@datagrok/sequence-translator 1.0.15 → 1.0.17
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/.eslintrc.json +16 -3
- package/detectors.js +0 -28
- package/dist/package-test.js +4372 -3957
- package/dist/package.js +3875 -3460
- package/package.json +4 -2
- package/setup-unlink-clean.sh +21 -0
- package/src/apps/oligo-sd-file-app.ts +58 -0
- package/src/autostart/calculations.ts +11 -8
- package/src/autostart/constants.ts +0 -12
- package/src/autostart/registration.ts +194 -157
- package/src/{axolabs/define-pattern.ts → axolabs-tab/axolabs-tab.ts} +2 -2
- package/src/axolabs-tab/define-pattern.ts +874 -0
- package/src/{axolabs → axolabs-tab}/draw-svg.ts +1 -1
- package/src/{axolabs → axolabs-tab}/helpers.ts +2 -2
- package/src/{autostart → hardcode-to-be-eliminated}/ICDs.ts +0 -0
- package/src/{autostart → hardcode-to-be-eliminated}/IDPs.ts +0 -0
- package/src/{structures-works → hardcode-to-be-eliminated}/const.ts +0 -0
- package/src/{axolabs → hardcode-to-be-eliminated}/constants.ts +0 -0
- package/src/{structures-works → hardcode-to-be-eliminated}/converters.ts +1 -1
- package/src/{structures-works → hardcode-to-be-eliminated}/map.ts +2 -2
- package/src/{autostart → hardcode-to-be-eliminated}/salts.ts +0 -0
- package/src/{autostart → hardcode-to-be-eliminated}/sources.ts +0 -0
- package/src/{autostart → hardcode-to-be-eliminated}/users.ts +0 -0
- package/src/{main/main-view.ts → main-tab/main-tab.ts} +28 -80
- package/src/package.ts +77 -13
- package/src/sdf-tab/sdf-tab.ts +163 -0
- package/src/{structures-works → sdf-tab}/sequence-codes-tools.ts +8 -5
- package/src/tests/smiles-tests.ts +2 -2
- package/src/utils/const.ts +0 -0
- package/src/{helpers.ts → utils/helpers.ts} +3 -3
- package/src/utils/parse.ts +27 -0
- package/src/utils/sdf-add-columns.ts +118 -0
- package/src/utils/sdf-save-table.ts +56 -0
- package/src/utils/structures-works/draw-molecule.ts +84 -0
- package/src/{structures-works → utils/structures-works}/from-monomers.ts +15 -16
- package/src/{structures-works → utils/structures-works}/mol-transformations.ts +34 -52
- package/{test-SequenceTranslator-91c83d8913ff-f94596bc.html → test-SequenceTranslator-6288c2fbe346-695b7b55.html} +10 -10
- package/src/structures-works/save-sense-antisense.ts +0 -91
package/.eslintrc.json
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"error",
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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": "off",
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"spaced-comment": "off",
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"linebreak-style": "off",
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"curly": [
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"error",
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"multi-or-nest"
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"multi-or-nest",
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"consistent"
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],
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"brace-style": [
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"error",
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"1tbs",
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{
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{
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"allowSingleLine": true
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}
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],
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"block-spacing": [2, "always"],
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"comma-dangle": ["error", {
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"arrays": "only-multiline",
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"functions": "never",
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"objects": "only-multiline",
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"imports": "only-multiline"
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}],
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"guard-for-in": "off"
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}
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}
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package/detectors.js
CHANGED
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class SequenceTranslatorPackageDetectors extends DG.Package {
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isDnaNucleotides(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|G|C){6,}$/.test(sequence);}
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isRnaNucleotides(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C){6,}$/.test(sequence);}
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isAsoGapmerBioSpring(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|\*|5|6|7|8|9|A|T|G|C){6,}$/.test(sequence);}
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isAsoGapmerGcrs(sequence) {return /^(?=.*moe)(?=.*5mC)(?=.*ps){6,}/.test(sequence);}
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isSiRnaBioSpring(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|\*|1|2|3|4|5|6|7|8){6,}$/.test(sequence);}
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isSiRnaAxolabs(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|f|s|A|C|G|U|a|c|g|u){6,}$/.test(sequence);}
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isSiRnaGcrs(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|f|m|p|s|A|C|G|U){6,}$/.test(sequence);}
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isGcrs(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|f|m|p|s|A|C|G|U){6,}$/.test(sequence);}
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isMermade12(sequence) {
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return /(\(invabasic\)|\(GalNAc-2-JNJ\)|I|i|J|j|K|k|L|l|E|e|F|f|G|g|H|h|Q|q){6,}$/.test(sequence);
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}
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//tags: semTypeDetector
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//input: column col
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//output: string semType
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detectNucleotides(col) {
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if (col.type === DG.TYPE.STRING) {
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if (DG.Detector.sampleCategories(col, (s) => this.isDnaNucleotides(s))) return 'DNA nucleotides';
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if (DG.Detector.sampleCategories(col, (s) => this.isRnaNucleotides(s))) return 'RNA nucleotides';
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if (DG.Detector.sampleCategories(col, (s) => this.isAsoGapmerBioSpring(s))) return 'BioSpring / Gapmers';
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if (DG.Detector.sampleCategories(col, (s) => this.isAsoGapmerGcrs(s))) return 'GCRS / Gapmers';
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if (DG.Detector.sampleCategories(col, (s) => this.isSiRnaBioSpring(s))) return 'BioSpring / siRNA';
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if (DG.Detector.sampleCategories(col, (s) => this.isSiRnaAxolabs(s))) return 'Axolabs / siRNA';
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if (DG.Detector.sampleCategories(col, (s) => this.isGcrs(s))) return 'GCRS';
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if (DG.Detector.sampleCategories(col, (s) => this.isMermade12(s))) return 'Mermade 12 / siRNA';
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}
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}
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}
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