jbrowse-plugin-msaview 3.4.0 → 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 (86) hide show
  1. package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js +4 -6
  2. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.d.ts +7 -0
  3. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.js +42 -0
  4. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.test.d.ts +1 -0
  5. package/dist/LaunchMsaView/components/BlastQuery/searchChoiceStorage.test.js +32 -0
  6. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +2 -1
  7. package/dist/LaunchMsaViewExtensionPoint/index.js +11 -6
  8. package/dist/LaunchMsaViewExtensionPoint/index.test.d.ts +1 -0
  9. package/dist/LaunchMsaViewExtensionPoint/index.test.js +43 -0
  10. package/dist/MsaViewPanel/afterCreateAutoruns.d.ts +15 -0
  11. package/dist/MsaViewPanel/afterCreateAutoruns.js +93 -70
  12. package/dist/MsaViewPanel/components/LaunchProgress.js +11 -2
  13. package/dist/MsaViewPanel/components/MsaViewPanel.test.js +19 -0
  14. package/dist/MsaViewPanel/doLaunchBlast.d.ts +3 -1
  15. package/dist/MsaViewPanel/doLaunchBlast.js +10 -12
  16. package/dist/MsaViewPanel/doLaunchOrthologs.d.ts +3 -1
  17. package/dist/MsaViewPanel/doLaunchOrthologs.js +6 -5
  18. package/dist/MsaViewPanel/doLaunchOrthologs.test.js +38 -24
  19. package/dist/MsaViewPanel/model.d.ts +160 -10
  20. package/dist/MsaViewPanel/model.js +51 -1
  21. package/dist/MsaViewPanel/msaDataStore.d.ts +5 -3
  22. package/dist/MsaViewPanel/msaDataStore.js +16 -7
  23. package/dist/MsaViewPanel/msaDataStore.test.d.ts +1 -0
  24. package/dist/MsaViewPanel/msaDataStore.test.js +44 -0
  25. package/dist/MsaViewPanel/runLaunch.d.ts +38 -0
  26. package/dist/MsaViewPanel/runLaunch.js +65 -0
  27. package/dist/MsaViewPanel/runLaunch.test.d.ts +1 -0
  28. package/dist/MsaViewPanel/runLaunch.test.js +129 -0
  29. package/dist/MsaViewPanel/storedData.test.d.ts +1 -0
  30. package/dist/MsaViewPanel/storedData.test.js +160 -0
  31. package/dist/jbrowse-plugin-msaview.umd.production.min.js +35 -35
  32. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  33. package/dist/utils/blastCache.js +32 -0
  34. package/dist/utils/blastCache.test.d.ts +1 -0
  35. package/dist/utils/blastCache.test.js +72 -0
  36. package/dist/utils/ebiBlast.d.ts +4 -2
  37. package/dist/utils/ebiBlast.js +6 -4
  38. package/dist/utils/ebiJobDispatcher.d.ts +6 -3
  39. package/dist/utils/ebiJobDispatcher.js +13 -6
  40. package/dist/utils/fetch.d.ts +8 -1
  41. package/dist/utils/fetch.js +28 -2
  42. package/dist/utils/msa.d.ts +4 -2
  43. package/dist/utils/msa.js +9 -5
  44. package/dist/utils/ncbiDomains.d.ts +2 -2
  45. package/dist/utils/ncbiOrthologs.d.ts +11 -1
  46. package/dist/utils/ncbiOrthologs.js +26 -7
  47. package/dist/utils/ncbiOrthologs.test.js +23 -1
  48. package/dist/utils/pantherOrthologs.js +2 -10
  49. package/dist/utils/phmmer.d.ts +2 -1
  50. package/dist/utils/phmmer.js +4 -2
  51. package/dist/utils/poll.d.ts +6 -1
  52. package/dist/utils/poll.js +7 -2
  53. package/dist/version.d.ts +1 -1
  54. package/dist/version.js +1 -1
  55. package/package.json +14 -14
  56. package/src/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.tsx +7 -11
  57. package/src/LaunchMsaView/components/BlastQuery/searchChoiceStorage.test.ts +43 -0
  58. package/src/LaunchMsaView/components/BlastQuery/searchChoiceStorage.ts +64 -0
  59. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +2 -2
  60. package/src/LaunchMsaViewExtensionPoint/index.test.ts +51 -0
  61. package/src/LaunchMsaViewExtensionPoint/index.ts +21 -6
  62. package/src/MsaViewPanel/afterCreateAutoruns.ts +100 -66
  63. package/src/MsaViewPanel/components/LaunchProgress.tsx +20 -2
  64. package/src/MsaViewPanel/components/MsaViewPanel.test.tsx +21 -0
  65. package/src/MsaViewPanel/doLaunchBlast.ts +14 -10
  66. package/src/MsaViewPanel/doLaunchOrthologs.test.ts +41 -26
  67. package/src/MsaViewPanel/doLaunchOrthologs.ts +8 -4
  68. package/src/MsaViewPanel/model.ts +54 -1
  69. package/src/MsaViewPanel/msaDataStore.test.ts +54 -0
  70. package/src/MsaViewPanel/msaDataStore.ts +22 -13
  71. package/src/MsaViewPanel/runLaunch.test.ts +154 -0
  72. package/src/MsaViewPanel/runLaunch.ts +102 -0
  73. package/src/MsaViewPanel/storedData.test.ts +196 -0
  74. package/src/utils/blastCache.test.ts +86 -0
  75. package/src/utils/blastCache.ts +34 -1
  76. package/src/utils/ebiBlast.ts +8 -2
  77. package/src/utils/ebiJobDispatcher.ts +18 -3
  78. package/src/utils/fetch.ts +29 -2
  79. package/src/utils/msa.ts +11 -3
  80. package/src/utils/ncbiDomains.ts +4 -2
  81. package/src/utils/ncbiOrthologs.test.ts +25 -0
  82. package/src/utils/ncbiOrthologs.ts +27 -7
  83. package/src/utils/pantherOrthologs.ts +6 -11
  84. package/src/utils/phmmer.ts +5 -1
  85. package/src/utils/poll.ts +8 -1
  86. package/src/version.ts +1 -1

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