jbrowse-plugin-msaview 2.1.0 → 2.2.1

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 (170) hide show
  1. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +3 -3
  2. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
  3. package/dist/AddHighlightModel/MsaToGenomeHighlight.js +3 -1
  4. package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
  5. package/dist/ExternalLink.d.ts +3 -0
  6. package/dist/ExternalLink.js +11 -0
  7. package/dist/ExternalLink.js.map +1 -0
  8. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +28 -33
  9. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +1 -1
  10. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js +0 -6
  11. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map +1 -1
  12. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts +1 -0
  13. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js +12 -22
  14. package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map +1 -1
  15. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts +2 -0
  16. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js +20 -0
  17. package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map +1 -0
  18. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts +24 -0
  19. package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map +1 -0
  20. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts +10 -0
  21. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +27 -0
  22. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +1 -0
  23. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +5 -5
  24. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
  25. package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/NcbiBlastPanel.d.ts → ManualMSALoader/ManualMSALoader.d.ts} +2 -2
  26. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +103 -0
  27. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -0
  28. package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.js.map +1 -1
  29. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts +14 -0
  30. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +12 -0
  31. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map +1 -0
  32. package/dist/LaunchMsaView/components/{MSALoader/MSALoader.d.ts → NCBIBlastQuery/NCBIBlastAutomaticPanel.d.ts} +4 -2
  33. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +89 -0
  34. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -0
  35. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.d.ts +10 -0
  36. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +55 -0
  37. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -0
  38. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.d.ts +5 -0
  39. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js +11 -0
  40. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js.map +1 -0
  41. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.d.ts +7 -0
  42. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js +30 -0
  43. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map +1 -0
  44. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.d.ts +5 -0
  45. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js +26 -0
  46. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map +1 -0
  47. package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.d.ts → NCBIBlastQuery/blastLaunchView.d.ts} +2 -1
  48. package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.js → NCBIBlastQuery/blastLaunchView.js} +3 -6
  49. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -0
  50. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts +1 -0
  51. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js +2 -0
  52. package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map +1 -0
  53. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +17 -16
  54. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  55. package/dist/LaunchMsaView/components/TranscriptSelector.d.ts +10 -0
  56. package/dist/LaunchMsaView/components/TranscriptSelector.js +45 -0
  57. package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -0
  58. package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/calculateProteinSequence.d.ts → calculateProteinSequence.d.ts} +1 -2
  59. package/dist/LaunchMsaView/components/calculateProteinSequence.js +39 -0
  60. package/dist/LaunchMsaView/components/calculateProteinSequence.js.map +1 -0
  61. package/dist/LaunchMsaView/components/fetchSeq.js.map +1 -0
  62. package/dist/LaunchMsaView/components/types.js +2 -0
  63. package/dist/LaunchMsaView/components/types.js.map +1 -0
  64. package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.d.ts → useFeatureSequence.d.ts} +2 -1
  65. package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.js → useFeatureSequence.js} +12 -1
  66. package/dist/LaunchMsaView/components/useFeatureSequence.js.map +1 -0
  67. package/dist/LaunchMsaView/components/util.js.map +1 -0
  68. package/dist/LaunchMsaView/util.d.ts +5 -1
  69. package/dist/LaunchMsaView/util.js +15 -1
  70. package/dist/LaunchMsaView/util.js.map +1 -1
  71. package/dist/MsaViewPanel/components/LoadingBLAST.d.ts +2 -1
  72. package/dist/MsaViewPanel/components/LoadingBLAST.js +6 -6
  73. package/dist/MsaViewPanel/components/LoadingBLAST.js.map +1 -1
  74. package/dist/MsaViewPanel/components/MsaViewPanel.js +1 -1
  75. package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
  76. package/dist/MsaViewPanel/components/RIDLink.d.ts +2 -1
  77. package/dist/MsaViewPanel/components/RIDLink.js +6 -9
  78. package/dist/MsaViewPanel/components/RIDLink.js.map +1 -1
  79. package/dist/MsaViewPanel/doLaunchBlast.js +18 -20
  80. package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
  81. package/dist/MsaViewPanel/model.d.ts +3 -4
  82. package/dist/MsaViewPanel/model.js.map +1 -1
  83. package/dist/ReadOnlyTextField2.d.ts +4 -0
  84. package/dist/ReadOnlyTextField2.js +20 -0
  85. package/dist/ReadOnlyTextField2.js.map +1 -0
  86. package/dist/jbrowse-plugin-msaview.umd.production.min.js +41 -51
  87. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  88. package/dist/utils/fetch.d.ts +1 -1
  89. package/dist/utils/fetch.js.map +1 -1
  90. package/dist/utils/ncbiBlast.d.ts +2 -2
  91. package/dist/utils/ncbiBlast.js +29 -15
  92. package/dist/utils/ncbiBlast.js.map +1 -1
  93. package/dist/utils/types.d.ts +20 -0
  94. package/dist/utils/types.js +2 -0
  95. package/dist/utils/types.js.map +1 -0
  96. package/package.json +3 -3
  97. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +3 -3
  98. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +2 -1
  99. package/src/ExternalLink.tsx +15 -0
  100. package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +39 -55
  101. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts +0 -6
  102. package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts +19 -54
  103. package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts +22 -0
  104. package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts +28 -0
  105. package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +29 -0
  106. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +9 -5
  107. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +219 -0
  108. package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +34 -0
  109. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +226 -0
  110. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +111 -0
  111. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.tsx +34 -0
  112. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx +82 -0
  113. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.tsx +75 -0
  114. package/src/LaunchMsaView/components/{NewNCBIBlastQuery/ncbiBlastLaunchView.ts → NCBIBlastQuery/blastLaunchView.ts} +4 -5
  115. package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts +1 -0
  116. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +27 -37
  117. package/src/LaunchMsaView/components/TranscriptSelector.tsx +99 -0
  118. package/src/LaunchMsaView/components/{NewNCBIBlastQuery/calculateProteinSequence.ts → calculateProteinSequence.ts} +12 -22
  119. package/src/LaunchMsaView/components/{NewNCBIBlastQuery/useFeatureSequence.ts → useFeatureSequence.ts} +16 -2
  120. package/src/LaunchMsaView/util.ts +22 -2
  121. package/src/MsaViewPanel/components/LoadingBLAST.tsx +26 -8
  122. package/src/MsaViewPanel/components/MsaViewPanel.tsx +5 -1
  123. package/src/MsaViewPanel/components/RIDLink.tsx +8 -8
  124. package/src/MsaViewPanel/doLaunchBlast.ts +29 -30
  125. package/src/MsaViewPanel/model.ts +1 -0
  126. package/src/ReadOnlyTextField2.tsx +33 -0
  127. package/src/utils/fetch.ts +2 -2
  128. package/src/utils/ncbiBlast.ts +40 -30
  129. package/src/utils/types.ts +14 -0
  130. package/dist/LaunchMsaView/components/MSALoader/MSALoader.js +0 -94
  131. package/dist/LaunchMsaView/components/MSALoader/MSALoader.js.map +0 -1
  132. package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.d.ts +0 -1
  133. package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js +0 -12
  134. package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js.map +0 -1
  135. package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.d.ts +0 -9
  136. package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js +0 -36
  137. package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js.map +0 -1
  138. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js +0 -85
  139. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map +0 -1
  140. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js +0 -47
  141. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map +0 -1
  142. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/fetchSeq.js.map +0 -1
  143. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.d.ts +0 -1
  144. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js +0 -2
  145. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js.map +0 -1
  146. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map +0 -1
  147. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/types.js.map +0 -1
  148. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map +0 -1
  149. package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.js.map +0 -1
  150. package/dist/OpenInNewIcon.d.ts +0 -3
  151. package/dist/OpenInNewIcon.js +0 -8
  152. package/dist/OpenInNewIcon.js.map +0 -1
  153. package/src/LaunchMsaView/components/MSALoader/MSALoader.tsx +0 -130
  154. package/src/LaunchMsaView/components/MSALoader/fetchGeneList.ts +0 -13
  155. package/src/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.ts +0 -55
  156. package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx +0 -171
  157. package/src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx +0 -1
  158. package/src/OpenInNewIcon.tsx +0 -14
  159. /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery → EnsemblGeneTree}/types.js +0 -0
  160. /package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.d.ts +0 -0
  161. /package/dist/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.js +0 -0
  162. /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/fetchSeq.d.ts → fetchSeq.d.ts} +0 -0
  163. /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/fetchSeq.js → fetchSeq.js} +0 -0
  164. /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/types.d.ts → types.d.ts} +0 -0
  165. /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/util.d.ts → util.d.ts} +0 -0
  166. /package/dist/LaunchMsaView/components/{NewNCBIBlastQuery/util.js → util.js} +0 -0
  167. /package/src/LaunchMsaView/components/{EnsemblGeneTree → ManualMSALoader}/fetchGeneList.ts +0 -0
  168. /package/src/LaunchMsaView/components/{NewNCBIBlastQuery/fetchSeq.ts → fetchSeq.ts} +0 -0
  169. /package/src/LaunchMsaView/components/{NewNCBIBlastQuery/types.ts → types.ts} +0 -0
  170. /package/src/LaunchMsaView/components/{NewNCBIBlastQuery/util.ts → util.ts} +0 -0

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