@datagrok/bio 2.20.1 → 2.20.2
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- package/CHANGELOG.md +5 -0
- package/detectors.js +10 -6
- package/dist/package-test.js +1 -1
- package/dist/package-test.js.map +1 -1
- package/dist/package.js +1 -1
- package/dist/package.js.map +1 -1
- package/package.json +1 -1
- package/src/package.ts +10 -0
- package/src/widgets/to-atomic-level-widget.ts +79 -0
- package/test-console-output-1.log +7361 -0
- package/test-record-1.mp4 +0 -0
package/CHANGELOG.md
CHANGED
package/detectors.js
CHANGED
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@@ -88,7 +88,9 @@ class BioPackageDetectors extends DG.Package {
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}
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/** Parts of the column name required in the column's name under the detector. It must be in lowercase. */
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-
likelyColNamePartList = ['seq', 'msa', 'dna', 'rna', 'fasta', 'helm', 'sense', 'protein'];
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+
likelyColNamePartList = ['seq', 'msa', 'dna', 'rna', 'fasta', 'helm', 'sense', 'protein', 'pep', 'enumerated'];
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+
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+
veryLikelyColNamePartList = ['peptide', 'oligo', 'sequence', 'enumerated'];
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peptideFastaAlphabet = new Set([
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'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
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@@ -152,7 +154,9 @@ class BioPackageDetectors extends DG.Package {
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const colName = col.name;
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const colNameLikely = this.likelyColNamePartList.some(
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(requiredColNamePart) => colName.toLowerCase().includes(requiredColNamePart));
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-
const
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const colNameVeryLikely = this.veryLikelyColNamePartList.some(
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(requiredColNamePart) => colName.toLowerCase().includes(requiredColNamePart));
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const seqMinLength = colNameVeryLikely ? 3 : colNameLikely ? 7 : 10;
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const maxBadRatio = colNameLikely ? 0.05 : 0.005;
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// Fail early
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@@ -188,11 +192,11 @@ class BioPackageDetectors extends DG.Package {
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col.setTag(DG.TAGS.CELL_RENDERER, 'helm');
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return DG.SEMTYPE.MACROMOLECULE;
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}
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-
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+
const multiplier = colNameVeryLikely ? 1.4 : colNameLikely ? 1.2 : 1.0;
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const decoyAlphabets = [
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-
['NUMBERS', this.numbersRawAlphabet, 0.25, undefined],
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['SMILES', this.smilesRawAlphabet, 0.25, (seq) => seq.replaceAll()],
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-
['SMARTS', this.smartsRawAlphabet, 0.45, undefined],
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+
['NUMBERS', this.numbersRawAlphabet, 0.25 * multiplier, undefined],
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['SMILES', this.smilesRawAlphabet, 0.25 * multiplier, (seq) => seq.replaceAll()],
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['SMARTS', this.smartsRawAlphabet, 0.45 * multiplier, undefined],
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];
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const candidateAlphabets = [
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