npm - @datagrok-libraries/bio - Versions diffs - 5.41.7 → 5.41.9 - Mend

@datagrok-libraries/bio 5.41.7 → 5.41.9

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.

Files changed (23) hide show

package/CHANGELOG.md +8 -0
package/package.json +2 -2
package/src/monomer-works/to-atomic-level-utils.js +5 -4
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.js +4 -4
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/types/index.js +5 -4
package/src/types/index.js.map +1 -1
package/src/utils/const.d.ts +4 -3
package/src/utils/const.d.ts.map +1 -1
package/src/utils/const.js.map +1 -1
package/src/utils/generator.js +8 -8
package/src/utils/generator.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts +2 -2
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +23 -3
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/index.js +1 -1
package/src/utils/macromolecule/index.js.map +1 -1
package/src/utils/macromolecule/utils.js +8 -8
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/seq-handler.js +55 -55
package/src/utils/seq-handler.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,13 @@
 # bio changelog
+## 5.41.9 (2024-05-29)
+Fix Monomer type
+## 5.41.8 (2024-05-29)
+Fix TAGS, ALPHABET enum
 ## 5.41.7 (2024-05-28)
 ### Bug fixes

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.41.7",
+  "version": "5.41.9",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
@@ -16,7 +16,7 @@
     "@datagrok-libraries/ml": "^6.6.5",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
-    "datagrok-api": "^1.17.4",
+    "datagrok-api": "^1.18.6",
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",

package/src/monomer-works/to-atomic-level-utils.js CHANGED Viewed

@@ -1,5 +1,6 @@
 import { monomerWorksConsts as C } from './consts';
 import { HELM_CORE_FIELDS, } from '../utils/const';
+import { ALPHABET } from '../utils/macromolecule/consts';
 /** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.
  * @param {IMonomerLib} monomerLib - Monomer library
  * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
@@ -11,8 +12,8 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
         const it = monomerLib.getMonomer(polymerType, monomerSymbol);
         if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ &&
             (it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === "Branch" /* HELM_MONOMER_TYPE.BRANCH */ ||
-                alphabet === "DNA" /* ALPHABET.DNA */ && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||
-                alphabet === "RNA" /* ALPHABET.RNA */ && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||
+                alphabet === ALPHABET.DNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||
+                alphabet === ALPHABET.RNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||
                 it["symbol" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||
             polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
                 it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */) {
@@ -51,7 +52,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     }
     else { // nucleotides
         addMonomerToMolblock = addNucleotideToMolblock;
-        sugar = (alphabet === "DNA" /* ALPHABET.DNA */) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
+        sugar = (alphabet === ALPHABET.DNA) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
         phosphate = monomersDict.get(C.PHOSPHATE);
     }
     const v = {
@@ -281,7 +282,7 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
         bondCount += monomerSeq.length;
     }
     else { // nucleotides
-        const sugar = (alphabet === "DNA" /* ALPHABET.DNA */) ?
+        const sugar = (alphabet === ALPHABET.DNA) ?
             monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
         const phosphate = monomersDict.get(C.PHOSPHATE);
         // add phosphate per each pair of nucleobase symbols

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package/src/monomer-works/to-atomic-level.js CHANGED Viewed

@@ -2,7 +2,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { NOTATION } from '../utils/macromolecule/consts';
+import { ALPHABET, NOTATION } from '../utils/macromolecule/consts';
 import { SeqHandler } from '../utils/seq-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
@@ -36,9 +36,9 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
     // determine the polymer type according to HELM specifications
     let polymerType;
     // todo: an exception from dart comes before this check if the alphabet is UN
-    if (alphabet === "PT" /* ALPHABET.PT */ || alphabet === "UN" /* ALPHABET.UN */)
+    if (alphabet === ALPHABET.PT || alphabet === ALPHABET.UN)
         polymerType = "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */;
-    else if (alphabet === "RNA" /* ALPHABET.RNA */ || alphabet === "DNA" /* ALPHABET.DNA */)
+    else if (alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA)
         polymerType = "RNA" /* HELM_POLYMER_TYPE.RNA */;
     else {
         const msg = `Unexpected column's '${srcCol.name}' alphabet '${alphabet}'.`;
@@ -96,7 +96,7 @@ export async function getMonomersDictFromLib(monomerSequencesArray, monomerLib,
     // this must NOT be placed after translating monomer sequences
     // because adding branch monomers for nucleobases relies on these data
     if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */) {
-        const symbols = (alphabet === "RNA" /* ALPHABET.RNA */) ?
+        const symbols = (alphabet === ALPHABET.RNA) ?
             [C.RIBOSE, C.PHOSPHATE] : [C.DEOXYRIBOSE, C.PHOSPHATE];
         for (const sym of symbols)
             addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle);

package/src/monomer-works/to-atomic-level.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/types/index.js CHANGED Viewed

@@ -1,8 +1,9 @@
 import './helm';
+import { ALPHABET } from '../utils/macromolecule';
 export const alphabetPolymerTypes = {
-    ["DNA" /* ALPHABET.DNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
-    ["RNA" /* ALPHABET.RNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
-    ["PT" /* ALPHABET.PT */]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
-    ["UN" /* ALPHABET.UN */]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
+    [ALPHABET.DNA]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
+    [ALPHABET.RNA]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
+    [ALPHABET.PT]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
+    [ALPHABET.UN]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
 };
 //# sourceMappingURL=index.js.map

package/src/types/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,QAAQ,CAAC;~~AAuEhB~~,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,~~0BAAc~~,mCAAuB;IACrC,~~0BAAc~~,mCAAuB;IACrC,~~wBAAa~~,2CAA2B;IACxC,~~wBAAa~~,2CAA2B;CACzC,CAAC"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,QAAQ,CAAC;AAehB,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAwDhD,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;IACxC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;CACzC,CAAC"}

package/src/utils/const.d.ts CHANGED Viewed

@@ -6,6 +6,7 @@ import MonomerTypes = org.helm.MonomerTypes;
 export { PolymerTypes, HelmTypes, MonomerTypes };
 import HELM_POLYMER_TYPE = org.helm.PolymerTypes;
 import HELM_MONOMER_TYPE = org.helm.MonomerTypes;
+import { RGroup } from '../types';
 export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
 /** Required HELM library monomer fields:
  * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
@@ -61,16 +62,16 @@ export declare const jsonSdfMonomerLibDict: {
     symbol: string;
 };
 export declare const DUMMY_MONOMER: {
-    monomerType: string;
+    monomerType: "Backbone" | "Branch" | "Terminal";
     smiles: string;
     name: string;
     author: string;
     molfile: string;
     naturalAnalog: string;
-    rgroups: never[];
+    rgroups: RGroup[];
     createDate: null;
     id: number;
-    polymerType: string;
+    polymerType: "G" | "RNA" | "PEPTIDE" | "CHEM" | "BLOB";
     symbol: string;
 };
 export declare const MONOMER_ENCODE_MIN = 256;

package/src/utils/const.d.ts.map CHANGED Viewed

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package/src/utils/const.js.map CHANGED Viewed

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package/src/utils/generator.js CHANGED Viewed

@@ -1,5 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import { getAlphabet, NOTATION } from './macromolecule';
+import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
 import wu from 'wu';
 import { GapOriginals, SeqHandler } from './seq-handler';
 import { StringListSeqSplitted } from './macromolecule/utils';
@@ -15,24 +15,24 @@ export function generateLongSequence(length = 10 ** 5) {
     const msaCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'MSA', new Array(10 ** 2).fill(longSequence));
     msaCol.semType = DG.SEMTYPE.MACROMOLECULE;
     msaCol.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
-    msaCol.setTag("separator" /* TAGS.separator */, '/');
-    msaCol.setTag("alphabet" /* TAGS.alphabet */, "UN" /* ALPHABET.UN */);
-    msaCol.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, 'true');
+    msaCol.setTag(TAGS.separator, '/');
+    msaCol.setTag(TAGS.alphabet, ALPHABET.UN);
+    msaCol.setTag(TAGS.alphabetIsMultichar, 'true');
     const columns = [];
     columns.push(msaCol);
     columns.push(DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'Activity', new Array(10 ** 2).fill(7.30751)));
     return columns;
 }
-export function generateLongSequence2(notation = NOTATION.SEPARATOR, alphabet = "PT" /* ALPHABET.PT */, separator = (notation === NOTATION.SEPARATOR ? '-' : undefined), monomerLib = undefined, colName = 'seq', rowCount = 100, seqLength = 10 ** 6) {
-    const alphabetSet = alphabet === "UN" /* ALPHABET.UN */ ?
+export function generateLongSequence2(notation = NOTATION.SEPARATOR, alphabet = ALPHABET.PT, separator = (notation === NOTATION.SEPARATOR ? '-' : undefined), monomerLib = undefined, colName = 'seq', rowCount = 100, seqLength = 10 ** 6) {
+    const alphabetSet = alphabet === ALPHABET.UN ?
         monomerLib?.getMonomerSymbolsByType("PEPTIDE" /* PolymerTypes.PEPTIDE */) ?? [] : Array.from(getAlphabet(alphabet));
     const alphabetSize = alphabetSet.length;
     const col = DG.Column.fromType(DG.COLUMN_TYPE.STRING, colName, rowCount);
     col.semType = DG.SEMTYPE.MACROMOLECULE;
     col.setTag(DG.TAGS.UNITS, notation);
-    col.setTag("alphabet" /* TAGS.alphabet */, alphabet);
+    col.setTag(TAGS.alphabet, alphabet);
     if (notation == NOTATION.SEPARATOR)
-        col.setTag("separator" /* TAGS.separator */, separator);
+        col.setTag(TAGS.separator, separator);
     const sh = SeqHandler.forColumn(col);
     for (let rowI = 0; rowI < rowCount; rowI++) {
         const seqMList = wu.count(0).take(seqLength)

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	@@ -1 +1 @@
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package/src/utils/macromolecule/consts.d.ts CHANGED Viewed

@@ -9,14 +9,14 @@ export declare const enum ALIGNMENT {
     SEQ_MSA = "SEQ.MSA",
     SEQ = "SEQ"
 }
-export declare const enum ALPHABET {
+export declare enum ALPHABET {
     DNA = "DNA",
     RNA = "RNA",
     PT = "PT",
     /** Unknown */
     UN = "UN"
 }
-export declare const enum TAGS {
+export declare enum TAGS {
     aligned = "aligned",
     alphabet = "alphabet",
     alphabetSize = ".alphabetSize",

package/src/utils/macromolecule/consts.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,~~0BAAkB~~,QAAQ;~~IACxB~~,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,~~0BAAkB~~,IAAI;~~IACpB~~,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;CACrB;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}
1	+ {"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,oBAAY,QAAQ;IAClB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;CACrB;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}

package/src/utils/macromolecule/consts.js CHANGED Viewed

@@ -6,6 +6,26 @@ export var NOTATION;
     NOTATION["SEPARATOR"] = "separator";
     NOTATION["HELM"] = "helm";
 })(NOTATION || (NOTATION = {}));
+export var ALPHABET;
+(function (ALPHABET) {
+    ALPHABET["DNA"] = "DNA";
+    ALPHABET["RNA"] = "RNA";
+    ALPHABET["PT"] = "PT";
+    /** Unknown */
+    ALPHABET["UN"] = "UN";
+})(ALPHABET || (ALPHABET = {}));
+export var TAGS;
+(function (TAGS) {
+    TAGS["aligned"] = "aligned";
+    TAGS["alphabet"] = "alphabet";
+    TAGS["alphabetSize"] = ".alphabetSize";
+    TAGS["alphabetIsMultichar"] = ".alphabetIsMultichar";
+    TAGS["separator"] = "separator";
+    TAGS["isHelmCompatible"] = ".isHelmCompatible";
+    TAGS["positionNames"] = ".positionNames";
+    TAGS["positionLabels"] = ".positionLabels";
+    TAGS["regions"] = ".regions";
+})(TAGS || (TAGS = {}));
 export const positionSeparator = ', ';
 export const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
 export const helmRe = /(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g;
@@ -23,8 +43,8 @@ export const Alphabets = new class {
     }
 }();
 export const candidateAlphabets = [
-    new CandidateType("PT" /* ALPHABET.PT */, Alphabets.fasta.peptide, 0.50),
-    new CandidateType("DNA" /* ALPHABET.DNA */, Alphabets.fasta.dna, 0.55),
-    new CandidateType("RNA" /* ALPHABET.RNA */, Alphabets.fasta.rna, 0.55),
+    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),
+    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),
+    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),
 ];
 //# sourceMappingURL=consts.js.map

package/src/utils/macromolecule/consts.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/index.js CHANGED Viewed

@@ -1,3 +1,3 @@
-export { NOTATION, candidateAlphabets, positionSeparator } from './consts';
+export { TAGS, NOTATION, ALPHABET, candidateAlphabets, positionSeparator } from './consts';
 export { splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType } from './utils';
 //# sourceMappingURL=index.js.map

package/src/utils/macromolecule/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,~~EAEL~~,QAAQ,~~EAGR~~,kBAAkB,EAClB,iBAAiB,EAClB,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEjB,MAAM,SAAS,CAAC"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EACL,IAAI,EACJ,QAAQ,EACR,QAAQ,EAER,kBAAkB,EAClB,iBAAiB,EAClB,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEjB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/utils.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { CandidateSimType, GAP_SYMBOL } from './types';
-import { Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
+import { ALPHABET, Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
 import { GapOriginals, SeqHandler } from '../seq-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
 import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
@@ -186,11 +186,11 @@ export function monomerToShort(amino, maxLengthOfMonomer) {
 /** */
 export function getAlphabet(alphabet) {
     switch (alphabet) {
-        case "DNA" /* ALPHABET.DNA */:
+        case ALPHABET.DNA:
             return Alphabets.fasta.dna;
-        case "RNA" /* ALPHABET.RNA */:
+        case ALPHABET.RNA:
             return Alphabets.fasta.rna;
-        case "PT" /* ALPHABET.PT */:
+        case ALPHABET.PT:
             return Alphabets.fasta.peptide;
         default:
             throw new Error(`Unsupported alphabet '${alphabet}'.`);
@@ -229,7 +229,7 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
         alphabetName = sim.name;
     }
     else
-        alphabetName = "UN" /* ALPHABET.UN */;
+        alphabetName = ALPHABET.UN;
     return alphabetName;
 }
 /** Selects a suitable palette based on column data
@@ -252,10 +252,10 @@ export function pickUpPalette(seqCol, minLength = 5) {
 }
 export function getPaletteByType(paletteType) {
     switch (paletteType) {
-        case "PT" /* ALPHABET.PT */:
+        case ALPHABET.PT:
             return AminoacidsPalettes.GrokGroups;
-        case "DNA" /* ALPHABET.DNA */:
-        case "RNA" /* ALPHABET.RNA */:
+        case ALPHABET.DNA:
+        case ALPHABET.RNA:
             return NucleotidesPalettes.Chromatogram;
         // other
         default:

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1	+ 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package/src/utils/seq-handler.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { NOTATION, candidateAlphabets, positionSeparator, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, } from './macromolecule';
+import { TAGS, ALPHABET, NOTATION, candidateAlphabets, positionSeparator, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, } from './macromolecule';
 import { GAP_SYMBOL, } from './macromolecule/types';
 import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
@@ -43,14 +43,14 @@ export class SeqHandler {
         this._defaultGapOriginal = (this.isFasta()) ? GapOriginals[NOTATION.FASTA] :
             (this.isHelm()) ? GapOriginals[NOTATION.HELM] :
                 GapOriginals[NOTATION.SEPARATOR];
-        if (!this.column.tags.has("aligned" /* TAGS.aligned */) || !this.column.tags.has("alphabet" /* TAGS.alphabet */) ||
-            (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) && !this.isHelm() && this.alphabet === "UN" /* ALPHABET.UN */)) {
+        if (!this.column.tags.has(TAGS.aligned) || !this.column.tags.has(TAGS.alphabet) ||
+            (!this.column.tags.has(TAGS.alphabetIsMultichar) && !this.isHelm() && this.alphabet === ALPHABET.UN)) {
             // The following detectors and setters are to be called because the column is likely
             // as the UnitsHandler constructor was called on the column.
             if (this.isFasta())
                 SeqHandler.setUnitsToFastaColumn(this);
             else if (this.isSeparator()) {
-                const separator = col.getTag("separator" /* TAGS.separator */);
+                const separator = col.getTag(TAGS.separator);
                 SeqHandler.setUnitsToSeparatorColumn(this, separator);
             }
             else if (this.isHelm())
@@ -66,12 +66,12 @@ export class SeqHandler {
         //     throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' ` +
         //       `tag '${TAGS.alphabetSize}' is mandatory.`);
         // }
-        if (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */)) {
+        if (!this.column.tags.has(TAGS.alphabetIsMultichar)) {
             if (this.isHelm())
-                this.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, 'true');
+                this.column.setTag(TAGS.alphabetIsMultichar, 'true');
             else if (['UN'].includes(this.alphabet)) {
                 throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' ` +
-                    `tag '${".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */}' is mandatory.`);
+                    `tag '${TAGS.alphabetIsMultichar}' is mandatory.`);
             }
         }
         this.notationProvider = this.column.temp[SeqTemps.notationProvider] ?? null;
@@ -89,7 +89,7 @@ export class SeqHandler {
         if (!separator)
             throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must have the separator tag.`);
         uh.column.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
-        uh.column.setTag("separator" /* TAGS.separator */, separator);
+        uh.column.setTag(TAGS.separator, separator);
         SeqHandler.setTags(uh);
     }
     static setUnitsToHelmColumn(uh) {
@@ -103,23 +103,23 @@ export class SeqHandler {
         const units = uh.column.getTag(DG.TAGS.UNITS);
         if ([NOTATION.FASTA, NOTATION.SEPARATOR].includes(units)) {
             // Empty monomer alphabet is allowed, only if alphabet tag is annotated
-            if (!uh.column.getTag("alphabet" /* TAGS.alphabet */) && Object.keys(uh.stats.freq).length === 0)
+            if (!uh.column.getTag(TAGS.alphabet) && Object.keys(uh.stats.freq).length === 0)
                 throw new Error('Alphabet is empty and not annotated.');
-            let aligned = uh.column.getTag("aligned" /* TAGS.aligned */);
+            let aligned = uh.column.getTag(TAGS.aligned);
             if (aligned === null) {
                 aligned = uh.stats.sameLength ? "SEQ.MSA" /* ALIGNMENT.SEQ_MSA */ : "SEQ" /* ALIGNMENT.SEQ */;
-                uh.column.setTag("aligned" /* TAGS.aligned */, aligned);
+                uh.column.setTag(TAGS.aligned, aligned);
             }
-            let alphabet = uh.column.getTag("alphabet" /* TAGS.alphabet */);
+            let alphabet = uh.column.getTag(TAGS.alphabet);
             if (alphabet === null) {
                 alphabet = detectAlphabet(uh.stats.freq, candidateAlphabets);
-                uh.column.setTag("alphabet" /* TAGS.alphabet */, alphabet);
+                uh.column.setTag(TAGS.alphabet, alphabet);
             }
-            if (alphabet === "UN" /* ALPHABET.UN */) {
+            if (alphabet === ALPHABET.UN) {
                 const alphabetSize = Object.keys(uh.stats.freq).length;
                 const alphabetIsMultichar = Object.keys(uh.stats.freq).some((m) => m.length > 1);
-                uh.column.setTag(".alphabetSize" /* TAGS.alphabetSize */, alphabetSize.toString());
-                uh.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, alphabetIsMultichar ? 'true' : 'false');
+                uh.column.setTag(TAGS.alphabetSize, alphabetSize.toString());
+                uh.column.setTag(TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
             }
         }
     }
@@ -129,13 +129,13 @@ export class SeqHandler {
     get notation() { return this._notation; }
     get defaultGapOriginal() { return this._defaultGapOriginal; }
     get separator() {
-        const separator = this.column.getTag("separator" /* TAGS.separator */) ?? undefined;
+        const separator = this.column.getTag(TAGS.separator) ?? undefined;
         if (this.notation === NOTATION.SEPARATOR && separator === undefined)
             throw new Error(`Separator is mandatory  for column '${this.column.name}' of notation '${this.notation}'.`);
         return separator;
     }
     get aligned() {
-        const aligned = this.column.getTag("aligned" /* TAGS.aligned */);
+        const aligned = this.column.getTag(TAGS.aligned);
         // TAGS.aligned is mandatory for columns of NOTATION.FASTA and NOTATION.SEPARATOR
         if (!aligned && (this.isFasta() || this.isSeparator()))
             throw new Error('Tag aligned not set');
@@ -143,18 +143,18 @@ export class SeqHandler {
     }
     /** Alphabet name (upper case) */
     get alphabet() {
-        const alphabet = this.column.getTag("alphabet" /* TAGS.alphabet */);
+        const alphabet = this.column.getTag(TAGS.alphabet);
         // TAGS.alphabet is mandatory for columns of NOTATION.FASTA and NOTATION.SEPARATOR
         if (!alphabet && (this.isFasta() || this.isSeparator()))
             throw new Error('Tag alphabet not set');
         return alphabet;
     }
     get helmCompatible() {
-        return this.column.getTag(".isHelmCompatible" /* TAGS.isHelmCompatible */);
+        return this.column.getTag(TAGS.isHelmCompatible);
     }
     getAlphabetSize() {
-        if (this.notation == NOTATION.HELM || this.alphabet == "UN" /* ALPHABET.UN */) {
-            const alphabetSizeStr = this.column.getTag(".alphabetSize" /* TAGS.alphabetSize */);
+        if (this.notation == NOTATION.HELM || this.alphabet == ALPHABET.UN) {
+            const alphabetSizeStr = this.column.getTag(TAGS.alphabetSize);
             let alphabetSize;
             if (alphabetSizeStr)
                 alphabetSize = parseInt(alphabetSizeStr);
@@ -167,10 +167,10 @@ export class SeqHandler {
         }
         else {
             switch (this.alphabet) {
-                case "PT" /* ALPHABET.PT */:
+                case ALPHABET.PT:
                     return 20;
-                case "DNA" /* ALPHABET.DNA */:
-                case "RNA" /* ALPHABET.RNA */:
+                case ALPHABET.DNA:
+                case ALPHABET.RNA:
                     return 4;
                 case 'NT':
                     console.warn(`Unexpected alphabet 'NT'.`);
@@ -183,10 +183,10 @@ export class SeqHandler {
     getAlphabetIsMultichar() {
         if (this.notation === NOTATION.HELM)
             return true;
-        else if (this.alphabet !== "UN" /* ALPHABET.UN */)
+        else if (this.alphabet !== ALPHABET.UN)
             return false;
         else
-            return this.column.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) === 'true';
+            return this.column.getTag(TAGS.alphabetIsMultichar) === 'true';
     }
     // /** */
     // public get splitted(): ISeqSplitted[] {
@@ -254,7 +254,7 @@ export class SeqHandler {
     }
     get posList() {
         if (this._posList === null) {
-            const posListTxt = this.column.getTag(".positionNames" /* TAGS.positionNames */);
+            const posListTxt = this.column.getTag(TAGS.positionNames);
             this._posList = posListTxt ? posListTxt.split(positionSeparator).map((p) => p.trim()) :
                 wu.count(1).take(this.maxLength).map((pos) => pos.toString()).toArray();
         }
@@ -263,9 +263,9 @@ export class SeqHandler {
     isFasta() { return this.notation === NOTATION.FASTA; }
     isSeparator() { return this.notation === NOTATION.SEPARATOR; }
     isHelm() { return this.notation === NOTATION.HELM; }
-    isRna() { return this.alphabet === "RNA" /* ALPHABET.RNA */; }
-    isDna() { return this.alphabet === "DNA" /* ALPHABET.DNA */; }
-    isPeptide() { return this.alphabet === "PT" /* ALPHABET.PT */; }
+    isRna() { return this.alphabet === ALPHABET.RNA; }
+    isDna() { return this.alphabet === ALPHABET.DNA; }
+    isPeptide() { return this.alphabet === ALPHABET.PT; }
     isMsa() { return this.aligned ? this.aligned.toUpperCase().includes('MSA') : false; }
     isHelmCompatible() { return this.helmCompatible === 'true'; }
     /** Checks {@link om} for being a gap
@@ -321,26 +321,26 @@ export class SeqHandler {
         if (tgtNotation === NOTATION.SEPARATOR) {
             if (!tgtSeparator)
                 throw new Error(`Notation \'${NOTATION.SEPARATOR}\' requires separator value.`);
-            newColumn.setTag("separator" /* TAGS.separator */, tgtSeparator);
+            newColumn.setTag(TAGS.separator, tgtSeparator);
         }
         newColumn.setTag(DG.TAGS.CELL_RENDERER, tgtNotation === NOTATION.HELM ? 'helm' : 'sequence'); // cell.renderer
-        const srcAligned = col.getTag("aligned" /* TAGS.aligned */);
+        const srcAligned = col.getTag(TAGS.aligned);
         if (srcAligned)
-            newColumn.setTag("aligned" /* TAGS.aligned */, srcAligned);
-        let srcAlphabet = col.getTag("alphabet" /* TAGS.alphabet */);
+            newColumn.setTag(TAGS.aligned, srcAligned);
+        let srcAlphabet = col.getTag(TAGS.alphabet);
         if (!srcAlphabet && this.notation === NOTATION.HELM && tgtNotation !== NOTATION.HELM)
-            srcAlphabet = "UN" /* ALPHABET.UN */;
+            srcAlphabet = ALPHABET.UN;
         if (srcAlphabet != null)
-            newColumn.setTag("alphabet" /* TAGS.alphabet */, srcAlphabet);
-        let srcAlphabetSize = col.getTag(".alphabetSize" /* TAGS.alphabetSize */);
+            newColumn.setTag(TAGS.alphabet, srcAlphabet);
+        let srcAlphabetSize = col.getTag(TAGS.alphabetSize);
         if (srcAlphabet != null && srcAlphabetSize)
-            newColumn.setTag(".alphabetSize" /* TAGS.alphabetSize */, srcAlphabetSize);
-        const srcAlphabetIsMultichar = col.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */);
+            newColumn.setTag(TAGS.alphabetSize, srcAlphabetSize);
+        const srcAlphabetIsMultichar = col.getTag(TAGS.alphabetIsMultichar);
         if (srcAlphabet != null && srcAlphabetIsMultichar !== undefined)
-            newColumn.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, srcAlphabetIsMultichar);
+            newColumn.setTag(TAGS.alphabetIsMultichar, srcAlphabetIsMultichar);
         if (tgtNotation == NOTATION.HELM) {
             srcAlphabetSize = this.getAlphabetSize().toString();
-            newColumn.setTag(".alphabetSize" /* TAGS.alphabetSize */, srcAlphabetSize);
+            newColumn.setTag(TAGS.alphabetSize, srcAlphabetSize);
         }
         return newColumn;
     }
@@ -400,7 +400,7 @@ export class SeqHandler {
         if (splitter)
             return splitter;
         if (this.units.toLowerCase().startsWith(NOTATION.FASTA)) {
-            const alphabet = this.column.getTag("alphabet" /* TAGS.alphabet */);
+            const alphabet = this.column.getTag(TAGS.alphabet);
             if (alphabet !== null && !this.getAlphabetIsMultichar())
                 return splitterAsFastaSimple;
             else
@@ -424,12 +424,12 @@ export class SeqHandler {
         if (this.isMsa())
             return MmDistanceFunctionsNames.HAMMING;
         switch (this.alphabet) {
-            case "DNA" /* ALPHABET.DNA */:
-            case "RNA" /* ALPHABET.RNA */:
+            case ALPHABET.DNA:
+            case ALPHABET.RNA:
                 // As DNA and RNA scoring matrices are same as identity matrices(mostly),
                 // we can use very fast and optimized Levenshtein distance library
                 return MmDistanceFunctionsNames.LEVENSHTEIN;
-            case "PT" /* ALPHABET.PT */:
+            case ALPHABET.PT:
                 return MmDistanceFunctionsNames.LEVENSHTEIN;
             // For default case, let's use Levenshtein distance
             default:
@@ -442,8 +442,8 @@ export class SeqHandler {
     // checks if the separator notation is compatible with helm library
     async checkHelmCompatibility() {
         // check first for the column tag to avoid extra processing
-        if (this.column.tags.has(".isHelmCompatible" /* TAGS.isHelmCompatible */))
-            return this.column.getTag(".isHelmCompatible" /* TAGS.isHelmCompatible */) === 'true';
+        if (this.column.tags.has(TAGS.isHelmCompatible))
+            return this.column.getTag(TAGS.isHelmCompatible) === 'true';
         // get the monomer lib and check against the column
         const monomerLibHelper = await getMonomerLibHelper();
         const bioLib = monomerLibHelper.getBioLib();
@@ -466,13 +466,13 @@ export class SeqHandler {
                 const monomers = this.getSplitted(rowIdx);
                 for (const cm of monomers.canonicals) {
                     if (!peptidesSet.has(cm)) {
-                        this.column.setTag(".isHelmCompatible" /* TAGS.isHelmCompatible */, 'false');
+                        this.column.setTag(TAGS.isHelmCompatible, 'false');
                         return false;
                     }
                 }
             }
         }
-        this.column.setTag(".isHelmCompatible" /* TAGS.isHelmCompatible */, 'true');
+        this.column.setTag(TAGS.isHelmCompatible, 'true');
         return true;
     }
     // -- Notation Converter --
@@ -572,12 +572,12 @@ export class SeqHandler {
             }
             return regPosList.join(positionSeparator);
         };
-        const srcPositionNamesStr = this.column.getTag(".positionNames" /* TAGS.positionNames */);
+        const srcPositionNamesStr = this.column.getTag(TAGS.positionNames);
         if (srcPositionNamesStr)
-            regCol.setTag(".positionNames" /* TAGS.positionNames */, getRegionOfPositionNames(srcPositionNamesStr));
-        const srcPositionLabelsStr = this.column.getTag(".positionLabels" /* TAGS.positionLabels */);
+            regCol.setTag(TAGS.positionNames, getRegionOfPositionNames(srcPositionNamesStr));
+        const srcPositionLabelsStr = this.column.getTag(TAGS.positionLabels);
         if (srcPositionLabelsStr)
-            regCol.setTag(".positionLabels" /* TAGS.positionLabels */, getRegionOfPositionNames(srcPositionLabelsStr));
+            regCol.setTag(TAGS.positionLabels, getRegionOfPositionNames(srcPositionLabelsStr));
         return regCol;
     }
     get joiner() {
@@ -602,7 +602,7 @@ export class SeqHandler {
                 break;
             }
             case NOTATION.HELM: {
-                const isDnaOrRna = srcSh.alphabet === "DNA" /* ALPHABET.DNA */ || srcSh.alphabet === "RNA" /* ALPHABET.RNA */;
+                const isDnaOrRna = srcSh.alphabet === ALPHABET.DNA || srcSh.alphabet === ALPHABET.RNA;
                 const wrappers = srcSh.getHelmWrappers();
                 res = function (srcSS) { return joinToHelm(srcSS, wrappers, isDnaOrRna); };
                 break;

package/src/utils/seq-handler.js.map CHANGED Viewed

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