@datagrok/bio 2.13.3 → 2.13.6

package/.eslintrc.json

@@ -8,7 +8,7 @@
   ],
   "parser": "@typescript-eslint/parser",
   "parserOptions": {
-    "ecmaVersion": 12,
+    "ecmaVersion": 2022,
     "sourceType": "module"
   },
   "plugins": [

package/CHANGELOG.md

@@ -1,5 +1,28 @@
 # Bio changelog
 
+## 2.13.6 (2024-07-29)
+
+* SequenceChemSimilarity: warning in case reference monomer not found in monomer library
+
+## 2.13.5 (2024-07-23)
+
+### Bug fixes
+
+* Fix tests for Helm package init wait
+* Add detectMacromolecule tests for fasta single char unknown alphabet
+* Fix detectMacromolecule checkBadMultichar wo RegExp and fail early
+* Fix use allowUnionTypes to allow union types in JSON schema
+* GROK-15793: Fix Calculate Identity, Similarity error Index out of bounds
+* Add progress indicator for loading monomer libraries
+
+## 2.13.4 (2024-07-02)
+
+### Bug fixes
+
+* GROK-15798: Fix To Atomic Level for units FASTA, UN alphabet
+* Fix detectMacromolecule to check for bad monomers on separator
+* Fix for review camelCase properties
+
 ## 2.13.3 (2024-06-28)
 
 ### Bug fixes

package/detectors.js

@@ -1,3 +1,4 @@
+'use strict';
 /**
  * The class contains semantic type detectors.
  * Detectors are functions tagged with `DG.FUNC_TYPES.SEM_TYPE_DETECTOR`.
@@ -7,6 +8,7 @@
  *
  * TODO: Use detectors from WebLogo pickUp.. methods
  */
+// eslint-disable-next-line max-lines
 
 const SEQ_SAMPLE_LIMIT = 100;
 const SEQ_SAMPLE_LENGTH_LIMIT = 100;
@@ -73,6 +75,12 @@ class BioPackageDetectors extends DG.Package {
 
   constructor() {
     super();
+
+    this.forbiddenMulticharAll = ' .:';
+    this.forbiddenMulticharFirst = ']' + this.forbiddenMulticharAll;
+    this.forbiddenMulticharMiddle = '][' + this.forbiddenMulticharAll;
+    this.forbiddenMulticharLast = '[' + this.forbiddenMulticharAll;
+
     // replace super._logger
     this._logger = new LoggerWrapper(this, this.logger, 'detectors');
   }
@@ -93,8 +101,8 @@ class BioPackageDetectors extends DG.Package {
   numbersRawAlphabet = new Set(['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']);
 
   smilesRawAlphabet = new Set([
-    'A', 'B', 'C', 'E', 'F', 'H', 'I', 'K', 'L', 'M', 'N', 'O', 'P', 'R', 'S', 'Z',
-    'a', 'c', 'e', 'g', 'i', 'l', 'n', 'o', 'r', 's', 't', 'u',
+    'C', 'F', 'H', 'N', 'O', 'P', 'S', 'B', /**/'A', 'E', 'I', 'K', 'L', 'M', 'R', 'Z',
+    'c', 'n', 'o', 's', /**/'a', 'e', 'g', 'i', 'l', 'r', 't', 'u',
     '0', '1', '2', '3', '4', '5', '6', '7', '8', '9',
     '+', '-', '.', , '/', '\\', '@', '[', ']', '(', ')', '#', '%', '=']);
 
@@ -167,7 +175,7 @@ class BioPackageDetectors extends DG.Package {
       ) {
         const statsAsHelm = this.getStats(categoriesSample, 2,
           this.getSplitterAsHelm(SEQ_SAMPLE_LENGTH_LIMIT));
-        col.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+        col.meta.units = NOTATION.HELM;
 
         // alphabetSize calculated on (sub)sample of data is incorrect
         // const alphabetSize = Object.keys(statsAsHelm.freq).length;
@@ -179,9 +187,9 @@ class BioPackageDetectors extends DG.Package {
       }
 
       const decoyAlphabets = [
-        ['NUMBERS', this.numbersRawAlphabet, 0.25],
-        ['SMILES', this.smilesRawAlphabet, 0.25],
-        ['SMARTS', this.smartsRawAlphabet, 0.45],
+        ['NUMBERS', this.numbersRawAlphabet, 0.25, undefined],
+        ['SMILES', this.smilesRawAlphabet, 0.25, (seq) => seq.replaceAll()],
+        ['SMARTS', this.smartsRawAlphabet, 0.45, undefined],
       ];
 
       const candidateAlphabets = [
@@ -246,7 +254,7 @@ class BioPackageDetectors extends DG.Package {
           return null;
         }
 
-        col.setTag(DG.TAGS.UNITS, units);
+        col.meta.units = units;
         if (separator) col.setTag(SeqHandler.TAGS.separator, separator);
         col.setTag(SeqHandler.TAGS.aligned, ALIGNMENT.SEQ_MSA);
         col.setTag(SeqHandler.TAGS.alphabet, alphabet);
@@ -265,24 +273,12 @@ class BioPackageDetectors extends DG.Package {
         }
         // Single- and multi-char monomer names for sequences with separators have constraints
         if (units === NOTATION.SEPARATOR || (units === NOTATION.FASTA && alphabetIsMultichar)) {
-          const badSet = this.checkBadMultichar(stats.freq);
-          const [badCount, allCount] = this.calcBad(stats.freq, badSet);
-          if (badCount / allCount > maxBadRatio) {
-            last.rejectReason = `Forbidden multi-char monomers: ` +
-              `${wu(badSet.keys()).map((m) => `'${m}'`).toArray().join(', ')}`;
-            return null;
-          }
-        }
-        if (units === NOTATION.FASTA && !alphabetIsMultichar) {
-          const badSet = this.checkBadSinglechar(stats.freq);
-          const [badCount, allCount] = this.calcBad(stats.freq, badSet);
-          if (badCount / allCount > maxBadRatio) {
-            last.rejectReason = `Forbidden single-char monomers: ` +
-              `${wu(badSet.keys()).map((m) => `'${m}'`).toArray().join(', ')}`;
+          const badSymbol /*: string | null*/ = this.checkBadMultichar(stats.freq);
+          if (badSymbol) {
+            last.rejectReason = `Forbidden multi-char monomer: '${badSymbol}'.`;
             return null;
           }
         }
-
         const aligned = stats.sameLength ? ALIGNMENT.SEQ_MSA : ALIGNMENT.SEQ;
 
         // TODO: If separator detected, then extra efforts to detect alphabet are allowed.
@@ -293,7 +289,7 @@ class BioPackageDetectors extends DG.Package {
         }
 
         // const forbidden = this.checkForbiddenWoSeparator(stats.freq);
-        col.setTag(DG.TAGS.UNITS, units);
+        col.meta.units = units;
         if (separator) col.setTag(SeqHandler.TAGS.separator, separator);
         col.setTag(SeqHandler.TAGS.aligned, aligned);
         col.setTag(SeqHandler.TAGS.alphabet, alphabet);
@@ -357,6 +353,8 @@ class BioPackageDetectors extends DG.Package {
     // Splitter with separator test application
     const splitter = this.getSplitterWithSeparator(sep, SEQ_SAMPLE_LENGTH_LIMIT);
     const stats = this.getStats(categoriesSample, seqMinLength, splitter);
+    const badSymbol = this.checkBadMultichar(stats.freq);
+    if (badSymbol) return null;
     // TODO: Test for Gamma/Erlang distribution
     const totalMonomerCount = wu(Object.values(stats.freq)).reduce((sum, a) => sum + a, 0);
     const mLengthAvg = wu.entries(stats.freq)
@@ -383,15 +381,22 @@ class BioPackageDetectors extends DG.Package {
   /** Dots and colons are nor allowed in multichar monomer names (but space is allowed).
    * The monomer name/label cannot contain digits only (but single digit is allowed).
    */
-  checkBadMultichar(freq) {
-    const badRe = /[ .:]|^\d+$/i;
-    return new Set(Object.keys(freq).filter((m) => badRe.test(m)));
-  }
-
-  /** Space, dot, colon, semicolon, digit, underscore are not allowed as singe char monomer names.*/
-  checkBadSinglechar(freq) {
-    const badRe = /[ .:;\d_]/i;
-    return new Set(Object.keys(freq).filter((m) => badRe.test(m)));
+  checkBadMultichar(freq) /* : string | null */ {
+    for (const symbol of Object.keys(freq)) {
+      if (symbol && !isNaN(symbol)) return symbol; // performance evaluated better with RegExp
+
+      const symbolLen = symbol.length;
+      if (this.forbiddenMulticharFirst.includes(symbol[0]))
+        return symbol;
+      if (this.forbiddenMulticharLast.includes(symbol[symbolLen - 1]))
+        return symbol;
+      for (let cI = 1; cI < symbolLen - 1; ++cI) {
+        const c = symbol[cI];
+        if (this.forbiddenMulticharMiddle.includes(c))
+          return symbol;
+      }
+    }
+    return null;
   }
 
   calcBad(freq, forbiddenSet) {
@@ -459,10 +464,11 @@ class BioPackageDetectors extends DG.Package {
     const keys = new Set([...new Set(Object.keys(freq)), ...alphabet]);
     keys.delete(gapSymbol);
 
+    const freqSum = Object.values(freq).reduce((a, b) => a + b, 0);
     const freqA = [];
     const alphabetA = [];
     for (const m of keys) {
-      freqA.push(m in freq ? freq[m] : -0.10);
+      freqA.push(m in freq ? freq[m] / freqSum : -0.001);
       alphabetA.push(alphabet.has(m) ? 10 : -20 /* penalty for character outside alphabet set*/);
     }
     /* There were a few ideas: chi-squared, pearson correlation (variance?), scalar product */
@@ -490,23 +496,27 @@ class BioPackageDetectors extends DG.Package {
 
   /** For trivial checks split by single chars*/
   getSplitterAsChars(lengthLimit) {
-    return function(seq) {
+    const resFunc = function(seq) {
       return seq.split('', lengthLimit);
     };
+    resFunc.T = 'splitterAsChars';
+    return resFunc;
   }
 
   getSplitterWithSeparator(separator, limit) {
-    return (seq) => {
+    const resFunc = function(seq) {
       return !seq ? [] : seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
     };
+    resFunc.T = 'splitterWithSeparator';
+    return resFunc;
   }
 
   // Multichar monomer names in square brackets, single char monomers or gap symbol
-  monomerRe = /\[(\w+)\]|(.)/g;
+  monomerRe = /\[([A-Za-z0-9_\-,()]+)\]|(.)/g;
 
   /** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol. */
   getSplitterAsFasta(lengthLimit) {
-    return function(seq) {
+    const resFunc = function(seq) {
       const res = wu(seq.toString().matchAll(this.monomerRe))
         .take(lengthLimit)
         .map((ma) => {
@@ -522,6 +532,8 @@ class BioPackageDetectors extends DG.Package {
 
       return res;
     }.bind(this);
+    resFunc.T = 'splitterAsFasta';
+    return resFunc;
   }
 
   /** Only some of the synonyms. These were obtained from the clustered oligopeptide dataset. */
@@ -535,7 +547,7 @@ class BioPackageDetectors extends DG.Package {
 
   /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA). */
   getSplitterAsHelm(lengthLimit) {
-    return function(seq) {
+    const resFunc = function(seq) {
       this.helmRe.lastIndex = 0;
       const ea = this.helmRe.exec(seq.toString());
       const inSeq = ea ? ea[2] : null;
@@ -553,6 +565,8 @@ class BioPackageDetectors extends DG.Package {
       const mmListRes = mmList.map(mmPostProcess);
       return mmListRes;
     }.bind(this);
+    resFunc.T = 'splitterAsHelm';
+    return resFunc;
   }
 
   sample(col, n) {

package/dist/111.js

@@ -0,0 +1,2 @@
+var bio;(()=>{"use strict";var e,r,t={4111:(e,r,t)=>{var n=t(6066);const o=e=>null==e;var a=t(2780),s=t(8774);onmessage=async e=>{const{values:r,startIdx:t,endIdx:i,threshold:l,fnNames:c,opts:h,aggregationMethod:p,weights:u}=e.data;try{const e=[],f=[],g=[],v=i-t,d=function(e,r){return e===n.G.MANHATTAN?e=>e.reduce(((e,t,n)=>e+t*r[n]),0):e=>{const t=e.reduce(((e,t,n)=>e+(t*r[n])**2),0);return Math.sqrt(t)}}(p,u);r.forEach(((e,t)=>{if((0,a.lW)(c[t]))for(let n=0;n<e.length;++n)o(e[n])||(r[t][n]=new s.A(r[t][n]._data,r[t][n]._length))}));let b=0;const w=new Array(c.length).fill(null).map(((e,r)=>new a.t$(c[r]).getMeasure(h[r]))),y=r[0].length-2-Math.floor(Math.sqrt(-8*t+4*r[0].length*(r[0].length-1)-7)/2-.5),m=t-r[0].length*y+Math.floor((y+1)*(y+2)/2);let x=y,O=m;for(;b<v;){const t=w.map(((e,t)=>o(r[t][x])||o(r[t][O])?1:e(r[t][x],r[t][O]))),n=1===t.length?t[0]:d(t);1-n>=l&&(e.push(x),f.push(O),g.push(n)),b++,O++,O===r[0].length&&(x++,O=x+1)}const A=new Int32Array(e),M=new Int32Array(f),j=new Float32Array(g);postMessage({i:A,j:M,distance:j})}catch(e){postMessage({error:e})}}}},n={};function o(e){var r=n[e];if(void 0!==r)return r.exports;var a=n[e]={exports:{}};return t[e](a,a.exports,o),a.exports}o.m=t,o.x=()=>{var e=o.O(void 0,[242,589],(()=>o(4111)));return o.O(e)},e=[],o.O=(r,t,n,a)=>{if(!t){var s=1/0;for(h=0;h<e.length;h++){for(var[t,n,a]=e[h],i=!0,l=0;l<t.length;l++)(!1&a||s>=a)&&Object.keys(o.O).every((e=>o.O[e](t[l])))?t.splice(l--,1):(i=!1,a<s&&(s=a));if(i){e.splice(h--,1);var c=n();void 0!==c&&(r=c)}}return r}a=a||0;for(var h=e.length;h>0&&e[h-1][2]>a;h--)e[h]=e[h-1];e[h]=[t,n,a]},o.d=(e,r)=>{for(var t in r)o.o(r,t)&&!o.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},o.f={},o.e=e=>Promise.all(Object.keys(o.f).reduce(((r,t)=>(o.f[t](e,r),r)),[])),o.u=e=>e+".js",o.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),o.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;o.g.importScripts&&(e=o.g.location+"");var r=o.g.document;if(!e&&r&&(r.currentScript&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var n=t.length-1;n>-1&&(!e||!/^http(s?):/.test(e));)e=t[n--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),o.p=e})(),(()=>{var e={111:1};o.f.i=(r,t)=>{e[r]||importScripts(o.p+o.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[n,a,s]=r;for(var i in a)o.o(a,i)&&(o.m[i]=a[i]);for(s&&s(o);n.length;)e[n.pop()]=1;t(r)}})(),r=o.x,o.x=()=>Promise.all([o.e(242),o.e(589)]).then(r);var a=o.x();bio=a})();
+//# sourceMappingURL=111.js.map

package/dist/111.js.map

@@ -0,0 +1 @@
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priority];\n\t\treturn;\n\t}\n\tvar notFulfilled = Infinity;\n\tfor (var i = 0; i < deferred.length; i++) {\n\t\tvar [chunkIds, fn, priority] = deferred[i];\n\t\tvar fulfilled = true;\n\t\tfor (var j = 0; j < chunkIds.length; j++) {\n\t\t\tif ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {\n\t\t\t\tchunkIds.splice(j--, 1);\n\t\t\t} else {\n\t\t\t\tfulfilled = false;\n\t\t\t\tif(priority < notFulfilled) notFulfilled = priority;\n\t\t\t}\n\t\t}\n\t\tif(fulfilled) {\n\t\t\tdeferred.splice(i--, 1)\n\t\t\tvar r = fn();\n\t\t\tif (r !== undefined) result = r;\n\t\t}\n\t}\n\treturn result;\n};","var next = __webpack_require__.x;\n__webpack_require__.x = () => {\n\treturn Promise.all([\n\t\t__webpack_require__.e(242),\n\t\t__webpack_require__.e(589)\n\t]).then(next);\n};","import { DistanceAggregationMethods } from './types';\nexport const isNil = (x) => x === null || x === undefined;\nexport function insertSmaller(distancesAr, indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num < v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n    if (num < distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num > v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function getAggregationFunction(aggregationMethod, weights) {\n    switch (aggregationMethod) {\n        case DistanceAggregationMethods.MANHATTAN:\n            return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n        default:\n            return (vs) => {\n                // euclidean\n                const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n                return Math.sqrt(sum);\n            };\n    }\n}\n//# 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{ getAggregationFunction, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, threshold, fnNames, opts, aggregationMethod, weights } = event.data;\n    try {\n        // if (startIdx != -1)\n        //   throw new Error('Error in sparse matrix worker'); // TODO: remove this line\n        const i = [];\n        const j = [];\n        const distances = [];\n        const chunkSize = endIdx - startIdx;\n        //const mi = startRow;\n        //const mj = startCol;\n        const aggregate = getAggregationFunction(aggregationMethod, weights);\n        values.forEach((v, colIdx) => {\n            if (isBitArrayMetric(fnNames[colIdx])) {\n                for (let i = 0; i < v.length; ++i) {\n                    if (isNil(v[i]))\n                        continue;\n                    values[colIdx][i] = new 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