@datagrok/bio 1.5.10 → 1.7.1

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Files changed (29) hide show
  1. package/detectors.js +1 -1
  2. package/dist/package-test.js +522 -475
  3. package/dist/package.js +312 -469
  4. package/files/samples/sample_FASTA.csv +0 -1
  5. package/files/samples/sample_FASTA.fasta +0 -3
  6. package/files/samples/sample_FASTA_DNA.csv +101 -0
  7. package/files/samples/sample_FASTA_PT.csv +101 -0
  8. package/files/samples/sample_FASTA_RNA.csv +101 -0
  9. package/files/{samples → tests}/peptides_complex_msa.csv +0 -0
  10. package/files/{samples → tests}/peptides_simple_msa.csv +0 -0
  11. package/files/{samples/testSmiles.csv → tests/sar-small.csv} +0 -0
  12. package/files/{samples → tests}/testDemog.csv +0 -0
  13. package/files/{samples → tests}/testHelm.csv +0 -0
  14. package/files/{samples → tests}/testId.csv +0 -0
  15. package/files/tests/testSmiles.csv +201 -0
  16. package/files/{samples → tests}/testSmiles2.csv +0 -0
  17. package/package.json +2 -2
  18. package/scripts/generate_fasta_csv_for_alphabets.R +70 -0
  19. package/src/package-test.ts +1 -0
  20. package/src/package.ts +89 -27
  21. package/src/tests/convert-test.ts +49 -8
  22. package/src/tests/detectors-test.ts +12 -6
  23. package/src/utils/cell-renderer.ts +58 -91
  24. package/src/utils/convert.ts +10 -14
  25. package/src/utils/multiple-sequence-alignment.ts +0 -1
  26. package/src/utils/notation-converter.ts +178 -65
  27. package/{test-Bio-34f75e5127b8-936bf89b.html → test-Bio-34f75e5127b8-726a0649.html} +2 -2
  28. package/src/utils/chem-palette.ts +0 -280
  29. package/src/utils/misc.ts +0 -29
package/detectors.js CHANGED
@@ -172,7 +172,7 @@ class BioPackageDetectors extends DG.Package {
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  * @param freq frequencies of monomers in sequence set
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  * @param candidates an array of pairs [name, monomer set]
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  * */
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- static detectAlphabet(freq, candidates, gapSymbol, cut = 0.65) {
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+ static detectAlphabet(freq, candidates, gapSymbol, cut = 0.55) {
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  const candidatesSims = candidates.map((c) => {
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  const sim = BioPackageDetectors.getAlphabetSimilarity(freq, c[1], gapSymbol);
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  return [c[0], c[1], freq, sim];