@datagrok/bio 2.0.25 → 2.0.26

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Files changed (23) hide show
  1. package/detectors.js +7 -2
  2. package/dist/package-test.js +2042 -833
  3. package/dist/package.js +2166 -684
  4. package/files/tests/nucleotidePairs.csv +146690 -0
  5. package/files/tests/peptidePairs.csv +103685 -0
  6. package/files/tests/toAtomicLevelTest.csv +7 -0
  7. package/package.json +5 -7
  8. package/setup.sh +1 -1
  9. package/src/calculations/monomerLevelMols.ts +7 -4
  10. package/src/package-test.ts +1 -1
  11. package/src/package.ts +13 -18
  12. package/src/substructure-search/substructure-search.ts +40 -13
  13. package/src/tests/{WebLogo-test.ts → bio-tests.ts} +16 -2
  14. package/src/tests/checkInputColumn-tests.ts +6 -7
  15. package/src/tests/detectors-test.ts +27 -19
  16. package/src/tests/renderers-test.ts +9 -5
  17. package/src/tests/test-sequnces-generators.ts +7 -4
  18. package/src/utils/cell-renderer.ts +5 -2
  19. package/src/widgets/bio-substructure-filter.ts +24 -5
  20. package/src/widgets/representations.ts +3 -2
  21. package/src/const.ts +0 -30
  22. package/src/monomer-library.ts +0 -199
  23. package/src/utils/utils.ts +0 -135
package/detectors.js CHANGED
@@ -22,6 +22,11 @@ const ALPHABET = {
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  UN: 'UN',
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  };
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+ const ALIGNMENT = {
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+ SEQ_MSA: 'SEQ.MSA',
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+ SEQ: 'SEQ',
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+ };
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+
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  /** Class for handling notation units in Macromolecule columns */
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  class UnitsHandler {
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  static TAGS = {
@@ -128,7 +133,7 @@ class BioPackageDetectors extends DG.Package {
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  const units = NOTATION.FASTA;
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  col.setTag(DG.TAGS.UNITS, units);
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- col.setTag(UnitsHandler.TAGS.aligned, 'SEQ.MSA');
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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;
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  }
@@ -145,7 +150,7 @@ class BioPackageDetectors extends DG.Package {
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  if (separator && BioPackageDetectors.checkForbiddenWithSeparators(stats.freq)) return null;
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  const format = separator ? NOTATION.SEPARATOR : NOTATION.FASTA;
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- const aligned = stats.sameLength ? 'SEQ.MSA' : 'SEQ';
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+ const aligned = stats.sameLength ? ALIGNMENT.SEQ_MSA : ALIGNMENT.SEQ;
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  // TODO: If separator detected, then extra efforts to detect alphabet are allowed.
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  const alphabet = BioPackageDetectors.detectAlphabet(stats.freq, candidateAlphabets, gapSymbol);