
  "path-browserify": "^1.0.1",
74
75
  "raw-loader": "^4.0.2",
75
76
  "react-draggable": "^4.4.6",
76
- "sass": "^1.86.0",
77
- "sass-loader": "^16.0.5",
77
+ "sass": "^1.77.8",
78
+ "sass-loader": "^16.0.1",
78
79
  "stream-browserify": "^3.0.0",
79
80
  "style-loader": "^4.0.0",
80
- "ts-loader": "^9.5.2",
81
+ "ts-loader": "^9.5.1",
81
82
  "ts-node": "^10.9.2",
82
- "typedoc": "^0.27.9",
83
- "typedoc-plugin-missing-exports": "^3.1.0",
84
- "typedoc-theme-hierarchy": "^5.0.4",
85
- "typescript": "^5.8.2",
83
+ "typedoc": "^0.26.6",
84
+ "typedoc-plugin-missing-exports": "^3.0.0",
85
+ "typedoc-theme-hierarchy": "^5.0.3",
86
+ "typescript": "^5.5.4",
86
87
  "uniqid": "^5.4.0",
87
- "webpack": "^5.98.0",
88
- "webpack-cli": "^6.0.1",
89
- "webpack-dev-server": "^5.2.0",
88
+ "webpack": "^5.93.0",
89
+ "webpack-cli": "^5.1.4",
90
+ "webpack-dev-server": "^5.0.4",
90
91
  "worker-loader": "^3.0.8"
91
92
  },
92
93
  "dependencies": {
93
- "@rcsb/rcsb-charts": "^0.2.26",
94
- "@rcsb/rcsb-saguaro": "^3.1.6",
94
+ "@rcsb/rcsb-charts": "^0.2.24",
95
+ "@rcsb/rcsb-saguaro": "^3.1.6-react-downgrade.1",
95
96
  "@rcsb/rcsb-search-tools": "^0.0.14",
96
- "ideogram": "^1.50.0",
97
- "react-bootstrap": "^2.10.9",
98
- "react-select": "^5.10.1",
99
- "rxjs": "^7.8.2",
97
+ "ideogram": "^1.47.0",
98
+ "react-bootstrap": "^2.10.4",
99
+ "react-select": "^5.8.0",
100
+ "rxjs": "^7.8.1",
100
101
  "string-to-color": "^2.2.2"
101
102
  },
102
103
  "peerDependencies": {
103
- "@rcsb/rcsb-api-tools": "^5.0.0-dev-js-seqcoord.3",
104
- "react": "^19.0.0",
105
- "react-dom": "^19.0.0"
104
+ "@rcsb/rcsb-api-tools": "^4.3.0",
105
+ "boxicons": "^2.1.4",
106
+ "react": "^18.3.1",
107
+ "react-dom": "^18.3.1"
106
108
  },
107
109
  "bugs": {
108
110
  "url": "https://github.com/rcsb/rcsb-saguaro-app/issues"
@@ -1 +0,0 @@
1
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