jbrowse-plugin-msaview 2.10.0 → 2.10.2

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Files changed (59) hide show
  1. package/dist/LaunchMsaView/components/BlastQuery/useCachedBlastResults.d.ts +1 -1
  2. package/dist/LaunchMsaView/components/BlastQuery/useCachedBlastResults.js +14 -17
  3. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +1 -1
  4. package/dist/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.d.ts +2 -1
  5. package/dist/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.js +48 -50
  6. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +4 -5
  7. package/dist/LaunchMsaView/components/useFeatureSequence.d.ts +6 -4
  8. package/dist/LaunchMsaView/components/useFeatureSequence.js +20 -11
  9. package/dist/LaunchMsaView/components/useTranscriptSelection.d.ts +1 -1
  10. package/dist/LaunchMsaView/extendStateModel.test.d.ts +1 -0
  11. package/dist/LaunchMsaView/extendStateModel.test.js +69 -0
  12. package/dist/LaunchMsaView/index.d.ts +2 -0
  13. package/dist/LaunchMsaView/index.js +44 -54
  14. package/dist/LaunchMsaView/launchTarget.d.ts +25 -0
  15. package/dist/LaunchMsaView/launchTarget.js +42 -0
  16. package/dist/LaunchMsaView/launchTarget.test.d.ts +1 -0
  17. package/dist/LaunchMsaView/launchTarget.test.js +54 -0
  18. package/dist/MsaViewPanel/doLaunchOrthologs.js +4 -2
  19. package/dist/MsaViewPanel/model.d.ts +4 -2
  20. package/dist/jbrowse-plugin-msaview.umd.production.min.js +29 -40
  21. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  22. package/dist/utils/ebiJobDispatcher.test.js +10 -1
  23. package/dist/utils/ncbiOrthologs.d.ts +1 -1
  24. package/dist/utils/ncbiOrthologs.js +1 -1
  25. package/dist/utils/ncbiTaxonomy.d.ts +19 -0
  26. package/dist/utils/ncbiTaxonomy.js +42 -9
  27. package/dist/utils/ncbiTaxonomy.test.d.ts +1 -0
  28. package/dist/utils/ncbiTaxonomy.test.js +69 -0
  29. package/dist/utils/useFetch.d.ts +22 -0
  30. package/dist/utils/useFetch.js +79 -0
  31. package/dist/utils/useFetch.test.d.ts +1 -0
  32. package/dist/utils/useFetch.test.js +23 -0
  33. package/dist/version.d.ts +1 -1
  34. package/dist/version.js +1 -1
  35. package/package.json +7 -6
  36. package/src/LaunchMsaView/components/BlastQuery/useCachedBlastResults.ts +16 -29
  37. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +1 -0
  38. package/src/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.tsx +63 -49
  39. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +3 -6
  40. package/src/LaunchMsaView/components/useFeatureSequence.ts +35 -15
  41. package/src/LaunchMsaView/extendStateModel.test.ts +76 -0
  42. package/src/LaunchMsaView/index.ts +47 -80
  43. package/src/LaunchMsaView/launchTarget.test.ts +77 -0
  44. package/src/LaunchMsaView/launchTarget.ts +65 -0
  45. package/src/MsaViewPanel/doLaunchOrthologs.ts +4 -2
  46. package/src/MsaViewPanel/model.ts +4 -2
  47. package/src/utils/ebiJobDispatcher.test.ts +10 -1
  48. package/src/utils/ncbiOrthologs.ts +1 -1
  49. package/src/utils/ncbiTaxonomy.test.ts +84 -0
  50. package/src/utils/ncbiTaxonomy.ts +52 -9
  51. package/src/utils/useFetch.test.ts +30 -0
  52. package/src/utils/useFetch.ts +116 -0
  53. package/src/version.ts +1 -1
  54. package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts +0 -12
  55. package/dist/LaunchMsaView/components/useSWRFeatureSequence.js +0 -25
  56. package/dist/utils/swrConfig.d.ts +0 -8
  57. package/dist/utils/swrConfig.js +0 -8
  58. package/src/LaunchMsaView/components/useSWRFeatureSequence.ts +0 -54
  59. package/src/utils/swrConfig.ts +0 -8
package/dist/MsaViewPanel/model.d.ts CHANGED
@@ -21,7 +21,8 @@ export interface OrthologParams {
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  /** NCBI taxon id of the assembly the query gene came from */
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  taxId: number;
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  /**
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- * taxon ids to include as rows (the query taxon is represented by QUERY).
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+ * taxon ids to include as rows. The query taxon has its own row already, so
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+ * it is excluded from this set whether or not it is named.
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  * Omitted means every species NCBI has an ortholog for, in its report order,
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  * which is what a launch that just wants "this gene across species" wants.
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  */
@@ -38,7 +39,8 @@ export interface OrthologParams {
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  msaAlgorithm: MsaAlgorithm;
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  selectedTranscript?: Feature;
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  /**
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- * The QUERY row. The launch dialog always supplies it, translated from the
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+ * The query row, named `<species>_query`. The launch dialog always supplies
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+ * it, translated from the
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  * transcript the user picked, which is what `connectedFeature` maps genome
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  * coordinates through. Omitted — a session spec naming a gene and nothing
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  * else — the query row becomes NCBI's representative protein for the resolved