jbrowse-plugin-msaview 2.3.2 → 2.3.5

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Files changed (43) hide show
  1. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +2 -11
  2. package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
  3. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +24 -47
  4. package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -1
  5. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +5 -20
  6. package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
  7. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.d.ts +7 -0
  8. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js +29 -0
  9. package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map +1 -0
  10. package/dist/LaunchMsaView/components/useTranscriptSelection.js +15 -14
  11. package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +1 -1
  12. package/dist/MsaViewPanel/afterCreateAutoruns.js +14 -9
  13. package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
  14. package/dist/MsaViewPanel/components/ErrorBoundary.d.ts +19 -0
  15. package/dist/MsaViewPanel/components/ErrorBoundary.js +22 -0
  16. package/dist/MsaViewPanel/components/ErrorBoundary.js.map +1 -0
  17. package/dist/MsaViewPanel/components/MsaViewPanel.js +4 -2
  18. package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
  19. package/dist/MsaViewPanel/model.d.ts +0 -12
  20. package/dist/MsaViewPanel/model.js +1 -1
  21. package/dist/MsaViewPanel/model.js.map +1 -1
  22. package/dist/MsaViewPanel/pairwiseAlignment.js +9 -4
  23. package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -1
  24. package/dist/jbrowse-plugin-msaview.umd.production.min.js +26 -26
  25. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  26. package/dist/utils/blastCache.js +2 -3
  27. package/dist/utils/blastCache.js.map +1 -1
  28. package/dist/version.d.ts +1 -1
  29. package/dist/version.js +1 -1
  30. package/dist/version.js.map +1 -1
  31. package/package.json +35 -34
  32. package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +2 -11
  33. package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +23 -49
  34. package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +6 -20
  35. package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts +49 -0
  36. package/src/LaunchMsaView/components/useTranscriptSelection.ts +25 -17
  37. package/src/MsaViewPanel/afterCreateAutoruns.ts +26 -9
  38. package/src/MsaViewPanel/components/ErrorBoundary.tsx +40 -0
  39. package/src/MsaViewPanel/components/MsaViewPanel.tsx +14 -11
  40. package/src/MsaViewPanel/model.ts +32 -21
  41. package/src/MsaViewPanel/pairwiseAlignment.ts +9 -4
  42. package/src/utils/blastCache.ts +2 -3
  43. package/src/version.ts +1 -1
package/dist/MsaViewPanel/pairwiseAlignment.js CHANGED
@@ -53,10 +53,11 @@ export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_
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  const matchScore = getScore(seq1[i - 1], seq2[j - 1]);
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  const prevM = M[i - 1][j - 1];
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  const prevIx = Ix[i - 1][j - 1];
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- if (M[i][j] === prevM + matchScore) {
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+ const currentScore = M[i][j];
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+ if (currentScore === prevM + matchScore) {
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  currentMatrix = 'M';
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  }
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- else if (M[i][j] === prevIx + matchScore) {
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+ else if (currentScore === prevIx + matchScore) {
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  currentMatrix = 'Ix';
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  }
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  else {
@@ -68,13 +69,17 @@ export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_
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  else if (currentMatrix === 'Ix' && i > 0) {
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  alignedSeq1 = seq1[i - 1] + alignedSeq1;
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  alignedSeq2 = '-' + alignedSeq2;
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- currentMatrix = Ix[i][j] === M[i - 1][j] + gapOpen ? 'M' : 'Ix';
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+ const ixScore = Ix[i][j];
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+ const mScore = M[i - 1][j] + gapOpen;
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+ currentMatrix = ixScore === mScore ? 'M' : 'Ix';
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  i--;
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  }
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  else if (j > 0) {
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  alignedSeq1 = '-' + alignedSeq1;
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  alignedSeq2 = seq2[j - 1] + alignedSeq2;
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- currentMatrix = Iy[i][j] === M[i][j - 1] + gapOpen ? 'M' : 'Iy';
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+ const iyScore = Iy[i][j];
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+ const mScore = M[i][j - 1] + gapOpen;
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+ currentMatrix = iyScore === mScore ? 'M' : 'Iy';
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  j--;
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  }
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  else {
package/dist/MsaViewPanel/pairwiseAlignment.js.map CHANGED
@@ -1 +1 @@
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