@datagrok/sequence-translator 1.0.3 → 1.0.6
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- package/detectors.js +26 -0
- package/dist/package-test.js +79 -67
- package/dist/package.js +768 -631
- package/package.json +28 -19
- package/src/__jest__/remote.test.ts +35 -16
- package/src/__jest__/test-node.ts +3 -2
- package/src/autostart/registration.ts +206 -0
- package/src/{axolabsMap.ts → axolabs/constants.ts} +1 -1
- package/src/{defineAxolabsPattern.ts → axolabs/define-pattern.ts} +87 -62
- package/src/{drawAxolabsPattern.ts → axolabs/draw-svg.ts} +1 -1
- package/src/main/main-view.ts +225 -0
- package/src/package.ts +11 -390
- package/src/structures-works/converters.ts +4 -1
- package/src/structures-works/from-monomers.ts +5 -4
- package/src/structures-works/map.ts +7 -0
- package/src/structures-works/mol-transformations.ts +19 -15
- package/src/structures-works/save-sense-antisense.ts +24 -11
- package/src/structures-works/sequence-codes-tools.ts +35 -27
- package/test-SequenceTranslator-d3cbf13cf137-2cb8277f.html +276 -0
- package/vendors/openchemlib-full.js +293 -0
- package/webpack.config.js +1 -1
- package/test-SequenceTranslator-46784acc64a5-c67dd897.html +0 -245
package/detectors.js
CHANGED
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@@ -1,2 +1,28 @@
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1
1
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class SequenceTranslatorPackageDetectors extends DG.Package {
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2
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isDnaNucleotides(sequence) {return /(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|G|C){6,}$/.test(sequence);}
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3
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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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