jbrowse-plugin-msaview 3.3.0 → 3.4.1

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 (149) hide show
  1. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +1 -1
  2. package/dist/AddHighlightModel/MsaToGenomeHighlight.js +1 -1
  3. package/dist/AddHighlightModel/index.js +1 -1
  4. package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js +60 -18
  5. package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.js +1 -1
  6. package/dist/LaunchMsaView/components/BlastQuery/BlastPanel.js +2 -2
  7. package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.d.ts +12 -0
  8. package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.js +21 -2
  9. package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.test.d.ts +1 -0
  10. package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.test.js +29 -0
  11. package/dist/LaunchMsaView/components/BlastQuery/MsaAlgorithmSelect.js +1 -1
  12. package/dist/LaunchMsaView/components/BlastQuery/consts.d.ts +28 -0
  13. package/dist/LaunchMsaView/components/BlastQuery/consts.js +21 -0
  14. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.d.ts +7 -0
  15. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.js +42 -0
  16. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.test.d.ts +1 -0
  17. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.test.js +32 -0
  18. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +1 -1
  19. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +5 -4
  20. package/dist/LaunchMsaView/components/SubmitCancelActions.test.js +1 -1
  21. package/dist/LaunchMsaView/components/useFeatureSequence.js +1 -1
  22. package/dist/LaunchMsaView/detectQueryRow.d.ts +15 -2
  23. package/dist/LaunchMsaView/detectQueryRow.js +20 -21
  24. package/dist/LaunchMsaView/detectQueryRow.test.js +15 -15
  25. package/dist/LaunchMsaView/useQueryRowName.js +5 -8
  26. package/dist/LaunchMsaViewExtensionPoint/index.js +11 -6
  27. package/dist/LaunchMsaViewExtensionPoint/index.test.d.ts +1 -0
  28. package/dist/LaunchMsaViewExtensionPoint/index.test.js +43 -0
  29. package/dist/MsaViewPanel/afterCreateAutoruns.d.ts +15 -0
  30. package/dist/MsaViewPanel/afterCreateAutoruns.js +95 -72
  31. package/dist/MsaViewPanel/components/ErrorBoundary.d.ts +2 -2
  32. package/dist/MsaViewPanel/components/JobLink.js +7 -1
  33. package/dist/MsaViewPanel/components/LaunchProgress.d.ts +17 -0
  34. package/dist/MsaViewPanel/components/LaunchProgress.js +50 -0
  35. package/dist/MsaViewPanel/components/MsaViewPanel.js +6 -3
  36. package/dist/MsaViewPanel/components/MsaViewPanel.test.d.ts +1 -0
  37. package/dist/MsaViewPanel/components/MsaViewPanel.test.js +87 -0
  38. package/dist/MsaViewPanel/doLaunchBlast.d.ts +4 -2
  39. package/dist/MsaViewPanel/doLaunchBlast.js +86 -56
  40. package/dist/MsaViewPanel/doLaunchOrthologs.d.ts +3 -1
  41. package/dist/MsaViewPanel/doLaunchOrthologs.js +6 -5
  42. package/dist/MsaViewPanel/doLaunchOrthologs.test.js +39 -25
  43. package/dist/MsaViewPanel/genomeToMSA.js +4 -2
  44. package/dist/MsaViewPanel/genomeToMSA.test.js +34 -0
  45. package/dist/MsaViewPanel/model.d.ts +190 -19
  46. package/dist/MsaViewPanel/model.js +51 -1
  47. package/dist/MsaViewPanel/msaDataStore.d.ts +5 -3
  48. package/dist/MsaViewPanel/msaDataStore.js +16 -7
  49. package/dist/MsaViewPanel/msaDataStore.test.d.ts +1 -0
  50. package/dist/MsaViewPanel/msaDataStore.test.js +44 -0
  51. package/dist/MsaViewPanel/observeProteinHighlights.test.js +11 -0
  52. package/dist/MsaViewPanel/runLaunch.d.ts +38 -0
  53. package/dist/MsaViewPanel/runLaunch.js +65 -0
  54. package/dist/MsaViewPanel/runLaunch.test.d.ts +1 -0
  55. package/dist/MsaViewPanel/runLaunch.test.js +129 -0
  56. package/dist/MsaViewPanel/storedData.test.d.ts +1 -0
  57. package/dist/MsaViewPanel/storedData.test.js +160 -0
  58. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js +1 -0
  59. package/dist/MsaViewPanel/util.d.ts +18 -0
  60. package/dist/MsaViewPanel/util.js +17 -0
  61. package/dist/jbrowse-plugin-msaview.umd.production.min.js +47 -35
  62. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  63. package/dist/utils/blastCache.d.ts +10 -6
  64. package/dist/utils/blastCache.js +47 -3
  65. package/dist/utils/blastCache.test.d.ts +1 -0
  66. package/dist/utils/blastCache.test.js +72 -0
  67. package/dist/utils/ebiBlast.d.ts +5 -3
  68. package/dist/utils/ebiBlast.js +6 -4
  69. package/dist/utils/ebiJobDispatcher.d.ts +6 -3
  70. package/dist/utils/ebiJobDispatcher.js +13 -6
  71. package/dist/utils/fetch.d.ts +8 -1
  72. package/dist/utils/fetch.js +28 -2
  73. package/dist/utils/msa.d.ts +15 -1
  74. package/dist/utils/msa.js +40 -13
  75. package/dist/utils/msaRows.d.ts +31 -0
  76. package/dist/utils/msaRows.js +67 -0
  77. package/dist/utils/ncbiDomains.d.ts +2 -2
  78. package/dist/utils/ncbiOrthologs.d.ts +11 -1
  79. package/dist/utils/ncbiOrthologs.js +26 -7
  80. package/dist/utils/ncbiOrthologs.test.js +23 -1
  81. package/dist/utils/pantherOrthologs.js +2 -10
  82. package/dist/utils/phmmer.d.ts +54 -0
  83. package/dist/utils/phmmer.js +120 -0
  84. package/dist/utils/poll.d.ts +6 -1
  85. package/dist/utils/poll.js +7 -2
  86. package/dist/utils/taxonomyNames.d.ts +1 -1
  87. package/dist/utils/taxonomyNames.js +6 -1
  88. package/dist/version.d.ts +1 -1
  89. package/dist/version.js +1 -1
  90. package/package.json +30 -24
  91. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +1 -1
  92. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +1 -1
  93. package/src/AddHighlightModel/index.tsx +1 -1
  94. package/src/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.tsx +85 -31
  95. package/src/LaunchMsaView/components/BlastQuery/BlastManualPanel.tsx +1 -1
  96. package/src/LaunchMsaView/components/BlastQuery/BlastPanel.tsx +4 -4
  97. package/src/LaunchMsaView/components/BlastQuery/CachedBlastResults.test.ts +50 -0
  98. package/src/LaunchMsaView/components/BlastQuery/CachedBlastResults.tsx +23 -3
  99. package/src/LaunchMsaView/components/BlastQuery/MsaAlgorithmSelect.tsx +1 -1
  100. package/src/LaunchMsaView/components/BlastQuery/consts.ts +40 -0
  101. package/src/LaunchMsaView/components/BlastQuery/searchChoiceStorage.test.ts +43 -0
  102. package/src/LaunchMsaView/components/BlastQuery/searchChoiceStorage.ts +64 -0
  103. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +1 -1
  104. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +7 -7
  105. package/src/LaunchMsaView/components/SubmitCancelActions.test.tsx +1 -1
  106. package/src/LaunchMsaView/components/useFeatureSequence.ts +1 -1
  107. package/src/LaunchMsaView/detectQueryRow.test.ts +17 -15
  108. package/src/LaunchMsaView/detectQueryRow.ts +34 -23
  109. package/src/LaunchMsaView/useQueryRowName.ts +6 -9
  110. package/src/LaunchMsaViewExtensionPoint/index.test.ts +51 -0
  111. package/src/LaunchMsaViewExtensionPoint/index.ts +21 -6
  112. package/src/MsaViewPanel/afterCreateAutoruns.ts +102 -68
  113. package/src/MsaViewPanel/components/ErrorBoundary.tsx +2 -1
  114. package/src/MsaViewPanel/components/JobLink.tsx +7 -2
  115. package/src/MsaViewPanel/components/LaunchProgress.tsx +80 -0
  116. package/src/MsaViewPanel/components/MsaViewPanel.test.tsx +104 -0
  117. package/src/MsaViewPanel/components/MsaViewPanel.tsx +7 -4
  118. package/src/MsaViewPanel/doLaunchBlast.ts +134 -72
  119. package/src/MsaViewPanel/doLaunchOrthologs.test.ts +43 -28
  120. package/src/MsaViewPanel/doLaunchOrthologs.ts +9 -5
  121. package/src/MsaViewPanel/genomeToMSA.test.ts +37 -0
  122. package/src/MsaViewPanel/genomeToMSA.ts +6 -2
  123. package/src/MsaViewPanel/model.ts +82 -6
  124. package/src/MsaViewPanel/msaDataStore.test.ts +54 -0
  125. package/src/MsaViewPanel/msaDataStore.ts +22 -13
  126. package/src/MsaViewPanel/observeProteinHighlights.test.ts +13 -0
  127. package/src/MsaViewPanel/runLaunch.test.ts +154 -0
  128. package/src/MsaViewPanel/runLaunch.ts +102 -0
  129. package/src/MsaViewPanel/storedData.test.ts +196 -0
  130. package/src/MsaViewPanel/syncGenomeHoverToMsaColumn.test.ts +1 -0
  131. package/src/MsaViewPanel/util.ts +18 -0
  132. package/src/utils/blastCache.test.ts +86 -0
  133. package/src/utils/blastCache.ts +67 -13
  134. package/src/utils/ebiBlast.ts +9 -3
  135. package/src/utils/ebiJobDispatcher.ts +18 -3
  136. package/src/utils/fetch.ts +29 -2
  137. package/src/utils/msa.ts +51 -12
  138. package/src/utils/msaRows.ts +95 -0
  139. package/src/utils/ncbiDomains.ts +4 -2
  140. package/src/utils/ncbiOrthologs.test.ts +25 -0
  141. package/src/utils/ncbiOrthologs.ts +27 -7
  142. package/src/utils/pantherOrthologs.ts +6 -11
  143. package/src/utils/phmmer.ts +178 -0
  144. package/src/utils/poll.ts +8 -1
  145. package/src/utils/taxonomyNames.ts +6 -1
  146. package/src/version.ts +1 -1
  147. package/dist/MsaViewPanel/components/LoadingBLAST.d.ts +0 -6
  148. package/dist/MsaViewPanel/components/LoadingBLAST.js +0 -26
  149. package/src/MsaViewPanel/components/LoadingBLAST.tsx +0 -48

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