jbrowse-plugin-msaview 2.2.11 → 2.3.2

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 (129) hide show
  1. package/dist/AddHighlightModel/index.d.ts +1 -1
  2. package/dist/AddHighlightModel/index.js.map +1 -1
  3. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts +2 -1
  4. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +1 -1
  5. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
  6. package/dist/BgzipFastaMsaAdapter/configSchema.d.ts +1 -1
  7. package/dist/BgzipFastaMsaAdapter/configSchema.js.map +1 -1
  8. package/dist/BgzipFastaMsaAdapter/index.d.ts +1 -1
  9. package/dist/BgzipFastaMsaAdapter/index.js.map +1 -1
  10. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts +1 -1
  11. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +1 -1
  12. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +1 -1
  13. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +1 -1
  14. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.d.ts +1 -1
  15. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
  16. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.d.ts +1 -1
  17. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +1 -1
  18. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
  19. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts +1 -1
  20. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map +1 -1
  21. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.d.ts +1 -2
  22. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +21 -14
  23. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -1
  24. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.d.ts +1 -1
  25. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +32 -35
  26. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
  27. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.d.ts +1 -1
  28. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js +2 -2
  29. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map +1 -1
  30. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +1 -1
  31. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
  32. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +2 -0
  33. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +1 -0
  34. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -1
  35. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.d.ts +1 -1
  36. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +6 -8
  37. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  38. package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.d.ts +2 -2
  39. package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js.map +1 -1
  40. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts +1 -1
  41. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map +1 -1
  42. package/dist/LaunchMsaView/components/TranscriptSelector.d.ts +3 -3
  43. package/dist/LaunchMsaView/components/TranscriptSelector.js +4 -4
  44. package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -1
  45. package/dist/LaunchMsaView/components/useTranscriptSelection.d.ts +1 -1
  46. package/dist/LaunchMsaView/components/useTranscriptSelection.js +1 -2
  47. package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +1 -1
  48. package/dist/LaunchMsaView/components/util.js +1 -1
  49. package/dist/LaunchMsaView/components/util.js.map +1 -1
  50. package/dist/LaunchMsaView/index.d.ts +1 -1
  51. package/dist/LaunchMsaView/index.js.map +1 -1
  52. package/dist/LaunchMsaView/util.d.ts +1 -0
  53. package/dist/LaunchMsaView/util.js +10 -0
  54. package/dist/LaunchMsaView/util.js.map +1 -1
  55. package/dist/MsaViewPanel/afterCreateAutoruns.d.ts +10 -0
  56. package/dist/MsaViewPanel/afterCreateAutoruns.js +258 -0
  57. package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -0
  58. package/dist/MsaViewPanel/blosum62.d.ts +2 -0
  59. package/dist/MsaViewPanel/blosum62.js +628 -0
  60. package/dist/MsaViewPanel/blosum62.js.map +1 -0
  61. package/dist/MsaViewPanel/components/LoadingBLAST.d.ts +1 -1
  62. package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
  63. package/dist/MsaViewPanel/components/MsaViewPanel.d.ts +1 -1
  64. package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
  65. package/dist/MsaViewPanel/doLaunchBlast.d.ts +1 -1
  66. package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
  67. package/dist/MsaViewPanel/genomeToMSA.d.ts +1 -1
  68. package/dist/MsaViewPanel/genomeToMSA.js.map +1 -1
  69. package/dist/MsaViewPanel/index.d.ts +1 -1
  70. package/dist/MsaViewPanel/index.js.map +1 -1
  71. package/dist/MsaViewPanel/model.d.ts +25 -39
  72. package/dist/MsaViewPanel/model.js +17 -309
  73. package/dist/MsaViewPanel/model.js.map +1 -1
  74. package/dist/MsaViewPanel/msaDataStore.d.ts +3 -4
  75. package/dist/MsaViewPanel/msaDataStore.js +59 -173
  76. package/dist/MsaViewPanel/msaDataStore.js.map +1 -1
  77. package/dist/MsaViewPanel/pairwiseAlignment.d.ts +0 -7
  78. package/dist/MsaViewPanel/pairwiseAlignment.js +1 -636
  79. package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -1
  80. package/dist/MsaViewPanel/structureConnection.js +1 -5
  81. package/dist/MsaViewPanel/structureConnection.js.map +1 -1
  82. package/dist/MsaViewPanel/util.d.ts +1 -1
  83. package/dist/index.d.ts +1 -1
  84. package/dist/index.js.map +1 -1
  85. package/dist/jbrowse-plugin-msaview.umd.production.min.js +30 -30
  86. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  87. package/dist/utils/msa.js +35 -77
  88. package/dist/utils/msa.js.map +1 -1
  89. package/dist/utils/ncbiBlast.js +1 -10
  90. package/dist/utils/ncbiBlast.js.map +1 -1
  91. package/package.json +31 -28
  92. package/src/AddHighlightModel/index.tsx +1 -1
  93. package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +3 -4
  94. package/src/BgzipFastaMsaAdapter/configSchema.ts +2 -1
  95. package/src/BgzipFastaMsaAdapter/index.ts +2 -1
  96. package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +2 -6
  97. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +2 -1
  98. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +2 -1
  99. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +6 -7
  100. package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +5 -2
  101. package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +22 -17
  102. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +40 -52
  103. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.tsx +6 -13
  104. package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +2 -1
  105. package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +2 -0
  106. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +7 -19
  107. package/src/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.ts +2 -2
  108. package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts +1 -2
  109. package/src/LaunchMsaView/components/TranscriptSelector.tsx +7 -6
  110. package/src/LaunchMsaView/components/useTranscriptSelection.ts +1 -6
  111. package/src/LaunchMsaView/components/util.ts +1 -1
  112. package/src/LaunchMsaView/index.ts +6 -5
  113. package/src/LaunchMsaView/util.ts +11 -0
  114. package/src/MsaViewPanel/afterCreateAutoruns.ts +299 -0
  115. package/src/MsaViewPanel/blosum62.ts +628 -0
  116. package/src/MsaViewPanel/components/LoadingBLAST.tsx +2 -1
  117. package/src/MsaViewPanel/components/MsaViewPanel.tsx +2 -1
  118. package/src/MsaViewPanel/doLaunchBlast.ts +1 -1
  119. package/src/MsaViewPanel/genomeToMSA.ts +2 -1
  120. package/src/MsaViewPanel/index.ts +2 -1
  121. package/src/MsaViewPanel/model.ts +30 -392
  122. package/src/MsaViewPanel/msaDataStore.ts +56 -196
  123. package/src/MsaViewPanel/pairwiseAlignment.ts +1 -637
  124. package/src/MsaViewPanel/structureConnection.ts +1 -5
  125. package/src/MsaViewPanel/util.ts +1 -1
  126. package/src/index.ts +4 -2
  127. package/src/utils/msa.ts +45 -100
  128. package/src/utils/ncbiBlast.ts +3 -13
  129. package/CHANGELOG.md +0 -101

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