jbrowse-plugin-msaview 2.8.2 → 2.10.0

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Files changed (108) hide show
  1. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastRIDPanel.d.ts → BlastQuery/BlastAutomaticPanel.d.ts} +2 -3
  2. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastAutomaticPanel.js → BlastQuery/BlastAutomaticPanel.js} +6 -25
  3. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastManualPanel.d.ts → BlastQuery/BlastManualPanel.d.ts} +2 -3
  4. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastManualPanel.js → BlastQuery/BlastManualPanel.js} +7 -4
  5. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastMethodSelector.d.ts → BlastQuery/BlastMethodSelector.d.ts} +2 -2
  6. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastMethodSelector.js → BlastQuery/BlastMethodSelector.js} +1 -2
  7. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastPanel.d.ts → BlastQuery/BlastPanel.d.ts} +3 -12
  8. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastPanel.js → BlastQuery/BlastPanel.js} +14 -16
  9. package/dist/LaunchMsaView/components/BlastQuery/BlastSettingsDialog.d.ts +8 -0
  10. package/dist/LaunchMsaView/components/{NCBIBlastQuery/NCBISettingsDialog.js → BlastQuery/BlastSettingsDialog.js} +13 -9
  11. package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/CachedBlastResults.js +1 -1
  12. package/dist/LaunchMsaView/components/BlastQuery/consts.d.ts +12 -0
  13. package/dist/LaunchMsaView/components/BlastQuery/consts.js +17 -0
  14. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +3 -3
  15. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +15 -35
  16. package/dist/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.d.ts +15 -0
  17. package/dist/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.js +67 -0
  18. package/dist/LaunchMsaView/index.js +19 -1
  19. package/dist/MsaViewPanel/components/JobLink.d.ts +5 -0
  20. package/dist/MsaViewPanel/components/JobLink.js +13 -0
  21. package/dist/MsaViewPanel/components/LoadingBLAST.d.ts +1 -2
  22. package/dist/MsaViewPanel/components/LoadingBLAST.js +8 -15
  23. package/dist/MsaViewPanel/components/MsaViewPanel.js +1 -1
  24. package/dist/MsaViewPanel/doLaunchBlast.js +11 -19
  25. package/dist/MsaViewPanel/doLaunchOrthologs.js +43 -12
  26. package/dist/MsaViewPanel/doLaunchOrthologs.test.d.ts +1 -0
  27. package/dist/MsaViewPanel/doLaunchOrthologs.test.js +201 -0
  28. package/dist/MsaViewPanel/model.d.ts +20 -12
  29. package/dist/jbrowse-plugin-msaview.umd.production.min.js +31 -33
  30. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  31. package/dist/utils/blastCache.d.ts +8 -4
  32. package/dist/utils/blastCache.js +4 -5
  33. package/dist/utils/ebiBlast.d.ts +52 -0
  34. package/dist/utils/ebiBlast.js +63 -0
  35. package/dist/utils/ebiJobDispatcher.d.ts +33 -0
  36. package/dist/utils/ebiJobDispatcher.js +80 -0
  37. package/dist/utils/ebiJobDispatcher.test.d.ts +1 -0
  38. package/dist/utils/ebiJobDispatcher.test.js +46 -0
  39. package/dist/utils/eutils.d.ts +9 -0
  40. package/dist/utils/eutils.js +18 -0
  41. package/dist/utils/fetch.js +24 -1
  42. package/dist/utils/msa.d.ts +1 -1
  43. package/dist/utils/msa.js +25 -32
  44. package/dist/utils/ncbiOrthologs.d.ts +17 -75
  45. package/dist/utils/ncbiOrthologs.js +67 -63
  46. package/dist/utils/ncbiOrthologs.test.js +82 -2
  47. package/dist/utils/ncbiTaxonomy.d.ts +11 -0
  48. package/dist/utils/ncbiTaxonomy.js +33 -0
  49. package/dist/utils/types.d.ts +9 -14
  50. package/dist/utils/useLocalStorage.d.ts +1 -0
  51. package/dist/utils/useLocalStorage.js +1 -1
  52. package/dist/version.d.ts +1 -1
  53. package/dist/version.js +1 -1
  54. package/package.json +3 -3
  55. package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx → BlastQuery/BlastAutomaticPanel.tsx} +13 -59
  56. package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastManualPanel.tsx → BlastQuery/BlastManualPanel.tsx} +7 -6
  57. package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastMethodSelector.tsx → BlastQuery/BlastMethodSelector.tsx} +2 -7
  58. package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastPanel.tsx → BlastQuery/BlastPanel.tsx} +21 -25
  59. package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBISettingsDialog.tsx → BlastQuery/BlastSettingsDialog.tsx} +26 -13
  60. package/src/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/CachedBlastResults.tsx +1 -1
  61. package/src/LaunchMsaView/components/BlastQuery/consts.ts +22 -0
  62. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +5 -7
  63. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +35 -73
  64. package/src/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.tsx +92 -0
  65. package/src/LaunchMsaView/index.ts +20 -2
  66. package/src/MsaViewPanel/components/JobLink.tsx +17 -0
  67. package/src/MsaViewPanel/components/LoadingBLAST.tsx +10 -41
  68. package/src/MsaViewPanel/components/MsaViewPanel.tsx +1 -1
  69. package/src/MsaViewPanel/doLaunchBlast.ts +12 -28
  70. package/src/MsaViewPanel/doLaunchOrthologs.test.ts +247 -0
  71. package/src/MsaViewPanel/doLaunchOrthologs.ts +56 -13
  72. package/src/MsaViewPanel/model.ts +10 -7
  73. package/src/utils/blastCache.ts +8 -9
  74. package/src/utils/ebiBlast.ts +114 -0
  75. package/src/utils/ebiJobDispatcher.test.ts +54 -0
  76. package/src/utils/ebiJobDispatcher.ts +120 -0
  77. package/src/utils/eutils.ts +19 -0
  78. package/src/utils/fetch.ts +26 -1
  79. package/src/utils/msa.ts +26 -47
  80. package/src/utils/ncbiOrthologs.test.ts +96 -2
  81. package/src/utils/ncbiOrthologs.ts +83 -71
  82. package/src/utils/ncbiTaxonomy.ts +37 -0
  83. package/src/utils/types.ts +8 -13
  84. package/src/utils/useLocalStorage.ts +1 -1
  85. package/src/version.ts +1 -1
  86. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.d.ts +0 -10
  87. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js +0 -74
  88. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.d.ts +0 -5
  89. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +0 -7
  90. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +0 -4
  91. package/dist/MsaViewPanel/components/RIDLink.d.ts +0 -6
  92. package/dist/MsaViewPanel/components/RIDLink.js +0 -12
  93. package/dist/utils/ncbiBlast.d.ts +0 -30
  94. package/dist/utils/ncbiBlast.js +0 -84
  95. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.tsx +0 -137
  96. package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +0 -10
  97. package/src/MsaViewPanel/components/RIDLink.tsx +0 -19
  98. package/src/utils/ncbiBlast.ts +0 -143
  99. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/CachedBlastResults.d.ts +0 -0
  100. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/MsaAlgorithmSelect.d.ts +0 -0
  101. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/MsaAlgorithmSelect.js +0 -0
  102. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/blastLaunchView.d.ts +0 -0
  103. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/blastLaunchView.js +0 -0
  104. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/useCachedBlastResults.d.ts +0 -0
  105. /package/dist/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/useCachedBlastResults.js +0 -0
  106. /package/src/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/MsaAlgorithmSelect.tsx +0 -0
  107. /package/src/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/blastLaunchView.ts +0 -0
  108. /package/src/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/useCachedBlastResults.ts +0 -0

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