jbrowse-plugin-msaview 3.2.0 → 3.4.0

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 (106) 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 +61 -17
  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/ManualMSALoader/ManualMSALoader.js +1 -1
  15. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +9 -4
  16. package/dist/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.d.ts +9 -0
  17. package/dist/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.js +20 -0
  18. package/dist/LaunchMsaView/components/SubmitCancelActions.test.js +1 -1
  19. package/dist/LaunchMsaView/components/useFeatureSequence.js +1 -1
  20. package/dist/LaunchMsaView/detectQueryRow.d.ts +15 -2
  21. package/dist/LaunchMsaView/detectQueryRow.js +20 -21
  22. package/dist/LaunchMsaView/detectQueryRow.test.js +15 -15
  23. package/dist/LaunchMsaView/useQueryRowName.js +5 -8
  24. package/dist/MsaViewPanel/afterCreateAutoruns.js +2 -2
  25. package/dist/MsaViewPanel/components/ErrorBoundary.d.ts +2 -2
  26. package/dist/MsaViewPanel/components/JobLink.js +7 -1
  27. package/dist/MsaViewPanel/components/LaunchProgress.d.ts +17 -0
  28. package/dist/MsaViewPanel/components/LaunchProgress.js +41 -0
  29. package/dist/MsaViewPanel/components/MsaViewPanel.js +6 -3
  30. package/dist/MsaViewPanel/components/MsaViewPanel.test.d.ts +1 -0
  31. package/dist/MsaViewPanel/components/MsaViewPanel.test.js +68 -0
  32. package/dist/MsaViewPanel/doLaunchBlast.d.ts +1 -1
  33. package/dist/MsaViewPanel/doLaunchBlast.js +84 -52
  34. package/dist/MsaViewPanel/doLaunchOrthologs.d.ts +7 -5
  35. package/dist/MsaViewPanel/doLaunchOrthologs.js +64 -30
  36. package/dist/MsaViewPanel/doLaunchOrthologs.test.js +106 -1
  37. package/dist/MsaViewPanel/genomeToMSA.js +4 -2
  38. package/dist/MsaViewPanel/genomeToMSA.test.js +34 -0
  39. package/dist/MsaViewPanel/model.d.ts +41 -11
  40. package/dist/MsaViewPanel/model.js +6 -0
  41. package/dist/MsaViewPanel/observeProteinHighlights.test.js +11 -0
  42. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js +1 -0
  43. package/dist/MsaViewPanel/util.d.ts +18 -0
  44. package/dist/MsaViewPanel/util.js +17 -0
  45. package/dist/jbrowse-plugin-msaview.umd.production.min.js +47 -35
  46. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  47. package/dist/utils/blastCache.d.ts +10 -6
  48. package/dist/utils/blastCache.js +15 -3
  49. package/dist/utils/ebiBlast.d.ts +1 -1
  50. package/dist/utils/msa.d.ts +12 -0
  51. package/dist/utils/msa.js +35 -12
  52. package/dist/utils/msaRows.d.ts +31 -0
  53. package/dist/utils/msaRows.js +67 -0
  54. package/dist/utils/pantherOrthologs.d.ts +79 -0
  55. package/dist/utils/pantherOrthologs.js +262 -0
  56. package/dist/utils/phmmer.d.ts +53 -0
  57. package/dist/utils/phmmer.js +118 -0
  58. package/dist/utils/taxonomyNames.d.ts +1 -1
  59. package/dist/utils/taxonomyNames.js +6 -1
  60. package/dist/version.d.ts +1 -1
  61. package/dist/version.js +1 -1
  62. package/package.json +27 -21
  63. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +1 -1
  64. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +1 -1
  65. package/src/AddHighlightModel/index.tsx +1 -1
  66. package/src/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.tsx +88 -30
  67. package/src/LaunchMsaView/components/BlastQuery/BlastManualPanel.tsx +1 -1
  68. package/src/LaunchMsaView/components/BlastQuery/BlastPanel.tsx +4 -4
  69. package/src/LaunchMsaView/components/BlastQuery/CachedBlastResults.test.ts +50 -0
  70. package/src/LaunchMsaView/components/BlastQuery/CachedBlastResults.tsx +23 -3
  71. package/src/LaunchMsaView/components/BlastQuery/MsaAlgorithmSelect.tsx +1 -1
  72. package/src/LaunchMsaView/components/BlastQuery/consts.ts +40 -0
  73. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +1 -1
  74. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +21 -5
  75. package/src/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.tsx +52 -0
  76. package/src/LaunchMsaView/components/SubmitCancelActions.test.tsx +1 -1
  77. package/src/LaunchMsaView/components/useFeatureSequence.ts +1 -1
  78. package/src/LaunchMsaView/detectQueryRow.test.ts +17 -15
  79. package/src/LaunchMsaView/detectQueryRow.ts +34 -23
  80. package/src/LaunchMsaView/useQueryRowName.ts +6 -9
  81. package/src/MsaViewPanel/afterCreateAutoruns.ts +2 -2
  82. package/src/MsaViewPanel/components/ErrorBoundary.tsx +2 -1
  83. package/src/MsaViewPanel/components/JobLink.tsx +7 -2
  84. package/src/MsaViewPanel/components/LaunchProgress.tsx +62 -0
  85. package/src/MsaViewPanel/components/MsaViewPanel.test.tsx +83 -0
  86. package/src/MsaViewPanel/components/MsaViewPanel.tsx +7 -4
  87. package/src/MsaViewPanel/doLaunchBlast.ts +127 -69
  88. package/src/MsaViewPanel/doLaunchOrthologs.test.ts +119 -2
  89. package/src/MsaViewPanel/doLaunchOrthologs.ts +100 -38
  90. package/src/MsaViewPanel/genomeToMSA.test.ts +37 -0
  91. package/src/MsaViewPanel/genomeToMSA.ts +6 -2
  92. package/src/MsaViewPanel/model.ts +38 -5
  93. package/src/MsaViewPanel/observeProteinHighlights.test.ts +13 -0
  94. package/src/MsaViewPanel/syncGenomeHoverToMsaColumn.test.ts +1 -0
  95. package/src/MsaViewPanel/util.ts +18 -0
  96. package/src/utils/blastCache.ts +33 -12
  97. package/src/utils/ebiBlast.ts +1 -1
  98. package/src/utils/msa.ts +43 -12
  99. package/src/utils/msaRows.ts +95 -0
  100. package/src/utils/pantherOrthologs.ts +399 -0
  101. package/src/utils/phmmer.ts +174 -0
  102. package/src/utils/taxonomyNames.ts +6 -1
  103. package/src/version.ts +1 -1
  104. package/dist/MsaViewPanel/components/LoadingBLAST.d.ts +0 -6
  105. package/dist/MsaViewPanel/components/LoadingBLAST.js +0 -26
  106. package/src/MsaViewPanel/components/LoadingBLAST.tsx +0 -48

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