@datagrok/sequence-translator 0.0.1 → 0.0.5

package/.eslintrc.json

@@ -0,0 +1,39 @@
+{
+  "env": {
+    "browser": true,
+    "es2021": true
+  },
+  "extends": [
+    "google"
+  ],
+  "parser": "@typescript-eslint/parser",
+  "parserOptions": {
+    "ecmaVersion": 12,
+    "sourceType": "module"
+  },
+  "plugins": [
+    "@typescript-eslint"
+  ],
+  "rules": {
+    "indent": [
+      "error",
+      2
+    ],
+    "max-len": [
+      "error",
+      120
+    ],
+    "require-jsdoc": "off",
+    "spaced-comment": "off",
+    "linebreak-style": "off",
+    "curly": [
+      "error",
+      "multi-or-nest"
+    ],
+    "brace-style": [
+      "error",
+      "1tbs",
+      { "allowSingleLine": true }
+    ]
+  }
+}

package/detectors.js

@@ -1,29 +1,25 @@
-class SequencetranslatorPackageDetectors extends DG.Package {
+class SequenceTranslatorPackageDetectors extends DG.Package {
   //tags: semTypeDetector
   //input: column col
   //output: string semType
   detectNucleotides(col) {
     if (col.type === DG.TYPE.STRING) {
-      if (DG.Detector.sampleCategories(col, (s) => /^[ATGC]{10,}$/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isDnaNucleotides(s)))
         return 'DNA nucleotides';
-      if (DG.Detector.sampleCategories(col, (s) => /^[AUGC]{10,}$/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isRnaNucleotides(s)))
         return 'RNA nucleotides';
-      if (DG.Detector.sampleCategories(col, (s) => /^[5678ATGC]{10,}$/.test(s)))
-        return 'ABI';
-      if (DG.Detector.sampleCategories(col, (s) => /^[*56789ATGC]{30,}$/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isAsoGapmerBioSpring(s)))
         return 'BioSpring / Gapmers';
-      if (DG.Detector.sampleCategories(col, (s) => /^(?=.*moe)(?=.*5mC)(?=.*ps){30,}/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isAsoGapmerGcrs(s)))
         return 'GCRS / Gapmers';
-      if (DG.Detector.sampleCategories(col, (s) => /^[*1-8]{30,}$/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isSiRnaBioSpring(s)))
         return 'BioSpring / siRNA';
-      if (DG.Detector.sampleCategories(col, (s) => /^[fsACGUacgu]{20,}$/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isSiRnaAxolabs(s)))
         return 'Axolabs / siRNA';
-      if (DG.Detector.sampleCategories(col, (s) => /^[fmpsACGU]{30,}$/.test(s)))
+      if (DG.Detector.sampleCategories(col, (s) => isGcrs(s)))
         return 'GCRS';
-      if (DG.Detector.sampleCategories(col, (s) => /^[acgu*]{10,}$/.test(s)))
-        return 'OP100';
-      if (DG.Detector.sampleCategories(col, (s) => /^[IiJjKkLlEeFfGgHhQq]{10,}$/.test(s)))
-        return 'MM12';
+      if (DG.Detector.sampleCategories(col, (s) => isMermade12(s)))
+        return 'Mermade 12 / siRNA';
     }
   }
-}
+}

package/package.json

@@ -1,18 +1,21 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "SequenceTranslator",
-  "version": "0.0.1",
+  "version": "0.0.5",
   "description": "",
   "dependencies": {
+    "@datagrok-libraries/utils": "^0.1.0",
     "@types/react": "latest",
-    "datagrok-api": "../../js-api",
+    "datagrok-api": ">0.94.10",
     "datagrok-tools": "^4.1.2",
     "npm": "^7.11.2",
     "save-svg-as-png": "^1.4.17",
     "ts-loader": "latest",
-    "typescript": "latest"
+    "typescript": "latest",
+    "openchemlib": "6.0.1"
   },
   "scripts": {
+    "link-api": "npm link datagrok-api",
     "debug-sequencetranslator": "grok publish --rebuild",
     "release-sequencetranslator": "grok publish --rebuild --release",
     "build-sequencetranslator": "webpack",
@@ -23,7 +26,11 @@
     "release-sequencetranslator-local": "grok publish local --rebuild --release"
   },
   "devDependencies": {
+    "@typescript-eslint/eslint-plugin": "^4.29.1",
+    "@typescript-eslint/parser": "^4.29.1",
     "cash-dom": "^8.1.0",
+    "eslint": "^7.32.0",
+    "eslint-config-google": "^0.14.0",
     "webpack": "^5.31.0",
     "webpack-cli": "^4.6.0"
   }

package/setup.cmd

@@ -0,0 +1,11 @@
+cd ../../js-api
+call npm install
+call npm link
+cd ../libraries/utils
+call npm install
+call npm link
+call npm link datagrok-api
+cd ../../packages/SequenceTranslator
+call npm install
+call npm link datagrok-api @datagrok-libraries/utils
+webpack

package/src/axolabsMap.ts

@@ -1,99 +1,101 @@
-const rnaColor = "rgb(255,230,153)";
-const invAbasicColor = "rgb(203,119,211)";
-export const axolabsMap: {[index: string]: {fullName: string, symbols: [string, string, string, string], color: string}} = {
-  "RNA": {
-    fullName: "RNA nucleotides",
-    symbols: ["A", "C", "G", "U"],
-    color: rnaColor
-  },
-  "DNA": {
-    fullName: "DNA nucleotides",
-    symbols: ["dA", "dC", "dG", "dT"],
-    color: "rgb(197,224,180)"
-  },
-  "2'-Fluoro": {
-    fullName: "2'-Fluoro nucleotides",
-    symbols: ["Af", "Cf", "Gf", "Uf"],
-    color: "rgb(68,114,196)"
-  },
-  "2'-O-Methyl": {
-    fullName: "2'-O-Methyl nucleotides",
-    symbols: ["a", "c", "g", "u"],
-    color: "rgb(166,166,166)"
-  },
-  "2'-O-MOE": {
-    fullName: "2'-O-MOE nucleotides (including 5-Methyl C)",
-    symbols: ["Am", "Cm", "Gm", "Tm"],
-    color: "rgb(112,48,160)"
-  },
-  "GNA": {
-    fullName: "Glycol nucleic acid",
-    symbols: ["(GNA-A)", "(GNA-C)", "(GNA-G)", "(GNA-T)"],
-    color: "rgb(255,192,0)"
-  },
-  "LNA": {
-    fullName: "Locked nucleic acid (including 5-Methyl C)",
-    symbols: ["Ab", "Cb", "Gb", "Tb"],
-    color: "rgb(54,229,238)"
-  },
-  "UNA": {
-    fullName: "Unlocked nucleotides",
-    symbols: ["Ao", "Co", "Go", "Uo"],
-    color: "rgb(255,192,0)"
-  },
-  "A": {
-    fullName: "Adenine",
-    symbols: ["a", "a", "a", "a"],
-    color: rnaColor
-  },
-  "C": {
-    fullName: "Cytosine",
-    symbols: ["c", "c", "c", "c"],
-    color: rnaColor
-  },
-  "G": {
-    fullName: "Guanine",
-    symbols: ["g", "g", "g", "g"],
-    color: rnaColor
-  },
-  "U": {
-    fullName: "Uracil",
-    symbols: ["u", "u", "u", "u"],
-    color: rnaColor
-  },
-  "X-New": {
-    fullName: "",
-    symbols: ["X", "X", "X", "X"],
-    color: "rgb(108,0,0)"
-  },
-  "Y-New": {
-    fullName: "",
-    symbols: ["Y", "Y", "Y", "Y"],
-    color: "rgb(210,146,146)"
-  },
-  "Z-New": {
-    fullName: "",
-    symbols: ["Z", "Z", "Z", "Z"],
-    color: "rgb(155,108,132)"
-  },
-  "InvAbasic": {
-    fullName: "Inverted abasic capped",
-    symbols: ["(invabasic)", "(invabasic)", "(invabasic)", "(invabasic)"],
-    color: invAbasicColor
-  },
-  "5'-vinylps": {
-    fullName: "5'-vinylphosphonate-2'-OMe-uridine",
-    symbols: ["(vinu)", "(vinu)", "(vinu)", "(vinu)"],
-    color: "rgb(0,0,139)"
-  },
-  "InvAbasic(o)": {
-    fullName: "Inverted abasic capped (overhang)",
-    symbols: ["(invabasic)", "(invabasic)", "(invabasic)", "(invabasic)"],
-    color: invAbasicColor
-  },
-  "2'-OMe-U(o)": {
-    fullName: "Nucleotide Uridine with 2’O-Methyl protection (overhang)",
-    symbols: ["mU", "mU", "mU", "mU"],
-    color: "rgb(65,233,80)"
-  }
-};
+const rnaColor = 'rgb(255,230,153)';
+const invAbasicColor = 'rgb(255,230,153)';
+export const axolabsMap:
+  {[index: string]: {fullName: string, symbols: [string, string, string, string], color: string}} =
+{
+  'RNA': {
+    fullName: 'RNA nucleotides',
+    symbols: ['A', 'C', 'G', 'U'],
+    color: rnaColor,
+  },
+  'DNA': {
+    fullName: 'DNA nucleotides',
+    symbols: ['dA', 'dC', 'dG', 'dT'],
+    color: 'rgb(197,224,180)',
+  },
+  '2\'-Fluoro': {
+    fullName: '2\'-Fluoro nucleotides',
+    symbols: ['Af', 'Cf', 'Gf', 'Uf'],
+    color: 'rgb(68,114,196)',
+  },
+  '2\'-O-Methyl': {
+    fullName: '2\'-O-Methyl nucleotides',
+    symbols: ['a', 'c', 'g', 'u'],
+    color: 'rgb(166,166,166)',
+  },
+  '2\'-O-MOE': {
+    fullName: '2\'-O-MOE nucleotides (including 5-Methyl C)',
+    symbols: ['Am', 'Cm', 'Gm', 'Tm'],
+    color: 'rgb(112,48,160)',
+  },
+  'GNA': {
+    fullName: 'Glycol nucleic acid',
+    symbols: ['(GNA-A)', '(GNA-C)', '(GNA-G)', '(GNA-T)'],
+    color: 'rgb(255,192,0)',
+  },
+  'LNA': {
+    fullName: 'Locked nucleic acid (including 5-Methyl C)',
+    symbols: ['Ab', 'Cb', 'Gb', 'Tb'],
+    color: 'rgb(54,229,238)',
+  },
+  'UNA': {
+    fullName: 'Unlocked nucleotides',
+    symbols: ['Ao', 'Co', 'Go', 'Uo'],
+    color: 'rgb(255,192,0)',
+  },
+  'A': {
+    fullName: 'Adenine',
+    symbols: ['a', 'a', 'a', 'a'],
+    color: rnaColor,
+  },
+  'C': {
+    fullName: 'Cytosine',
+    symbols: ['c', 'c', 'c', 'c'],
+    color: rnaColor,
+  },
+  'G': {
+    fullName: 'Guanine',
+    symbols: ['g', 'g', 'g', 'g'],
+    color: rnaColor,
+  },
+  'U': {
+    fullName: 'Uracil',
+    symbols: ['u', 'u', 'u', 'u'],
+    color: rnaColor,
+  },
+  'X-New': {
+    fullName: '',
+    symbols: ['X', 'X', 'X', 'X'],
+    color: 'rgb(108,0,0)',
+  },
+  'Y-New': {
+    fullName: '',
+    symbols: ['Y', 'Y', 'Y', 'Y'],
+    color: 'rgb(210,146,146)',
+  },
+  'Z-New': {
+    fullName: '',
+    symbols: ['Z', 'Z', 'Z', 'Z'],
+    color: 'rgb(155,108,132)',
+  },
+  'InvAbasic': {
+    fullName: 'Inverted abasic capped',
+    symbols: ['(invabasic)', '(invabasic)', '(invabasic)', '(invabasic)'],
+    color: invAbasicColor,
+  },
+  '5\'-vinylps': {
+    fullName: '5\'-vinylphosphonate-2\'-OMe-uridine',
+    symbols: ['(vinu)', '(vinu)', '(vinu)', '(vinu)'],
+    color: 'rgb(0,0,139)',
+  },
+  'InvAbasic(o)': {
+    fullName: 'Inverted abasic capped (overhang)',
+    symbols: ['(invabasic)', '(invabasic)', '(invabasic)', '(invabasic)'],
+    color: invAbasicColor,
+  },
+  '2\'-OMe-U(o)': {
+    fullName: 'Nucleotide Uridine with 2’O-Methyl protection (overhang)',
+    symbols: ['mU', 'mU', 'mU', 'mU'],
+    color: 'rgb(65,233,80)',
+  },
+};