@datagrok/bio 2.1.9 → 2.1.11

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Files changed (9) hide show
  1. package/.eslintrc.json +1 -0
  2. package/detectors.js +12 -12
  3. package/dist/package-test.js +7 -2
  4. package/dist/package.js +3 -2
  5. package/files/tests/testSmilesShort.csv +11 -0
  6. package/package.json +1 -1
  7. package/src/package.ts +3 -1
  8. package/src/tests/detectors-tests.ts +6 -0
  9. package/{test-Bio-62cc009524f3-820f73b0.html → test-Bio-91c83d8913ff-bb573307.html} +100 -99
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
@@ -138,7 +138,8 @@ class BioPackageDetectors extends DG.Package {
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  // TODO: Lazy calculations could be helpful for performance and convenient for expressing classification logic.
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  const statsAsChars = this.getStats(categoriesSample, 5,
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  this.getSplitterAsChars(SEQ_SAMPLE_LENGTH_LIMIT));
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- // if (Object.keys(statsAsChars.freq).length === 0) return;
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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 null;
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  const decoy = this.detectAlphabet(statsAsChars.freq, decoyAlphabets, null);
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  if (decoy != ALPHABET.UN) return null;
@@ -149,19 +150,16 @@ 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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- if (Object.keys(statsAsChars.freq).length > 0) { // require non empty alphabet
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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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+ 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(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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- }
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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;
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  } else {
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  const stats = this.getStats(categoriesSample, 5, splitter);
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  // Empty monomer alphabet is not allowed
@@ -176,6 +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) {