jbrowse-plugin-msaview 2.3.8 → 2.4.1

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 (128) 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 +11 -13
  4. package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
  5. package/dist/AddHighlightModel/util.d.ts +6 -0
  6. package/dist/AddHighlightModel/util.js +6 -0
  7. package/dist/AddHighlightModel/util.js.map +1 -1
  8. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts +2 -0
  9. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +8 -4
  10. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
  11. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +3 -8
  12. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
  13. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +7 -10
  14. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
  15. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +2 -5
  16. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
  17. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +0 -3
  18. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
  19. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +4 -4
  20. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +2 -2
  21. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
  22. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +4 -0
  23. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +2 -0
  24. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -1
  25. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +10 -21
  26. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  27. package/dist/LaunchMsaView/components/PreLoadedMSA/types.d.ts +1 -0
  28. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js +4 -1
  29. package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map +1 -1
  30. package/dist/LaunchMsaView/components/types.d.ts +0 -3
  31. package/dist/LaunchMsaView/components/useFeatureSequence.d.ts +4 -4
  32. package/dist/LaunchMsaView/components/useFeatureSequence.js +2 -4
  33. package/dist/LaunchMsaView/components/useFeatureSequence.js.map +1 -1
  34. package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts +4 -5
  35. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +11 -30
  36. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +1 -1
  37. package/dist/MsaViewPanel/afterCreateAutoruns.js +13 -17
  38. package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
  39. package/dist/MsaViewPanel/components/ConnectStructureDialog.js +2 -2
  40. package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -1
  41. package/dist/MsaViewPanel/components/LoadingBLAST.js +2 -3
  42. package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
  43. package/dist/MsaViewPanel/model.d.ts +9 -11
  44. package/dist/MsaViewPanel/model.js +22 -23
  45. package/dist/MsaViewPanel/model.js.map +1 -1
  46. package/dist/MsaViewPanel/msaDataStore.d.ts +0 -1
  47. package/dist/MsaViewPanel/msaDataStore.js +0 -9
  48. package/dist/MsaViewPanel/msaDataStore.js.map +1 -1
  49. package/dist/MsaViewPanel/structureConnection.d.ts +6 -4
  50. package/dist/MsaViewPanel/structureConnection.js +6 -6
  51. package/dist/MsaViewPanel/structureConnection.js.map +1 -1
  52. package/dist/MsaViewPanel/structureConnection.test.js +1 -19
  53. package/dist/MsaViewPanel/structureConnection.test.js.map +1 -1
  54. package/dist/MsaViewPanel/util.d.ts +11 -0
  55. package/dist/MsaViewPanel/util.js +11 -3
  56. package/dist/MsaViewPanel/util.js.map +1 -1
  57. package/dist/jbrowse-plugin-msaview.umd.production.min.js +25 -27
  58. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  59. package/dist/utils/blastCache.d.ts +7 -13
  60. package/dist/utils/blastCache.js +0 -12
  61. package/dist/utils/blastCache.js.map +1 -1
  62. package/dist/utils/msa.d.ts +2 -1
  63. package/dist/utils/msa.js +0 -3
  64. package/dist/utils/msa.js.map +1 -1
  65. package/dist/utils/ncbiBlast.d.ts +3 -2
  66. package/dist/utils/ncbiBlast.js +7 -7
  67. package/dist/utils/ncbiBlast.js.map +1 -1
  68. package/dist/utils/taxonomyNames.js +9 -7
  69. package/dist/utils/taxonomyNames.js.map +1 -1
  70. package/dist/version.d.ts +1 -1
  71. package/dist/version.js +1 -1
  72. package/package.json +22 -20
  73. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +8 -25
  74. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +16 -16
  75. package/src/AddHighlightModel/util.ts +11 -0
  76. package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +10 -4
  77. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +3 -16
  78. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +8 -12
  79. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +6 -15
  80. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +0 -9
  81. package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +6 -6
  82. package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +7 -0
  83. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +12 -27
  84. package/src/LaunchMsaView/components/PreLoadedMSA/types.ts +6 -0
  85. package/src/LaunchMsaView/components/types.ts +0 -3
  86. package/src/LaunchMsaView/components/useFeatureSequence.ts +1 -7
  87. package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +10 -37
  88. package/src/MsaViewPanel/afterCreateAutoruns.ts +15 -17
  89. package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +2 -2
  90. package/src/MsaViewPanel/components/LoadingBLAST.tsx +4 -3
  91. package/src/MsaViewPanel/model.ts +33 -33
  92. package/src/MsaViewPanel/msaDataStore.ts +0 -9
  93. package/src/MsaViewPanel/structureConnection.test.ts +0 -21
  94. package/src/MsaViewPanel/structureConnection.ts +7 -7
  95. package/src/MsaViewPanel/util.ts +27 -2
  96. package/src/utils/blastCache.ts +14 -37
  97. package/src/utils/msa.ts +5 -6
  98. package/src/utils/ncbiBlast.ts +18 -11
  99. package/src/utils/taxonomyNames.ts +13 -6
  100. package/src/version.ts +1 -1
  101. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts +0 -8
  102. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +0 -70
  103. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +0 -1
  104. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts +0 -13
  105. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js +0 -12
  106. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map +0 -1
  107. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts +0 -6
  108. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js +0 -25
  109. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +0 -1
  110. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts +0 -2
  111. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js +0 -20
  112. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map +0 -1
  113. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts +0 -24
  114. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js +0 -2
  115. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map +0 -1
  116. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts +0 -10
  117. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +0 -11
  118. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +0 -1
  119. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts +0 -1
  120. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js +0 -2
  121. package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map +0 -1
  122. package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +0 -123
  123. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts +0 -30
  124. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +0 -47
  125. package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts +0 -22
  126. package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts +0 -28
  127. package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +0 -17
  128. package/src/LaunchMsaView/components/EnsemblGeneTree/util.ts +0 -6

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