@datagrok/bio 1.7.8 → 1.7.12

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Files changed (16) hide show
  1. package/detectors.js +17 -2
  2. package/dist/package-test.js +373 -81
  3. package/dist/package.js +289 -62
  4. package/files/tests/testSpgi100.csv +8437 -0
  5. package/files/tests/testUnichemSources.csv +36 -0
  6. package/package.json +3 -3
  7. package/src/const.ts +5 -0
  8. package/src/package.ts +83 -4
  9. package/src/tests/activity-cliffs-tests.ts +3 -0
  10. package/src/tests/convert-test.ts +55 -22
  11. package/src/tests/detectors-test.ts +37 -4
  12. package/src/utils/cell-renderer.ts +114 -1
  13. package/src/utils/constants.ts +2 -1
  14. package/src/utils/convert.ts +8 -6
  15. package/src/utils/utils.ts +29 -2
  16. package/{test-Bio-34f75e5127b8-cdc230d8.html → test-Bio-34f75e5127b8-6fa72ec4.html} +22 -14
package/detectors.js CHANGED
@@ -30,7 +30,8 @@ class BioPackageDetectors extends DG.Package {
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  /** @param s {String} - string to check
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  * @returns {boolean} */
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  static isHelm(s) {
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- return s.startsWith('PEPTIDE1{') || s.startsWith('RNA1{') || s.startsWith('CHEM1{') || s.startsWith('BLOB1{');
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+ return s.startsWith('PEPTIDE1{') || s.startsWith('CHEM1{') || s.startsWith('BLOB1{') ||
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+ s.startsWith('RNA1{') || s.startsWith('DNA1{');
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  }
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  //tags: semTypeDetector
@@ -54,6 +55,20 @@ class BioPackageDetectors extends DG.Package {
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  ['RNA', BioPackageDetectors.RnaFastaAlphabet],
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  ];
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+ // Check for url column, maybe it is too heavy check
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+ const isUrlCheck = (s) => {
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+ let res = true;
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+ try {
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+ const url = new URL(s);
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+ res = true;
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+ } catch {
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+ res = false;
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+ }
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+ return res;
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+ };
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+ const isUrl = DG.Detector.sampleCategories(col, isUrlCheck, 1);
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+ if (isUrl) return null;
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+
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  // TODO: Detect HELM sequence
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  // TODO: Lazy calculations could be helpful for performance and convenient for expressing classification logic.
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  const statsAsChars = BioPackageDetectors.getStats(col, 5, BioPackageDetectors.splitterAsChars);
@@ -198,7 +213,7 @@ class BioPackageDetectors extends DG.Package {
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  const alphabetA = [];
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  for (const m of keys) {
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  freqA.push(m in freq ? freq[m] : 0);
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- alphabetA.push(alphabet.has(m) ? 1 : 0);
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+ alphabetA.push(alphabet.has(m) ? 10 : -10 /* penalty for character outside alphabet set*/);
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  }
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  /* There were a few ideas: chi-squared, pearson correlation (variance?), scalar product */
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  const cos = BioPackageDetectors.vectorDotProduct(freqA, alphabetA) / (BioPackageDetectors.vectorLength(freqA) * BioPackageDetectors.vectorLength(alphabetA));