@datagrok/bio 2.20.1 → 2.20.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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 +2 -2
- package/src/package.ts +10 -0
- package/src/widgets/to-atomic-level-widget.ts +79 -0
- package/test-console-output-1.log +7364 -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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