jbrowse-plugin-msaview 2.2.3 → 2.2.4

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 (162) hide show
  1. package/CHANGELOG.md +1 -1
  2. package/README.md +229 -0
  3. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js +23 -18
  4. package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
  5. package/dist/AddHighlightModel/MsaToGenomeHighlight.js +23 -13
  6. package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
  7. package/dist/AddHighlightModel/index.js +8 -1
  8. package/dist/AddHighlightModel/index.js.map +1 -1
  9. package/dist/AddHighlightModel/util.d.ts +2 -2
  10. package/dist/BgzipFastaMsaAdapter/configSchema.d.ts +2 -2
  11. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js +5 -11
  12. package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map +1 -1
  13. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js +5 -1
  14. package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map +1 -1
  15. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js +16 -16
  16. package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map +1 -1
  17. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +38 -46
  18. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map +1 -1
  19. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts +4 -3
  20. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +4 -3
  21. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map +1 -1
  22. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.d.ts +9 -0
  23. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +76 -0
  24. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -0
  25. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +35 -13
  26. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
  27. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js +6 -12
  28. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map +1 -1
  29. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts +6 -0
  30. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js +15 -0
  31. package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map +1 -1
  32. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +12 -34
  33. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map +1 -1
  34. package/dist/LaunchMsaView/components/PreLoadedMSA/consts.d.ts +1 -0
  35. package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js +1 -0
  36. package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js.map +1 -1
  37. package/dist/LaunchMsaView/components/TabPanel.d.ts +2 -2
  38. package/dist/LaunchMsaView/components/TranscriptSelector.d.ts +2 -2
  39. package/dist/LaunchMsaView/components/TranscriptSelector.js +3 -6
  40. package/dist/LaunchMsaView/components/TranscriptSelector.js.map +1 -1
  41. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +6 -4
  42. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map +1 -1
  43. package/dist/LaunchMsaView/components/useTranscriptSelection.d.ts +16 -0
  44. package/dist/LaunchMsaView/components/useTranscriptSelection.js +31 -0
  45. package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +1 -0
  46. package/dist/LaunchMsaView/components/util.d.ts +3 -1
  47. package/dist/LaunchMsaView/components/util.js +12 -2
  48. package/dist/LaunchMsaView/components/util.js.map +1 -1
  49. package/dist/LaunchMsaView/util.d.ts +2 -0
  50. package/dist/LaunchMsaView/util.js +16 -4
  51. package/dist/LaunchMsaView/util.js.map +1 -1
  52. package/dist/LaunchMsaViewExtensionPoint/index.d.ts +2 -0
  53. package/dist/LaunchMsaViewExtensionPoint/index.js +31 -0
  54. package/dist/LaunchMsaViewExtensionPoint/index.js.map +1 -0
  55. package/dist/MsaViewPanel/components/ConnectStructureDialog.d.ts +7 -0
  56. package/dist/MsaViewPanel/components/ConnectStructureDialog.js +56 -0
  57. package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map +1 -0
  58. package/dist/MsaViewPanel/components/MsaViewPanel.js +4 -2
  59. package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
  60. package/dist/MsaViewPanel/doLaunchBlast.d.ts +1 -0
  61. package/dist/MsaViewPanel/doLaunchBlast.js +65 -19
  62. package/dist/MsaViewPanel/doLaunchBlast.js.map +1 -1
  63. package/dist/MsaViewPanel/genomeToMSA.d.ts +6 -0
  64. package/dist/MsaViewPanel/genomeToMSA.js +38 -8
  65. package/dist/MsaViewPanel/genomeToMSA.js.map +1 -1
  66. package/dist/MsaViewPanel/genomeToMSA.test.d.ts +1 -0
  67. package/dist/MsaViewPanel/genomeToMSA.test.js +244 -0
  68. package/dist/MsaViewPanel/genomeToMSA.test.js.map +1 -0
  69. package/dist/MsaViewPanel/model.d.ts +717 -226
  70. package/dist/MsaViewPanel/model.js +467 -39
  71. package/dist/MsaViewPanel/model.js.map +1 -1
  72. package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts +7 -2
  73. package/dist/MsaViewPanel/msaCoordToGenomeCoord.js +26 -27
  74. package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map +1 -1
  75. package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.d.ts +1 -0
  76. package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js +240 -0
  77. package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js.map +1 -0
  78. package/dist/MsaViewPanel/msaDataStore.d.ts +14 -0
  79. package/dist/MsaViewPanel/msaDataStore.js +197 -0
  80. package/dist/MsaViewPanel/msaDataStore.js.map +1 -0
  81. package/dist/MsaViewPanel/pairwiseAlignment.d.ts +27 -0
  82. package/dist/MsaViewPanel/pairwiseAlignment.js +776 -0
  83. package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -0
  84. package/dist/MsaViewPanel/pairwiseAlignment.test.d.ts +1 -0
  85. package/dist/MsaViewPanel/pairwiseAlignment.test.js +112 -0
  86. package/dist/MsaViewPanel/pairwiseAlignment.test.js.map +1 -0
  87. package/dist/MsaViewPanel/structureConnection.d.ts +27 -0
  88. package/dist/MsaViewPanel/structureConnection.js +46 -0
  89. package/dist/MsaViewPanel/structureConnection.js.map +1 -0
  90. package/dist/MsaViewPanel/structureConnection.test.d.ts +1 -0
  91. package/dist/MsaViewPanel/structureConnection.test.js +122 -0
  92. package/dist/MsaViewPanel/structureConnection.test.js.map +1 -0
  93. package/dist/MsaViewPanel/types.d.ts +13 -0
  94. package/dist/MsaViewPanel/types.js +2 -0
  95. package/dist/MsaViewPanel/types.js.map +1 -0
  96. package/dist/MsaViewPanel/util.d.ts +7 -0
  97. package/dist/MsaViewPanel/util.js +10 -0
  98. package/dist/MsaViewPanel/util.js.map +1 -1
  99. package/dist/index.d.ts +5 -5
  100. package/dist/index.js +3 -1
  101. package/dist/index.js.map +1 -1
  102. package/dist/jbrowse-plugin-msaview.umd.production.min.js +39 -90
  103. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  104. package/dist/utils/blastCache.d.ts +34 -0
  105. package/dist/utils/blastCache.js +58 -0
  106. package/dist/utils/blastCache.js.map +1 -0
  107. package/dist/utils/fetch.d.ts +1 -1
  108. package/dist/utils/fetch.js +1 -1
  109. package/dist/utils/fetch.js.map +1 -1
  110. package/dist/utils/ncbiBlast.d.ts +1 -5
  111. package/dist/utils/taxonomyNames.d.ts +5 -0
  112. package/dist/utils/taxonomyNames.js +79 -0
  113. package/dist/utils/taxonomyNames.js.map +1 -0
  114. package/dist/utils/types.d.ts +8 -5
  115. package/package.json +50 -54
  116. package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +37 -21
  117. package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +38 -17
  118. package/src/AddHighlightModel/index.tsx +9 -4
  119. package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx +13 -13
  120. package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts +6 -0
  121. package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx +30 -23
  122. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +64 -51
  123. package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +9 -6
  124. package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +146 -0
  125. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +53 -22
  126. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx +8 -13
  127. package/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts +25 -0
  128. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +27 -47
  129. package/src/LaunchMsaView/components/PreLoadedMSA/consts.ts +1 -0
  130. package/src/LaunchMsaView/components/TabPanel.tsx +2 -2
  131. package/src/LaunchMsaView/components/TranscriptSelector.tsx +13 -20
  132. package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +5 -5
  133. package/src/LaunchMsaView/components/useTranscriptSelection.ts +48 -0
  134. package/src/LaunchMsaView/components/util.ts +17 -2
  135. package/src/LaunchMsaView/index.ts +1 -1
  136. package/src/LaunchMsaView/util.ts +25 -6
  137. package/src/LaunchMsaViewExtensionPoint/index.ts +74 -0
  138. package/src/MsaViewPanel/components/ConnectStructureDialog.tsx +156 -0
  139. package/src/MsaViewPanel/components/MsaViewPanel.tsx +6 -1
  140. package/src/MsaViewPanel/doLaunchBlast.ts +83 -23
  141. package/src/MsaViewPanel/genomeToMSA.test.ts +281 -0
  142. package/src/MsaViewPanel/genomeToMSA.ts +43 -10
  143. package/src/MsaViewPanel/model.ts +590 -43
  144. package/src/MsaViewPanel/msaCoordToGenomeCoord.test.ts +256 -0
  145. package/src/MsaViewPanel/msaCoordToGenomeCoord.ts +43 -29
  146. package/src/MsaViewPanel/msaDataStore.ts +236 -0
  147. package/src/MsaViewPanel/pairwiseAlignment.test.ts +140 -0
  148. package/src/MsaViewPanel/pairwiseAlignment.ts +818 -0
  149. package/src/MsaViewPanel/structureConnection.test.ts +143 -0
  150. package/src/MsaViewPanel/structureConnection.ts +72 -0
  151. package/src/MsaViewPanel/types.ts +14 -0
  152. package/src/MsaViewPanel/util.ts +11 -0
  153. package/src/index.ts +3 -1
  154. package/src/utils/blastCache.ts +114 -0
  155. package/src/utils/fetch.ts +1 -1
  156. package/src/utils/taxonomyNames.ts +111 -0
  157. package/src/utils/types.ts +9 -1
  158. package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.d.ts +0 -5
  159. package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.js +0 -16
  160. package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.js.map +0 -1
  161. package/dist/out.js +0 -55381
  162. package/src/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.ts +0 -25
@@ -1,25 +0,0 @@
1
- import { getId } from '../../util'
2
-
3
- import type { Feature } from '@jbrowse/core/util'
4
-
5
- // Function to find a valid transcript ID that exists in the MSA list
6
- export function findValidTranscriptId({
7
- transcriptsList,
8
- validMsaList,
9
- }: {
10
- transcriptsList: Feature[]
11
- validMsaList?: string[]
12
- }) {
13
- if (!validMsaList || validMsaList.length === 0) {
14
- return null
15
- }
16
-
17
- // Try to find a transcript ID that exists in the MSA list
18
- for (const transcript of transcriptsList) {
19
- const id = getId(transcript)
20
- if (id && validMsaList.includes(id)) {
21
- return id
22
- }
23
- }
24
- return null
25
- }