jbrowse-plugin-msaview 2.3.8 → 2.4.0

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 (120) hide show
  1. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +4 -15
  2. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
  3. package/dist/AddHighlightModel/MsaToGenomeHighlight.js +5 -8
  4. package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
  5. package/dist/AddHighlightModel/util.d.ts +3 -0
  6. package/dist/AddHighlightModel/util.js +3 -0
  7. package/dist/AddHighlightModel/util.js.map +1 -1
  8. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +3 -8
  9. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
  10. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +7 -10
  11. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
  12. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +2 -5
  13. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
  14. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +0 -3
  15. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
  16. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +4 -4
  17. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +2 -2
  18. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
  19. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +4 -0
  20. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +2 -0
  21. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -1
  22. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +10 -21
  23. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  24. package/dist/LaunchMsaView/components/PreLoadedMSA/types.d.ts +1 -0
  25. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js +4 -1
  26. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map +1 -1
  27. package/dist/LaunchMsaView/components/types.d.ts +0 -3
  28. package/dist/LaunchMsaView/components/useFeatureSequence.d.ts +4 -4
  29. package/dist/LaunchMsaView/components/useFeatureSequence.js +2 -4
  30. package/dist/LaunchMsaView/components/useFeatureSequence.js.map +1 -1
  31. package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts +4 -5
  32. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +11 -30
  33. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +1 -1
  34. package/dist/MsaViewPanel/afterCreateAutoruns.js +4 -13
  35. package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
  36. package/dist/MsaViewPanel/components/ConnectStructureDialog.js +2 -2
  37. package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -1
  38. package/dist/MsaViewPanel/components/LoadingBLAST.js +2 -3
  39. package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
  40. package/dist/MsaViewPanel/model.d.ts +4 -11
  41. package/dist/MsaViewPanel/model.js +6 -20
  42. package/dist/MsaViewPanel/model.js.map +1 -1
  43. package/dist/MsaViewPanel/msaDataStore.d.ts +0 -1
  44. package/dist/MsaViewPanel/msaDataStore.js +0 -9
  45. package/dist/MsaViewPanel/msaDataStore.js.map +1 -1
  46. package/dist/MsaViewPanel/structureConnection.d.ts +6 -4
  47. package/dist/MsaViewPanel/structureConnection.js +6 -6
  48. package/dist/MsaViewPanel/structureConnection.js.map +1 -1
  49. package/dist/MsaViewPanel/structureConnection.test.js +1 -19
  50. package/dist/MsaViewPanel/structureConnection.test.js.map +1 -1
  51. package/dist/jbrowse-plugin-msaview.umd.production.min.js +25 -27
  52. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  53. package/dist/utils/blastCache.d.ts +7 -13
  54. package/dist/utils/blastCache.js +0 -12
  55. package/dist/utils/blastCache.js.map +1 -1
  56. package/dist/utils/msa.d.ts +2 -1
  57. package/dist/utils/msa.js +0 -3
  58. package/dist/utils/msa.js.map +1 -1
  59. package/dist/utils/ncbiBlast.d.ts +3 -2
  60. package/dist/utils/ncbiBlast.js +1 -1
  61. package/dist/utils/ncbiBlast.js.map +1 -1
  62. package/dist/utils/taxonomyNames.js +9 -4
  63. package/dist/utils/taxonomyNames.js.map +1 -1
  64. package/dist/version.d.ts +1 -1
  65. package/dist/version.js +1 -1
  66. package/package.json +22 -20
  67. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +7 -21
  68. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +10 -10
  69. package/src/AddHighlightModel/util.ts +6 -0
  70. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +3 -16
  71. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +8 -12
  72. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +6 -15
  73. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +0 -9
  74. package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +6 -6
  75. package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +7 -0
  76. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +12 -27
  77. package/src/LaunchMsaView/components/PreLoadedMSA/types.ts +6 -0
  78. package/src/LaunchMsaView/components/types.ts +0 -3
  79. package/src/LaunchMsaView/components/useFeatureSequence.ts +1 -7
  80. package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +10 -37
  81. package/src/MsaViewPanel/afterCreateAutoruns.ts +7 -15
  82. package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +2 -2
  83. package/src/MsaViewPanel/components/LoadingBLAST.tsx +4 -3
  84. package/src/MsaViewPanel/model.ts +16 -29
  85. package/src/MsaViewPanel/msaDataStore.ts +0 -9
  86. package/src/MsaViewPanel/structureConnection.test.ts +0 -21
  87. package/src/MsaViewPanel/structureConnection.ts +7 -7
  88. package/src/utils/blastCache.ts +14 -37
  89. package/src/utils/msa.ts +5 -6
  90. package/src/utils/ncbiBlast.ts +9 -5
  91. package/src/utils/taxonomyNames.ts +13 -4
  92. package/src/version.ts +1 -1
  93. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts +0 -8
  94. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +0 -70
  95. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +0 -1
  96. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts +0 -13
  97. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js +0 -12
  98. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map +0 -1
  99. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts +0 -6
  100. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js +0 -25
  101. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +0 -1
  102. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts +0 -2
  103. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js +0 -20
  104. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map +0 -1
  105. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts +0 -24
  106. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js +0 -2
  107. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map +0 -1
  108. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts +0 -10
  109. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +0 -11
  110. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +0 -1
  111. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts +0 -1
  112. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js +0 -2
  113. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map +0 -1
  114. package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +0 -123
  115. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts +0 -30
  116. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +0 -47
  117. package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts +0 -22
  118. package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts +0 -28
  119. package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +0 -17
  120. package/src/LaunchMsaView/components/EnsemblGeneTree/util.ts +0 -6

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