jbrowse-plugin-protein3d 0.0.3 → 0.0.5

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 (196) hide show
  1. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +3 -9
  2. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
  3. package/dist/AddHighlightModel/HighlightComponents.d.ts +1 -2
  4. package/dist/AddHighlightModel/HighlightComponents.js.map +1 -1
  5. package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js +4 -3
  6. package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js.map +1 -1
  7. package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.d.ts +1 -2
  8. package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js +4 -3
  9. package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js.map +1 -1
  10. package/dist/AddHighlightModel/util.js +1 -1
  11. package/dist/AddHighlightModel/util.js.map +1 -1
  12. package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.d.ts +16 -0
  13. package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js +43 -0
  14. package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js.map +1 -0
  15. package/dist/AlphaFoldConfidenceAdapter/configSchema.d.ts +13 -0
  16. package/dist/AlphaFoldConfidenceAdapter/configSchema.js +16 -0
  17. package/dist/AlphaFoldConfidenceAdapter/configSchema.js.map +1 -0
  18. package/dist/AlphaFoldConfidenceAdapter/index.d.ts +2 -0
  19. package/dist/AlphaFoldConfidenceAdapter/index.js +11 -0
  20. package/dist/AlphaFoldConfidenceAdapter/index.js.map +1 -0
  21. package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.d.ts +30 -0
  22. package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js +78 -0
  23. package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js.map +1 -0
  24. package/dist/AlphaMissensePathogenicityAdapter/configSchema.d.ts +13 -0
  25. package/dist/AlphaMissensePathogenicityAdapter/configSchema.js +16 -0
  26. package/dist/AlphaMissensePathogenicityAdapter/configSchema.js.map +1 -0
  27. package/dist/AlphaMissensePathogenicityAdapter/index.d.ts +2 -0
  28. package/dist/AlphaMissensePathogenicityAdapter/index.js +11 -0
  29. package/dist/AlphaMissensePathogenicityAdapter/index.js.map +1 -0
  30. package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js +162 -13
  31. package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js.map +1 -1
  32. package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js +8 -6
  33. package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js.map +1 -1
  34. package/dist/LaunchProteinView/components/HelpButton.js +6 -2
  35. package/dist/LaunchProteinView/components/HelpButton.js.map +1 -1
  36. package/dist/LaunchProteinView/components/HelpDialog.js +3 -1
  37. package/dist/LaunchProteinView/components/HelpDialog.js.map +1 -1
  38. package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js +12 -4
  39. package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js.map +1 -1
  40. package/dist/LaunchProteinView/components/MSATable.js +3 -1
  41. package/dist/LaunchProteinView/components/MSATable.js.map +1 -1
  42. package/dist/LaunchProteinView/components/ManualUniProtIDEntry.d.ts +8 -0
  43. package/dist/LaunchProteinView/components/ManualUniProtIDEntry.js +225 -0
  44. package/dist/LaunchProteinView/components/ManualUniProtIDEntry.js.map +1 -0
  45. package/dist/LaunchProteinView/components/TranscriptSelector.js +3 -1
  46. package/dist/LaunchProteinView/components/TranscriptSelector.js.map +1 -1
  47. package/dist/LaunchProteinView/components/UserProvidedStructure.js +19 -12
  48. package/dist/LaunchProteinView/components/UserProvidedStructure.js.map +1 -1
  49. package/dist/LaunchProteinView/components/calculateProteinSequence.js +5 -3
  50. package/dist/LaunchProteinView/components/calculateProteinSequence.js.map +1 -1
  51. package/dist/LaunchProteinView/components/useLocalStructureFileSequence.d.ts +1 -1
  52. package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js +29 -9
  53. package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js.map +1 -1
  54. package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.d.ts +1 -1
  55. package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js +25 -8
  56. package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js.map +1 -1
  57. package/dist/LaunchProteinView/components/util.js +1 -1
  58. package/dist/LaunchProteinView/index.js +7 -3
  59. package/dist/LaunchProteinView/index.js.map +1 -1
  60. package/dist/ProteinView/{loadStructureFromData.d.ts → addStructureFromData.d.ts} +2 -2
  61. package/dist/ProteinView/{loadStructureFromData.js → addStructureFromData.js} +3 -8
  62. package/dist/ProteinView/addStructureFromData.js.map +1 -0
  63. package/dist/ProteinView/{loadStructureFromURL.d.ts → addStructureFromURL.d.ts} +2 -2
  64. package/dist/ProteinView/{loadStructureFromURL.js → addStructureFromURL.js} +11 -9
  65. package/dist/ProteinView/addStructureFromURL.js.map +1 -0
  66. package/dist/ProteinView/clearSelection.js +1 -1
  67. package/dist/ProteinView/clearSelection.js.map +1 -1
  68. package/dist/ProteinView/components/ProteinAlignment.d.ts +2 -2
  69. package/dist/ProteinView/components/ProteinAlignment.js +37 -26
  70. package/dist/ProteinView/components/ProteinAlignment.js.map +1 -1
  71. package/dist/ProteinView/components/ProteinAlignmentHelpButton.d.ts +2 -2
  72. package/dist/ProteinView/components/ProteinAlignmentHelpButton.js +6 -4
  73. package/dist/ProteinView/components/ProteinAlignmentHelpButton.js.map +1 -1
  74. package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js +6 -5
  75. package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js.map +1 -1
  76. package/dist/ProteinView/components/ProteinView.js +18 -60
  77. package/dist/ProteinView/components/ProteinView.js.map +1 -1
  78. package/dist/ProteinView/components/{Header.js → ProteinViewHeader.js} +29 -12
  79. package/dist/ProteinView/components/ProteinViewHeader.js.map +1 -0
  80. package/dist/ProteinView/components/SplitString.d.ts +4 -4
  81. package/dist/ProteinView/components/SplitString.js +3 -3
  82. package/dist/ProteinView/components/SplitString.js.map +1 -1
  83. package/dist/ProteinView/genomeToProtein.d.ts +2 -2
  84. package/dist/ProteinView/genomeToProtein.js +4 -5
  85. package/dist/ProteinView/genomeToProtein.js.map +1 -1
  86. package/dist/ProteinView/highlightResidue.js +2 -2
  87. package/dist/ProteinView/highlightResidue.js.map +1 -1
  88. package/dist/ProteinView/launchRemotePairwiseAlignment.d.ts +2 -5
  89. package/dist/ProteinView/launchRemotePairwiseAlignment.js +7 -3
  90. package/dist/ProteinView/launchRemotePairwiseAlignment.js.map +1 -1
  91. package/dist/ProteinView/model.d.ts +492 -160
  92. package/dist/ProteinView/model.js +62 -246
  93. package/dist/ProteinView/model.js.map +1 -1
  94. package/dist/ProteinView/proteinToGenomeMapping.d.ts +6 -6
  95. package/dist/ProteinView/proteinToGenomeMapping.js +29 -28
  96. package/dist/ProteinView/proteinToGenomeMapping.js.map +1 -1
  97. package/dist/ProteinView/selectResidue.js +1 -1
  98. package/dist/ProteinView/selectResidue.js.map +1 -1
  99. package/dist/ProteinView/structureModel.d.ts +183 -0
  100. package/dist/ProteinView/structureModel.js +407 -0
  101. package/dist/ProteinView/structureModel.js.map +1 -0
  102. package/dist/ProteinView/useProteinView.d.ts +1 -4
  103. package/dist/ProteinView/useProteinView.js +3 -15
  104. package/dist/ProteinView/useProteinView.js.map +1 -1
  105. package/dist/ProteinView/util.d.ts +3 -3
  106. package/dist/ProteinView/util.js +8 -6
  107. package/dist/ProteinView/util.js.map +1 -1
  108. package/dist/UniProtVariationAdapter/UniProtVariationAdapter.d.ts +15 -0
  109. package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js +55 -0
  110. package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js.map +1 -0
  111. package/dist/UniProtVariationAdapter/configSchema.d.ts +17 -0
  112. package/dist/UniProtVariationAdapter/configSchema.js +20 -0
  113. package/dist/UniProtVariationAdapter/configSchema.js.map +1 -0
  114. package/dist/UniProtVariationAdapter/index.d.ts +2 -0
  115. package/dist/UniProtVariationAdapter/index.js +11 -0
  116. package/dist/UniProtVariationAdapter/index.js.map +1 -0
  117. package/dist/genomeToTranscriptMapping.d.ts +2 -2
  118. package/dist/genomeToTranscriptMapping.js +3 -3
  119. package/dist/genomeToTranscriptMapping.js.map +1 -1
  120. package/dist/index.js +6 -0
  121. package/dist/index.js.map +1 -1
  122. package/dist/jbrowse-plugin-protein3d.umd.production.min.js +2506 -1658
  123. package/dist/jbrowse-plugin-protein3d.umd.production.min.js.map +4 -4
  124. package/dist/mappings.d.ts +12 -10
  125. package/dist/mappings.js +7 -7
  126. package/dist/mappings.js.map +1 -1
  127. package/dist/mappings.test.js +7 -5
  128. package/dist/mappings.test.js.map +1 -1
  129. package/dist/test_data/gene.d.ts +577 -64
  130. package/dist/test_data/gene.js +1 -1
  131. package/dist/test_data/gene.js.map +1 -1
  132. package/package.json +20 -19
  133. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +4 -17
  134. package/src/AddHighlightModel/HighlightComponents.tsx +1 -3
  135. package/src/AddHighlightModel/ProteinToGenomeClickHighlight.tsx +17 -14
  136. package/src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx +18 -17
  137. package/src/AddHighlightModel/util.ts +1 -1
  138. package/src/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.ts +63 -0
  139. package/src/AlphaFoldConfidenceAdapter/configSchema.ts +21 -0
  140. package/src/AlphaFoldConfidenceAdapter/index.ts +19 -0
  141. package/src/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.ts +109 -0
  142. package/src/AlphaMissensePathogenicityAdapter/configSchema.ts +21 -0
  143. package/src/AlphaMissensePathogenicityAdapter/index.ts +19 -0
  144. package/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx +173 -12
  145. package/src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx +8 -6
  146. package/src/LaunchProteinView/components/HelpButton.tsx +10 -2
  147. package/src/LaunchProteinView/components/HelpDialog.tsx +6 -1
  148. package/src/LaunchProteinView/components/LaunchProteinViewDialog.tsx +20 -4
  149. package/src/LaunchProteinView/components/MSATable.tsx +3 -1
  150. package/src/LaunchProteinView/components/ManualUniProtIDEntry.tsx +332 -0
  151. package/src/LaunchProteinView/components/TranscriptSelector.tsx +9 -7
  152. package/src/LaunchProteinView/components/UserProvidedStructure.tsx +18 -13
  153. package/src/LaunchProteinView/components/calculateProteinSequence.ts +6 -4
  154. package/src/LaunchProteinView/components/useLocalStructureFileSequence.ts +28 -9
  155. package/src/LaunchProteinView/components/useRemoteStructureFileSequence.ts +23 -8
  156. package/src/LaunchProteinView/components/util.ts +1 -1
  157. package/src/LaunchProteinView/index.ts +36 -26
  158. package/src/ProteinView/{loadStructureFromData.ts → addStructureFromData.ts} +2 -8
  159. package/src/ProteinView/{loadStructureFromURL.ts → addStructureFromURL.ts} +11 -11
  160. package/src/ProteinView/clearSelection.ts +1 -1
  161. package/src/ProteinView/components/ProteinAlignment.tsx +51 -35
  162. package/src/ProteinView/components/ProteinAlignmentHelpButton.tsx +4 -4
  163. package/src/ProteinView/components/ProteinAlignmentHelpDialog.tsx +15 -11
  164. package/src/ProteinView/components/ProteinView.tsx +22 -82
  165. package/src/ProteinView/components/{Header.tsx → ProteinViewHeader.tsx} +44 -23
  166. package/src/ProteinView/components/SplitString.tsx +8 -8
  167. package/src/ProteinView/genomeToProtein.ts +5 -9
  168. package/src/ProteinView/highlightResidue.ts +2 -2
  169. package/src/ProteinView/launchRemotePairwiseAlignment.ts +6 -3
  170. package/src/ProteinView/model.ts +75 -287
  171. package/src/ProteinView/proteinToGenomeMapping.ts +40 -38
  172. package/src/ProteinView/selectResidue.ts +1 -1
  173. package/src/ProteinView/structureModel.ts +512 -0
  174. package/src/ProteinView/useProteinView.ts +2 -19
  175. package/src/ProteinView/util.ts +20 -9
  176. package/src/UniProtVariationAdapter/UniProtVariationAdapter.ts +99 -0
  177. package/src/UniProtVariationAdapter/configSchema.ts +25 -0
  178. package/src/UniProtVariationAdapter/index.ts +17 -0
  179. package/src/__snapshots__/mappings.test.ts.snap +224 -224
  180. package/src/genomeToTranscriptMapping.ts +9 -9
  181. package/src/index.ts +6 -0
  182. package/src/mappings.test.ts +7 -5
  183. package/src/mappings.ts +25 -23
  184. package/src/test_data/gene.ts +3 -3
  185. package/dist/ProteinView/components/Header.js.map +0 -1
  186. package/dist/ProteinView/loadStructureFromData.js.map +0 -1
  187. package/dist/ProteinView/loadStructureFromURL.js.map +0 -1
  188. package/dist/ProteinView/useProteinViewClickBehavior.d.ts +0 -8
  189. package/dist/ProteinView/useProteinViewClickBehavior.js +0 -34
  190. package/dist/ProteinView/useProteinViewClickBehavior.js.map +0 -1
  191. package/dist/ProteinView/useProteinViewHoverBehavior.d.ts +0 -6
  192. package/dist/ProteinView/useProteinViewHoverBehavior.js +0 -31
  193. package/dist/ProteinView/useProteinViewHoverBehavior.js.map +0 -1
  194. package/src/ProteinView/useProteinViewClickBehavior.ts +0 -48
  195. package/src/ProteinView/useProteinViewHoverBehavior.ts +0 -44
  196. /package/dist/ProteinView/components/{Header.d.ts → ProteinViewHeader.d.ts} +0 -0

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