@datagrok/bio 1.7.13 → 1.7.14
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package/detectors.js
CHANGED
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@@ -11,8 +11,6 @@
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11
11
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12
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class BioPackageDetectors extends DG.Package {
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13
13
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14
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-
static mmSemType = 'Macromolecule';
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15
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-
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14
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static PeptideFastaAlphabet = new Set([
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'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
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'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',
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@@ -40,9 +38,12 @@ class BioPackageDetectors extends DG.Package {
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detectMacromolecule(col) {
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// To collect alphabet freq three strategies can be used:
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// as chars, as fasta (single or within square brackets), as with the separator.
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43
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-
if (
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41
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if (
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!(col.categories.length == 1 && !col.categories[0]) && // TODO: Remove with tests for single empty category value
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DG.Detector.sampleCategories(col, (s) => BioPackageDetectors.isHelm(s), 1)
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) {
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col.setTag(DG.TAGS.UNITS, 'HELM');
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45
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-
return
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return DG.SEMTYPE.MACROMOLECULE;
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}
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const decoyAlphabets = [
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@@ -72,6 +73,7 @@ class BioPackageDetectors extends DG.Package {
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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);
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76
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+
// if (Object.keys(statsAsChars.freq).length === 0) return;
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const decoy = BioPackageDetectors.detectAlphabet(statsAsChars.freq, decoyAlphabets, null, 0.35);
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if (decoy != 'UN') return null;
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@@ -83,7 +85,7 @@ class BioPackageDetectors extends DG.Package {
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const units = `fasta:SEQ.MSA:${alphabet}`;
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col.setTag(DG.TAGS.UNITS, units);
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86
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-
return
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return DG.SEMTYPE.MACROMOLECULE;
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}
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} else {
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const separator = BioPackageDetectors.detectSeparator(statsAsChars.freq);
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@@ -107,7 +109,7 @@ class BioPackageDetectors extends DG.Package {
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const units = `${format}:${seqType}:${alphabet}`;
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col.setTag(DG.TAGS.UNITS, units);
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if (separator) col.setTag('separator', separator);
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110
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-
return
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112
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return DG.SEMTYPE.MACROMOLECULE;
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}
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}
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}
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