@datagrok/bio 2.1.10 → 2.1.12

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Files changed (34) hide show
  1. package/.eslintrc.json +1 -0
  2. package/detectors.js +5 -4
  3. package/dist/package-test.js +2182 -57664
  4. package/dist/package.js +1773 -57252
  5. package/dist/vendors-node_modules_datagrok-libraries_ml_src_workers_dimensionality-reducer_js.js +301 -250
  6. package/package.json +10 -12
  7. package/src/analysis/sequence-activity-cliffs.ts +5 -5
  8. package/src/analysis/sequence-diversity-viewer.ts +3 -2
  9. package/src/analysis/sequence-search-base-viewer.ts +2 -1
  10. package/src/analysis/sequence-similarity-viewer.ts +2 -2
  11. package/src/calculations/monomerLevelMols.ts +3 -3
  12. package/src/package.ts +28 -25
  13. package/src/substructure-search/substructure-search.ts +9 -9
  14. package/src/tests/Palettes-test.ts +9 -9
  15. package/src/tests/WebLogo-positions-test.ts +64 -57
  16. package/src/tests/bio-tests.ts +31 -21
  17. package/src/tests/checkInputColumn-tests.ts +17 -17
  18. package/src/tests/converters-test.ts +30 -30
  19. package/src/tests/detectors-benchmark-tests.ts +15 -16
  20. package/src/tests/detectors-tests.ts +31 -24
  21. package/src/tests/fasta-export-tests.ts +2 -3
  22. package/src/tests/renderers-test.ts +17 -15
  23. package/src/tests/splitters-test.ts +3 -3
  24. package/src/tests/utils/sequences-generators.ts +7 -7
  25. package/src/utils/cell-renderer.ts +33 -24
  26. package/src/utils/convert.ts +10 -10
  27. package/src/utils/multiple-sequence-alignment.ts +6 -7
  28. package/src/utils/save-as-fasta.ts +8 -8
  29. package/src/viewers/vd-regions-viewer.ts +15 -14
  30. package/tsconfig.json +1 -1
  31. package/jest.config.js +0 -33
  32. package/src/__jest__/remote.test.ts +0 -77
  33. package/src/__jest__/test-node.ts +0 -98
  34. package/test-Bio-62cc009524f3-e7a922ae.html +0 -392
package/.eslintrc.json CHANGED
@@ -25,6 +25,7 @@
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  ],
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  "no-unused-vars": "warn",
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  "require-jsdoc": "off",
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+ "valid-jsdoc": "warn",
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  "spaced-comment": "off",
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  "linebreak-style": "off",
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  "curly": [
package/detectors.js CHANGED
@@ -139,7 +139,7 @@ class BioPackageDetectors extends DG.Package {
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  const statsAsChars = this.getStats(categoriesSample, 5,
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  this.getSplitterAsChars(SEQ_SAMPLE_LENGTH_LIMIT));
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  // Empty statsAsShars.freq alphabet means no strings of enough length presented in the data
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- if (Object.keys(statsAsChars.freq).length === 0) return;
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+ if (Object.keys(statsAsChars.freq).length === 0) return null;
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  const decoy = this.detectAlphabet(statsAsChars.freq, decoyAlphabets, null);
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  if (decoy != ALPHABET.UN) return null;
@@ -150,14 +150,13 @@ class BioPackageDetectors extends DG.Package {
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  const splitter = separator ? this.getSplitterWithSeparator(separator, SEQ_SAMPLE_LENGTH_LIMIT) :
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  this.getSplitterAsFasta(SEQ_SAMPLE_LENGTH_LIMIT);
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- col.setTag(DG.TAGS.UNITS, units);
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- if (separator) col.setTag(UnitsHandler.TAGS.separator, separator);
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-
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  if (statsAsChars.sameLength) {
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  const stats = this.getStats(categoriesSample, 5, splitter);
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  const alphabet = this.detectAlphabet(stats.freq, candidateAlphabets, '-');
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  if (alphabet === ALPHABET.UN) return null;
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+ col.setTag(DG.TAGS.UNITS, units);
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+ if (separator) col.setTag(UnitsHandler.TAGS.separator, separator);
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  col.setTag(UnitsHandler.TAGS.aligned, ALIGNMENT.SEQ_MSA);
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  col.setTag(UnitsHandler.TAGS.alphabet, alphabet);
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  return DG.SEMTYPE.MACROMOLECULE;
@@ -175,6 +174,8 @@ class BioPackageDetectors extends DG.Package {
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  // const forbidden = this.checkForbiddenWoSeparator(stats.freq);
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  if (separator || alphabet != 'UN') {
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+ col.setTag(DG.TAGS.UNITS, units);
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+ if (separator) col.setTag(UnitsHandler.TAGS.separator, separator);
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  col.setTag(UnitsHandler.TAGS.aligned, aligned);
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  col.setTag(UnitsHandler.TAGS.alphabet, alphabet);
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  if (alphabet === ALPHABET.UN) {