jbrowse-plugin-msaview 3.6.0 → 3.7.0

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 (156) hide show
  1. package/README.md +8 -0
  2. package/dist/LaunchMsaView/cleanProteinSequence.test.d.ts +1 -0
  3. package/dist/LaunchMsaView/cleanProteinSequence.test.js +77 -0
  4. package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js +29 -32
  5. package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.js +10 -15
  6. package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.js +14 -13
  7. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +25 -22
  8. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +14 -19
  9. package/dist/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.d.ts +2 -1
  10. package/dist/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.js +18 -2
  11. package/dist/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.test.d.ts +1 -0
  12. package/dist/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.test.js +13 -0
  13. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +19 -14
  14. package/dist/LaunchMsaView/components/SubmitCancelActions.d.ts +3 -1
  15. package/dist/LaunchMsaView/components/SubmitCancelActions.js +10 -7
  16. package/dist/LaunchMsaView/components/SubmitCancelActions.test.js +20 -2
  17. package/dist/LaunchMsaView/components/calculateProteinSequence.d.ts +8 -1
  18. package/dist/LaunchMsaView/components/calculateProteinSequence.js +25 -20
  19. package/dist/LaunchMsaView/components/launchConnectedView.d.ts +23 -0
  20. package/dist/LaunchMsaView/components/launchConnectedView.js +39 -0
  21. package/dist/LaunchMsaView/detectQueryRow.js +4 -7
  22. package/dist/LaunchMsaView/util.d.ts +6 -0
  23. package/dist/LaunchMsaView/util.js +7 -1
  24. package/dist/LaunchMsaViewExtensionPoint/index.test.js +15 -0
  25. package/dist/MsaViewPanel/afterCreateAutoruns.js +12 -3
  26. package/dist/MsaViewPanel/applyRegion.d.ts +23 -0
  27. package/dist/MsaViewPanel/applyRegion.js +19 -0
  28. package/dist/MsaViewPanel/applyRegion.test.d.ts +1 -0
  29. package/dist/MsaViewPanel/applyRegion.test.js +45 -0
  30. package/dist/MsaViewPanel/doLaunchBlast.js +2 -1
  31. package/dist/MsaViewPanel/doLaunchBlast.test.js +12 -0
  32. package/dist/MsaViewPanel/doLaunchOrthologs.test.js +1 -1
  33. package/dist/MsaViewPanel/genomeToMSA.js +3 -3
  34. package/dist/MsaViewPanel/genomeToMSA.test.js +69 -23
  35. package/dist/MsaViewPanel/launchAutoruns.test.d.ts +1 -0
  36. package/dist/MsaViewPanel/launchAutoruns.test.js +36 -0
  37. package/dist/MsaViewPanel/model.d.ts +18 -14
  38. package/dist/MsaViewPanel/model.js +17 -0
  39. package/dist/MsaViewPanel/msaDataStore.d.ts +5 -3
  40. package/dist/MsaViewPanel/msaDataStore.js +3 -12
  41. package/dist/MsaViewPanel/msaDataStore.test.js +8 -1
  42. package/dist/MsaViewPanel/observeProteinHighlights.test.js +4 -4
  43. package/dist/MsaViewPanel/regionSnapshot.test.d.ts +1 -0
  44. package/dist/MsaViewPanel/regionSnapshot.test.js +29 -0
  45. package/dist/MsaViewPanel/resolveConnectedTranscript.d.ts +41 -4
  46. package/dist/MsaViewPanel/resolveConnectedTranscript.js +103 -68
  47. package/dist/MsaViewPanel/resolveConnectedTranscript.test.d.ts +1 -0
  48. package/dist/MsaViewPanel/resolveConnectedTranscript.test.js +149 -0
  49. package/dist/MsaViewPanel/runLaunch.d.ts +8 -4
  50. package/dist/MsaViewPanel/runLaunch.js +15 -4
  51. package/dist/MsaViewPanel/runLaunch.test.js +16 -0
  52. package/dist/MsaViewPanel/storedData.test.js +23 -0
  53. package/dist/MsaViewPanel/syncGenomeHoverToMsaColumn.test.js +3 -2
  54. package/dist/MsaViewPanel/util.d.ts +23 -23
  55. package/dist/MsaViewPanel/util.js +23 -24
  56. package/dist/index.js +17 -10
  57. package/dist/jbrowse-plugin-msaview.umd.production.min.js +36 -36
  58. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  59. package/dist/utils/blastCache.d.ts +26 -2
  60. package/dist/utils/blastCache.js +51 -39
  61. package/dist/utils/blastCache.test.js +46 -19
  62. package/dist/utils/domainCache.d.ts +1 -1
  63. package/dist/utils/domainCache.js +18 -14
  64. package/dist/utils/ebiJobDispatcher.d.ts +11 -0
  65. package/dist/utils/ebiJobDispatcher.js +12 -13
  66. package/dist/utils/ebiJobDispatcher.test.js +17 -3
  67. package/dist/utils/eutils.d.ts +14 -0
  68. package/dist/utils/eutils.js +48 -14
  69. package/dist/utils/eutils.test.d.ts +1 -0
  70. package/dist/utils/eutils.test.js +31 -0
  71. package/dist/utils/idb.d.ts +16 -3
  72. package/dist/utils/idb.js +51 -5
  73. package/dist/utils/idb.test.d.ts +1 -0
  74. package/dist/utils/idb.test.js +78 -0
  75. package/dist/utils/ncbiDomains.js +4 -4
  76. package/dist/utils/ncbiOrthologs.d.ts +1 -1
  77. package/dist/utils/ncbiOrthologs.js +18 -17
  78. package/dist/utils/ncbiOrthologs.test.js +17 -1
  79. package/dist/utils/ncbiTaxonomy.js +14 -15
  80. package/dist/utils/taxonomyNames.js +23 -19
  81. package/dist/utils/taxonomyNames.test.d.ts +1 -0
  82. package/dist/utils/taxonomyNames.test.js +33 -0
  83. package/dist/utils/unirefHomologs.js +2 -2
  84. package/dist/utils/unirefHomologs.test.js +8 -1
  85. package/dist/version.d.ts +1 -1
  86. package/dist/version.js +1 -1
  87. package/package.json +9 -9
  88. package/src/LaunchMsaView/cleanProteinSequence.test.ts +91 -0
  89. package/src/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.tsx +35 -32
  90. package/src/LaunchMsaView/components/BlastQuery/BlastManualPanel.tsx +10 -14
  91. package/src/LaunchMsaView/components/BlastQuery/CachedBlastResults.tsx +16 -15
  92. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +34 -21
  93. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +18 -21
  94. package/src/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.test.ts +16 -0
  95. package/src/LaunchMsaView/components/OrthologQuery/OrthologSourceSelect.tsx +24 -2
  96. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +19 -13
  97. package/src/LaunchMsaView/components/SubmitCancelActions.test.tsx +27 -2
  98. package/src/LaunchMsaView/components/SubmitCancelActions.tsx +12 -7
  99. package/src/LaunchMsaView/components/calculateProteinSequence.ts +28 -18
  100. package/src/LaunchMsaView/components/launchConnectedView.ts +56 -0
  101. package/src/LaunchMsaView/detectQueryRow.ts +5 -7
  102. package/src/LaunchMsaView/util.ts +7 -1
  103. package/src/LaunchMsaViewExtensionPoint/index.test.ts +16 -0
  104. package/src/LaunchMsaViewExtensionPoint/index.ts +28 -1
  105. package/src/MsaViewPanel/afterCreateAutoruns.ts +12 -3
  106. package/src/MsaViewPanel/applyRegion.test.ts +55 -0
  107. package/src/MsaViewPanel/applyRegion.ts +33 -0
  108. package/src/MsaViewPanel/doLaunchBlast.test.ts +20 -1
  109. package/src/MsaViewPanel/doLaunchBlast.ts +2 -1
  110. package/src/MsaViewPanel/doLaunchOrthologs.test.ts +1 -1
  111. package/src/MsaViewPanel/genomeToMSA.test.ts +75 -23
  112. package/src/MsaViewPanel/genomeToMSA.ts +3 -2
  113. package/src/MsaViewPanel/launchAutoruns.test.ts +45 -0
  114. package/src/MsaViewPanel/model.ts +22 -0
  115. package/src/MsaViewPanel/msaDataStore.test.ts +14 -2
  116. package/src/MsaViewPanel/msaDataStore.ts +4 -12
  117. package/src/MsaViewPanel/observeProteinHighlights.test.ts +4 -4
  118. package/src/MsaViewPanel/regionSnapshot.test.ts +34 -0
  119. package/src/MsaViewPanel/resolveConnectedTranscript.test.ts +183 -0
  120. package/src/MsaViewPanel/resolveConnectedTranscript.ts +154 -71
  121. package/src/MsaViewPanel/runLaunch.test.ts +19 -0
  122. package/src/MsaViewPanel/runLaunch.ts +21 -4
  123. package/src/MsaViewPanel/storedData.test.ts +32 -0
  124. package/src/MsaViewPanel/syncGenomeHoverToMsaColumn.test.ts +3 -2
  125. package/src/MsaViewPanel/util.ts +38 -29
  126. package/src/index.ts +19 -10
  127. package/src/utils/blastCache.test.ts +59 -20
  128. package/src/utils/blastCache.ts +62 -39
  129. package/src/utils/domainCache.ts +27 -15
  130. package/src/utils/ebiJobDispatcher.test.ts +18 -3
  131. package/src/utils/ebiJobDispatcher.ts +12 -16
  132. package/src/utils/eutils.test.ts +39 -0
  133. package/src/utils/eutils.ts +64 -14
  134. package/src/utils/idb.test.ts +106 -0
  135. package/src/utils/idb.ts +57 -5
  136. package/src/utils/ncbiDomains.ts +4 -4
  137. package/src/utils/ncbiOrthologs.test.ts +20 -0
  138. package/src/utils/ncbiOrthologs.ts +26 -28
  139. package/src/utils/ncbiTaxonomy.ts +17 -20
  140. package/src/utils/taxonomyNames.test.ts +41 -0
  141. package/src/utils/taxonomyNames.ts +33 -19
  142. package/src/utils/unirefHomologs.test.ts +11 -1
  143. package/src/utils/unirefHomologs.ts +2 -2
  144. package/src/version.ts +1 -1
  145. package/dist/LaunchMsaView/components/BlastQuery/blastLaunchView.d.ts +0 -16
  146. package/dist/LaunchMsaView/components/BlastQuery/blastLaunchView.js +0 -31
  147. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts +0 -16
  148. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +0 -16
  149. package/dist/LaunchMsaView/components/OrthologQuery/orthologLaunchView.d.ts +0 -9
  150. package/dist/LaunchMsaView/components/OrthologQuery/orthologLaunchView.js +0 -15
  151. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts +0 -13
  152. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js +0 -22
  153. package/src/LaunchMsaView/components/BlastQuery/blastLaunchView.ts +0 -59
  154. package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +0 -43
  155. package/src/LaunchMsaView/components/OrthologQuery/orthologLaunchView.ts +0 -31
  156. package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts +0 -42

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