jbrowse-plugin-msaview 2.4.4 → 2.5.0

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 (180) hide show
  1. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +2 -2
  2. package/dist/AddHighlightModel/HighlightComponents.js +0 -1
  3. package/dist/AddHighlightModel/MsaToGenomeHighlight.js +5 -3
  4. package/dist/AddHighlightModel/index.js +2 -2
  5. package/dist/AddHighlightModel/util.d.ts +1 -6
  6. package/dist/AddHighlightModel/util.js +1 -7
  7. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +0 -1
  8. package/dist/BgzipFastaMsaAdapter/configSchema.js +0 -1
  9. package/dist/BgzipFastaMsaAdapter/index.js +0 -1
  10. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +0 -1
  11. package/dist/LaunchMsaView/components/LaunchPanelContent.js +0 -1
  12. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +0 -1
  13. package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.js +0 -1
  14. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +0 -1
  15. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +0 -1
  16. package/dist/LaunchMsaView/components/NCBIBlastQuery/MsaAlgorithmSelect.js +0 -1
  17. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +0 -1
  18. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +0 -1
  19. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js +0 -1
  20. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js +0 -1
  21. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js +0 -1
  22. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js +0 -1
  23. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +0 -1
  24. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +0 -1
  25. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js +0 -1
  26. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +0 -1
  27. package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js +0 -1
  28. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js +0 -1
  29. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js +0 -1
  30. package/dist/LaunchMsaView/components/SubmitCancelActions.js +0 -1
  31. package/dist/LaunchMsaView/components/TabPanel.js +1 -2
  32. package/dist/LaunchMsaView/components/TranscriptSelector.js +0 -1
  33. package/dist/LaunchMsaView/components/calculateProteinSequence.js +0 -1
  34. package/dist/LaunchMsaView/components/fetchSeq.js +0 -1
  35. package/dist/LaunchMsaView/components/types.js +0 -1
  36. package/dist/LaunchMsaView/components/useFeatureSequence.js +0 -1
  37. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +0 -1
  38. package/dist/LaunchMsaView/components/useTranscriptSelection.js +0 -1
  39. package/dist/LaunchMsaView/components/util.js +0 -1
  40. package/dist/LaunchMsaView/index.js +0 -1
  41. package/dist/LaunchMsaView/util.js +1 -2
  42. package/dist/LaunchMsaViewExtensionPoint/index.js +0 -1
  43. package/dist/MsaViewPanel/afterCreateAutoruns.d.ts +8 -1
  44. package/dist/MsaViewPanel/afterCreateAutoruns.js +25 -21
  45. package/dist/MsaViewPanel/blosum62.js +0 -1
  46. package/dist/MsaViewPanel/components/ConnectStructureDialog.js +0 -1
  47. package/dist/MsaViewPanel/components/ErrorBoundary.d.ts +1 -1
  48. package/dist/MsaViewPanel/components/ErrorBoundary.js +0 -1
  49. package/dist/MsaViewPanel/components/LoadingBLAST.js +0 -1
  50. package/dist/MsaViewPanel/components/MsaViewPanel.js +0 -1
  51. package/dist/MsaViewPanel/components/RIDLink.js +0 -1
  52. package/dist/MsaViewPanel/doLaunchBlast.js +0 -1
  53. package/dist/MsaViewPanel/genomeToMSA.d.ts +0 -6
  54. package/dist/MsaViewPanel/genomeToMSA.js +8 -30
  55. package/dist/MsaViewPanel/genomeToMSA.test.js +0 -1
  56. package/dist/MsaViewPanel/index.js +0 -1
  57. package/dist/MsaViewPanel/model.d.ts +143 -514
  58. package/dist/MsaViewPanel/model.js +18 -61
  59. package/dist/MsaViewPanel/msaCoordToGenomeCoord.js +5 -22
  60. package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js +0 -1
  61. package/dist/MsaViewPanel/msaDataStore.js +0 -1
  62. package/dist/MsaViewPanel/pairwiseAlignment.js +2 -10
  63. package/dist/MsaViewPanel/pairwiseAlignment.test.js +0 -1
  64. package/dist/MsaViewPanel/structureConnection.d.ts +0 -6
  65. package/dist/MsaViewPanel/structureConnection.js +0 -17
  66. package/dist/MsaViewPanel/structureConnection.test.js +1 -52
  67. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.d.ts +1 -0
  68. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js +92 -0
  69. package/dist/MsaViewPanel/types.js +0 -1
  70. package/dist/MsaViewPanel/util.d.ts +1 -3
  71. package/dist/MsaViewPanel/util.js +1 -3
  72. package/dist/components/ExternalLink.js +0 -1
  73. package/dist/components/ReadOnlyTextField2.js +0 -1
  74. package/dist/components/TextField2.js +0 -1
  75. package/dist/index.js +0 -1
  76. package/dist/jbrowse-plugin-msaview.umd.production.min.js +40 -40
  77. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  78. package/dist/utils/blastCache.js +2 -5
  79. package/dist/utils/fetch.js +0 -1
  80. package/dist/utils/msa.js +9 -9
  81. package/dist/utils/ncbiBlast.js +5 -6
  82. package/dist/utils/swrConfig.js +0 -1
  83. package/dist/utils/taxonomyNames.js +0 -1
  84. package/dist/utils/types.js +0 -1
  85. package/dist/version.d.ts +1 -1
  86. package/dist/version.js +1 -2
  87. package/package.json +11 -11
  88. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +4 -1
  89. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +5 -8
  90. package/src/AddHighlightModel/index.tsx +4 -1
  91. package/src/AddHighlightModel/util.ts +1 -10
  92. package/src/LaunchMsaView/components/TabPanel.tsx +1 -1
  93. package/src/LaunchMsaView/util.ts +1 -3
  94. package/src/MsaViewPanel/afterCreateAutoruns.ts +24 -21
  95. package/src/MsaViewPanel/genomeToMSA.ts +10 -29
  96. package/src/MsaViewPanel/model.ts +21 -66
  97. package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +5 -21
  98. package/src/MsaViewPanel/pairwiseAlignment.ts +2 -7
  99. package/src/MsaViewPanel/structureConnection.test.ts +1 -61
  100. package/src/MsaViewPanel/structureConnection.ts +0 -22
  101. package/src/MsaViewPanel/syncGenomeHoverToMsaColumn.test.ts +112 -0
  102. package/src/MsaViewPanel/util.ts +3 -7
  103. package/src/utils/blastCache.ts +2 -4
  104. package/src/utils/msa.ts +10 -8
  105. package/src/utils/ncbiBlast.ts +5 -6
  106. package/src/version.ts +1 -1
  107. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +0 -1
  108. package/dist/AddHighlightModel/HighlightComponents.js.map +0 -1
  109. package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +0 -1
  110. package/dist/AddHighlightModel/index.js.map +0 -1
  111. package/dist/AddHighlightModel/util.js.map +0 -1
  112. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +0 -1
  113. package/dist/BgzipFastaMsaAdapter/configSchema.js.map +0 -1
  114. package/dist/BgzipFastaMsaAdapter/index.js.map +0 -1
  115. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +0 -1
  116. package/dist/LaunchMsaView/components/LaunchPanelContent.js.map +0 -1
  117. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +0 -1
  118. package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.js.map +0 -1
  119. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map +0 -1
  120. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +0 -1
  121. package/dist/LaunchMsaView/components/NCBIBlastQuery/MsaAlgorithmSelect.js.map +0 -1
  122. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +0 -1
  123. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +0 -1
  124. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js.map +0 -1
  125. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map +0 -1
  126. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map +0 -1
  127. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map +0 -1
  128. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +0 -1
  129. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +0 -1
  130. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map +0 -1
  131. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +0 -1
  132. package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js.map +0 -1
  133. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map +0 -1
  134. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map +0 -1
  135. package/dist/LaunchMsaView/components/SubmitCancelActions.js.map +0 -1
  136. package/dist/LaunchMsaView/components/TabPanel.js.map +0 -1
  137. package/dist/LaunchMsaView/components/TranscriptSelector.js.map +0 -1
  138. package/dist/LaunchMsaView/components/calculateProteinSequence.js.map +0 -1
  139. package/dist/LaunchMsaView/components/fetchSeq.js.map +0 -1
  140. package/dist/LaunchMsaView/components/types.js.map +0 -1
  141. package/dist/LaunchMsaView/components/useFeatureSequence.js.map +0 -1
  142. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +0 -1
  143. package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +0 -1
  144. package/dist/LaunchMsaView/components/util.js.map +0 -1
  145. package/dist/LaunchMsaView/index.js.map +0 -1
  146. package/dist/LaunchMsaView/util.js.map +0 -1
  147. package/dist/LaunchMsaViewExtensionPoint/index.js.map +0 -1
  148. package/dist/MsaViewPanel/afterCreateAutoruns.js.map +0 -1
  149. package/dist/MsaViewPanel/blosum62.js.map +0 -1
  150. package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +0 -1
  151. package/dist/MsaViewPanel/components/ErrorBoundary.js.map +0 -1
  152. package/dist/MsaViewPanel/components/LoadingBLAST.js.map +0 -1
  153. package/dist/MsaViewPanel/components/MsaViewPanel.js.map +0 -1
  154. package/dist/MsaViewPanel/components/RIDLink.js.map +0 -1
  155. package/dist/MsaViewPanel/doLaunchBlast.js.map +0 -1
  156. package/dist/MsaViewPanel/genomeToMSA.js.map +0 -1
  157. package/dist/MsaViewPanel/genomeToMSA.test.js.map +0 -1
  158. package/dist/MsaViewPanel/index.js.map +0 -1
  159. package/dist/MsaViewPanel/model.js.map +0 -1
  160. package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map +0 -1
  161. package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js.map +0 -1
  162. package/dist/MsaViewPanel/msaDataStore.js.map +0 -1
  163. package/dist/MsaViewPanel/pairwiseAlignment.js.map +0 -1
  164. package/dist/MsaViewPanel/pairwiseAlignment.test.js.map +0 -1
  165. package/dist/MsaViewPanel/structureConnection.js.map +0 -1
  166. package/dist/MsaViewPanel/structureConnection.test.js.map +0 -1
  167. package/dist/MsaViewPanel/types.js.map +0 -1
  168. package/dist/MsaViewPanel/util.js.map +0 -1
  169. package/dist/components/ExternalLink.js.map +0 -1
  170. package/dist/components/ReadOnlyTextField2.js.map +0 -1
  171. package/dist/components/TextField2.js.map +0 -1
  172. package/dist/index.js.map +0 -1
  173. package/dist/utils/blastCache.js.map +0 -1
  174. package/dist/utils/fetch.js.map +0 -1
  175. package/dist/utils/msa.js.map +0 -1
  176. package/dist/utils/ncbiBlast.js.map +0 -1
  177. package/dist/utils/swrConfig.js.map +0 -1
  178. package/dist/utils/taxonomyNames.js.map +0 -1
  179. package/dist/utils/types.js.map +0 -1
  180. package/dist/version.js.map +0 -1

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