jbrowse-plugin-protein3d 0.0.2 → 0.0.4

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Files changed (220) hide show
  1. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +3 -9
  2. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
  3. package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js +4 -3
  4. package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js.map +1 -1
  5. package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.d.ts +1 -2
  6. package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js +4 -3
  7. package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js.map +1 -1
  8. package/dist/AddHighlightModel/util.js +1 -1
  9. package/dist/AddHighlightModel/util.js.map +1 -1
  10. package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.d.ts +16 -0
  11. package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js +43 -0
  12. package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js.map +1 -0
  13. package/dist/AlphaFoldConfidenceAdapter/configSchema.d.ts +13 -0
  14. package/dist/AlphaFoldConfidenceAdapter/configSchema.js +16 -0
  15. package/dist/AlphaFoldConfidenceAdapter/configSchema.js.map +1 -0
  16. package/dist/AlphaFoldConfidenceAdapter/index.d.ts +2 -0
  17. package/dist/AlphaFoldConfidenceAdapter/index.js +11 -0
  18. package/dist/AlphaFoldConfidenceAdapter/index.js.map +1 -0
  19. package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.d.ts +30 -0
  20. package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js +78 -0
  21. package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js.map +1 -0
  22. package/dist/AlphaMissensePathogenicityAdapter/configSchema.d.ts +13 -0
  23. package/dist/AlphaMissensePathogenicityAdapter/configSchema.js +16 -0
  24. package/dist/AlphaMissensePathogenicityAdapter/configSchema.js.map +1 -0
  25. package/dist/AlphaMissensePathogenicityAdapter/index.d.ts +2 -0
  26. package/dist/AlphaMissensePathogenicityAdapter/index.js +11 -0
  27. package/dist/AlphaMissensePathogenicityAdapter/index.js.map +1 -0
  28. package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js +201 -34
  29. package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js.map +1 -1
  30. package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.d.ts +7 -4
  31. package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js +35 -14
  32. package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js.map +1 -1
  33. package/dist/LaunchProteinView/components/HelpButton.js +6 -2
  34. package/dist/LaunchProteinView/components/HelpButton.js.map +1 -1
  35. package/dist/LaunchProteinView/components/HelpDialog.js +13 -4
  36. package/dist/LaunchProteinView/components/HelpDialog.js.map +1 -1
  37. package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js +9 -9
  38. package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js.map +1 -1
  39. package/dist/LaunchProteinView/components/MSATable.d.ts +10 -0
  40. package/dist/LaunchProteinView/components/MSATable.js +55 -0
  41. package/dist/LaunchProteinView/components/MSATable.js.map +1 -0
  42. package/dist/LaunchProteinView/components/TranscriptSelector.d.ts +7 -3
  43. package/dist/LaunchProteinView/components/TranscriptSelector.js +25 -8
  44. package/dist/LaunchProteinView/components/TranscriptSelector.js.map +1 -1
  45. package/dist/LaunchProteinView/components/UserProvidedStructure.js +67 -47
  46. package/dist/LaunchProteinView/components/UserProvidedStructure.js.map +1 -1
  47. package/dist/LaunchProteinView/{calculateProteinSequence.js → components/calculateProteinSequence.js} +5 -3
  48. package/dist/LaunchProteinView/components/calculateProteinSequence.js.map +1 -0
  49. package/dist/LaunchProteinView/components/useIsoformProteinSequences.d.ts +14 -0
  50. package/dist/LaunchProteinView/{useProteinSequences.js → components/useIsoformProteinSequences.js} +11 -6
  51. package/dist/LaunchProteinView/components/useIsoformProteinSequences.js.map +1 -0
  52. package/dist/LaunchProteinView/components/useLocalStructureFileSequence.d.ts +7 -0
  53. package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js +64 -0
  54. package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js.map +1 -0
  55. package/dist/LaunchProteinView/{useMyGeneInfo.d.ts → components/useMyGeneInfoUniprotIdLookup.d.ts} +2 -2
  56. package/dist/LaunchProteinView/{useMyGeneInfo.js → components/useMyGeneInfoUniprotIdLookup.js} +15 -10
  57. package/dist/LaunchProteinView/components/useMyGeneInfoUniprotIdLookup.js.map +1 -0
  58. package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.d.ts +7 -0
  59. package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js +59 -0
  60. package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js.map +1 -0
  61. package/dist/LaunchProteinView/{util.d.ts → components/util.d.ts} +0 -10
  62. package/dist/LaunchProteinView/{util.js → components/util.js} +4 -25
  63. package/dist/LaunchProteinView/components/util.js.map +1 -0
  64. package/dist/LaunchProteinView/index.js +6 -2
  65. package/dist/LaunchProteinView/index.js.map +1 -1
  66. package/dist/ProteinView/{loadStructureFromData.d.ts → addStructureFromData.d.ts} +2 -2
  67. package/dist/ProteinView/{loadStructureFromData.js → addStructureFromData.js} +3 -8
  68. package/dist/ProteinView/addStructureFromData.js.map +1 -0
  69. package/dist/ProteinView/{loadStructureFromURL.d.ts → addStructureFromURL.d.ts} +2 -2
  70. package/dist/ProteinView/{loadStructureFromURL.js → addStructureFromURL.js} +11 -9
  71. package/dist/ProteinView/addStructureFromURL.js.map +1 -0
  72. package/dist/ProteinView/clearSelection.js +1 -1
  73. package/dist/ProteinView/clearSelection.js.map +1 -1
  74. package/dist/ProteinView/components/ProteinAlignment.d.ts +2 -2
  75. package/dist/ProteinView/components/ProteinAlignment.js +37 -26
  76. package/dist/ProteinView/components/ProteinAlignment.js.map +1 -1
  77. package/dist/ProteinView/components/ProteinAlignmentHelpButton.d.ts +2 -2
  78. package/dist/ProteinView/components/ProteinAlignmentHelpButton.js +6 -4
  79. package/dist/ProteinView/components/ProteinAlignmentHelpButton.js.map +1 -1
  80. package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js +6 -5
  81. package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js.map +1 -1
  82. package/dist/ProteinView/components/ProteinView.js +18 -60
  83. package/dist/ProteinView/components/ProteinView.js.map +1 -1
  84. package/dist/ProteinView/components/{Header.js → ProteinViewHeader.js} +29 -12
  85. package/dist/ProteinView/components/ProteinViewHeader.js.map +1 -0
  86. package/dist/ProteinView/components/SplitString.d.ts +4 -4
  87. package/dist/ProteinView/components/SplitString.js +4 -4
  88. package/dist/ProteinView/components/SplitString.js.map +1 -1
  89. package/dist/ProteinView/genomeToProtein.d.ts +2 -2
  90. package/dist/ProteinView/genomeToProtein.js +4 -5
  91. package/dist/ProteinView/genomeToProtein.js.map +1 -1
  92. package/dist/ProteinView/highlightResidue.js +2 -2
  93. package/dist/ProteinView/highlightResidue.js.map +1 -1
  94. package/dist/ProteinView/launchRemotePairwiseAlignment.d.ts +2 -5
  95. package/dist/ProteinView/launchRemotePairwiseAlignment.js +7 -3
  96. package/dist/ProteinView/launchRemotePairwiseAlignment.js.map +1 -1
  97. package/dist/ProteinView/model.d.ts +496 -156
  98. package/dist/ProteinView/model.js +66 -225
  99. package/dist/ProteinView/model.js.map +1 -1
  100. package/dist/ProteinView/proteinToGenomeMapping.d.ts +6 -6
  101. package/dist/ProteinView/proteinToGenomeMapping.js +29 -28
  102. package/dist/ProteinView/proteinToGenomeMapping.js.map +1 -1
  103. package/dist/ProteinView/selectResidue.js +1 -1
  104. package/dist/ProteinView/selectResidue.js.map +1 -1
  105. package/dist/ProteinView/structureModel.d.ts +183 -0
  106. package/dist/ProteinView/structureModel.js +407 -0
  107. package/dist/ProteinView/structureModel.js.map +1 -0
  108. package/dist/ProteinView/useProteinView.d.ts +1 -4
  109. package/dist/ProteinView/useProteinView.js +3 -15
  110. package/dist/ProteinView/useProteinView.js.map +1 -1
  111. package/dist/ProteinView/util.d.ts +3 -3
  112. package/dist/ProteinView/util.js +8 -6
  113. package/dist/ProteinView/util.js.map +1 -1
  114. package/dist/UniProtVariationAdapter/UniProtVariationAdapter.d.ts +15 -0
  115. package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js +55 -0
  116. package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js.map +1 -0
  117. package/dist/UniProtVariationAdapter/configSchema.d.ts +17 -0
  118. package/dist/UniProtVariationAdapter/configSchema.js +20 -0
  119. package/dist/UniProtVariationAdapter/configSchema.js.map +1 -0
  120. package/dist/UniProtVariationAdapter/index.d.ts +2 -0
  121. package/dist/UniProtVariationAdapter/index.js +11 -0
  122. package/dist/UniProtVariationAdapter/index.js.map +1 -0
  123. package/dist/genomeToTranscriptMapping.d.ts +2 -2
  124. package/dist/genomeToTranscriptMapping.js +3 -3
  125. package/dist/genomeToTranscriptMapping.js.map +1 -1
  126. package/dist/index.js +6 -9
  127. package/dist/index.js.map +1 -1
  128. package/dist/jbrowse-plugin-protein3d.umd.production.min.js +1473 -1489
  129. package/dist/jbrowse-plugin-protein3d.umd.production.min.js.map +4 -4
  130. package/dist/mappings.d.ts +12 -10
  131. package/dist/mappings.js +7 -7
  132. package/dist/mappings.js.map +1 -1
  133. package/dist/mappings.test.js +7 -5
  134. package/dist/mappings.test.js.map +1 -1
  135. package/dist/test_data/gene.d.ts +577 -64
  136. package/dist/test_data/gene.js +1 -1
  137. package/dist/test_data/gene.js.map +1 -1
  138. package/package.json +17 -16
  139. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +4 -17
  140. package/src/AddHighlightModel/ProteinToGenomeClickHighlight.tsx +17 -14
  141. package/src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx +18 -17
  142. package/src/AddHighlightModel/util.ts +1 -1
  143. package/src/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.ts +63 -0
  144. package/src/AlphaFoldConfidenceAdapter/configSchema.ts +21 -0
  145. package/src/AlphaFoldConfidenceAdapter/index.ts +19 -0
  146. package/src/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.ts +109 -0
  147. package/src/AlphaMissensePathogenicityAdapter/configSchema.ts +21 -0
  148. package/src/AlphaMissensePathogenicityAdapter/index.ts +19 -0
  149. package/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx +266 -53
  150. package/src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx +71 -29
  151. package/src/LaunchProteinView/components/HelpButton.tsx +10 -2
  152. package/src/LaunchProteinView/components/HelpDialog.tsx +41 -8
  153. package/src/LaunchProteinView/components/LaunchProteinViewDialog.tsx +10 -12
  154. package/src/LaunchProteinView/components/MSATable.tsx +98 -0
  155. package/src/LaunchProteinView/components/TranscriptSelector.tsx +39 -11
  156. package/src/LaunchProteinView/components/UserProvidedStructure.tsx +119 -68
  157. package/src/LaunchProteinView/{calculateProteinSequence.ts → components/calculateProteinSequence.ts} +6 -4
  158. package/src/LaunchProteinView/{useProteinSequences.ts → components/useIsoformProteinSequences.ts} +12 -7
  159. package/src/LaunchProteinView/components/useLocalStructureFileSequence.ts +72 -0
  160. package/src/LaunchProteinView/{useMyGeneInfo.ts → components/useMyGeneInfoUniprotIdLookup.ts} +16 -11
  161. package/src/LaunchProteinView/components/useRemoteStructureFileSequence.ts +59 -0
  162. package/src/LaunchProteinView/{util.ts → components/util.ts} +4 -36
  163. package/src/LaunchProteinView/index.ts +36 -26
  164. package/src/ProteinView/{loadStructureFromData.ts → addStructureFromData.ts} +2 -8
  165. package/src/ProteinView/{loadStructureFromURL.ts → addStructureFromURL.ts} +11 -11
  166. package/src/ProteinView/clearSelection.ts +1 -1
  167. package/src/ProteinView/components/ProteinAlignment.tsx +51 -35
  168. package/src/ProteinView/components/ProteinAlignmentHelpButton.tsx +4 -4
  169. package/src/ProteinView/components/ProteinAlignmentHelpDialog.tsx +15 -11
  170. package/src/ProteinView/components/ProteinView.tsx +22 -82
  171. package/src/ProteinView/components/{Header.tsx → ProteinViewHeader.tsx} +44 -21
  172. package/src/ProteinView/components/SplitString.tsx +9 -9
  173. package/src/ProteinView/genomeToProtein.ts +5 -9
  174. package/src/ProteinView/highlightResidue.ts +2 -2
  175. package/src/ProteinView/launchRemotePairwiseAlignment.ts +6 -3
  176. package/src/ProteinView/model.ts +80 -265
  177. package/src/ProteinView/proteinToGenomeMapping.ts +40 -38
  178. package/src/ProteinView/selectResidue.ts +1 -1
  179. package/src/ProteinView/structureModel.ts +512 -0
  180. package/src/ProteinView/useProteinView.ts +2 -19
  181. package/src/ProteinView/util.ts +20 -9
  182. package/src/UniProtVariationAdapter/UniProtVariationAdapter.ts +99 -0
  183. package/src/UniProtVariationAdapter/configSchema.ts +25 -0
  184. package/src/UniProtVariationAdapter/index.ts +17 -0
  185. package/src/__snapshots__/mappings.test.ts.snap +224 -224
  186. package/src/genomeToTranscriptMapping.ts +9 -9
  187. package/src/index.ts +7 -12
  188. package/src/mappings.test.ts +7 -5
  189. package/src/mappings.ts +25 -23
  190. package/src/test_data/gene.ts +3 -3
  191. package/dist/LaunchProteinView/calculateProteinSequence.js.map +0 -1
  192. package/dist/LaunchProteinView/components/PreLoadedStructureMapping.d.ts +0 -8
  193. package/dist/LaunchProteinView/components/PreLoadedStructureMapping.js +0 -72
  194. package/dist/LaunchProteinView/components/PreLoadedStructureMapping.js.map +0 -1
  195. package/dist/LaunchProteinView/components/useCheckAlphaFoldDBExistence.d.ts +0 -7
  196. package/dist/LaunchProteinView/components/useCheckAlphaFoldDBExistence.js +0 -26
  197. package/dist/LaunchProteinView/components/useCheckAlphaFoldDBExistence.js.map +0 -1
  198. package/dist/LaunchProteinView/useMyGeneInfo.js.map +0 -1
  199. package/dist/LaunchProteinView/useProteinSequences.d.ts +0 -10
  200. package/dist/LaunchProteinView/useProteinSequences.js.map +0 -1
  201. package/dist/LaunchProteinView/util.js.map +0 -1
  202. package/dist/ProteinModelSessionExtension.d.ts +0 -11
  203. package/dist/ProteinModelSessionExtension.js +0 -53
  204. package/dist/ProteinModelSessionExtension.js.map +0 -1
  205. package/dist/ProteinView/components/Header.js.map +0 -1
  206. package/dist/ProteinView/loadStructureFromData.js.map +0 -1
  207. package/dist/ProteinView/loadStructureFromURL.js.map +0 -1
  208. package/dist/ProteinView/useProteinViewClickBehavior.d.ts +0 -8
  209. package/dist/ProteinView/useProteinViewClickBehavior.js +0 -34
  210. package/dist/ProteinView/useProteinViewClickBehavior.js.map +0 -1
  211. package/dist/ProteinView/useProteinViewHoverBehavior.d.ts +0 -6
  212. package/dist/ProteinView/useProteinViewHoverBehavior.js +0 -31
  213. package/dist/ProteinView/useProteinViewHoverBehavior.js.map +0 -1
  214. package/src/LaunchProteinView/components/PreLoadedStructureMapping.tsx +0 -153
  215. package/src/LaunchProteinView/components/useCheckAlphaFoldDBExistence.ts +0 -31
  216. package/src/ProteinModelSessionExtension.ts +0 -71
  217. package/src/ProteinView/useProteinViewClickBehavior.ts +0 -48
  218. package/src/ProteinView/useProteinViewHoverBehavior.ts +0 -44
  219. /package/dist/LaunchProteinView/{calculateProteinSequence.d.ts → components/calculateProteinSequence.d.ts} +0 -0
  220. /package/dist/ProteinView/components/{Header.d.ts → ProteinViewHeader.d.ts} +0 -0

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