@datagrok/sequence-translator 1.0.16 → 1.0.17

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Files changed (34) hide show
  1. package/detectors.js +0 -28
  2. package/dist/package-test.js +3830 -3738
  3. package/dist/package.js +3826 -3734
  4. package/package.json +3 -1
  5. package/setup-unlink-clean.sh +21 -0
  6. package/src/autostart/calculations.ts +2 -2
  7. package/src/autostart/registration.ts +102 -37
  8. package/src/{axolabs/define-pattern.ts → axolabs-tab/axolabs-tab.ts} +2 -2
  9. package/src/axolabs-tab/define-pattern.ts +874 -0
  10. package/src/{axolabs → axolabs-tab}/draw-svg.ts +1 -1
  11. package/src/{axolabs → axolabs-tab}/helpers.ts +2 -2
  12. package/src/{autostart → hardcode-to-be-eliminated}/ICDs.ts +0 -0
  13. package/src/{autostart → hardcode-to-be-eliminated}/IDPs.ts +0 -0
  14. package/src/{structures-works → hardcode-to-be-eliminated}/const.ts +0 -0
  15. package/src/{axolabs → hardcode-to-be-eliminated}/constants.ts +0 -0
  16. package/src/{structures-works → hardcode-to-be-eliminated}/converters.ts +1 -1
  17. package/src/{structures-works → hardcode-to-be-eliminated}/map.ts +2 -2
  18. package/src/{autostart → hardcode-to-be-eliminated}/salts.ts +0 -0
  19. package/src/{autostart → hardcode-to-be-eliminated}/sources.ts +0 -0
  20. package/src/{autostart → hardcode-to-be-eliminated}/users.ts +0 -0
  21. package/src/{main/main-view.ts → main-tab/main-tab.ts} +27 -79
  22. package/src/package.ts +40 -23
  23. package/src/sdf-tab/sdf-tab.ts +163 -0
  24. package/src/{structures-works → sdf-tab}/sequence-codes-tools.ts +8 -5
  25. package/src/tests/smiles-tests.ts +2 -2
  26. package/src/utils/const.ts +0 -0
  27. package/src/{helpers.ts → utils/helpers.ts} +3 -3
  28. package/src/utils/sdf-add-columns.ts +3 -3
  29. package/src/utils/sdf-save-table.ts +4 -4
  30. package/src/utils/structures-works/draw-molecule.ts +84 -0
  31. package/src/{structures-works → utils/structures-works}/from-monomers.ts +15 -16
  32. package/src/{structures-works → utils/structures-works}/mol-transformations.ts +34 -52
  33. package/{test-SequenceTranslator-6288c2fbe346-cce4ac1d.html → test-SequenceTranslator-6288c2fbe346-695b7b55.html} +10 -10
  34. package/src/structures-works/save-sense-antisense.ts +0 -91
package/detectors.js CHANGED
@@ -1,28 +0,0 @@
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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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- }