npm - @datagrok-libraries/bio - Versions diffs - 5.34.2 → 5.35.0 - Mend

@datagrok-libraries/bio 5.34.2 → 5.35.0

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 (41) hide show

package/.eslintrc.json +4 -3
package/CHANGELOG.md +7 -2
package/package.json +1 -1
package/src/monomer-works/monomer-utils.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.js +10 -13
package/src/monomer-works/monomer-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts +1 -1
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +7 -8
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +7 -8
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/cell-renderer.d.ts +3 -2
package/src/utils/cell-renderer.d.ts.map +1 -1
package/src/utils/cell-renderer.js +1 -1
package/src/utils/cell-renderer.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +1 -1
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/index.d.ts +1 -1
package/src/utils/macromolecule/index.d.ts.map +1 -1
package/src/utils/macromolecule/index.js +1 -1
package/src/utils/macromolecule/index.js.map +1 -1
package/src/utils/macromolecule/types.d.ts +5 -1
package/src/utils/macromolecule/types.d.ts.map +1 -1
package/src/utils/macromolecule/types.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts +2 -8
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +18 -31
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/notation-converter.d.ts.map +1 -1
package/src/utils/notation-converter.js +5 -7
package/src/utils/notation-converter.js.map +1 -1
package/src/utils/splitter.d.ts.map +1 -1
package/src/utils/splitter.js +3 -2
package/src/utils/splitter.js.map +1 -1
package/src/utils/units-handler.d.ts +3 -3
package/src/utils/units-handler.d.ts.map +1 -1
package/src/utils/units-handler.js +26 -18
package/src/utils/units-handler.js.map +1 -1

package/.eslintrc.json CHANGED Viewed

@@ -18,15 +18,16 @@
     "indent": ["error", 2, {"SwitchCase": 1}],
     "max-len": ["error", 120],
     "no-unused-vars": "off",
-    "@typescript-eslint/no-unused-vars": ["warn", { "varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}],
+    "@typescript-eslint/no-unused-vars": [
+      "warn", {"varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}
+    ],
     "require-jsdoc": "off",
     "valid-jsdoc": "warn",
     "spaced-comment": "off",
     "linebreak-style": "off",
     "curly": [
       "error",
-      "multi-or-nest",
-      "consistent"
+      "multi-or-nest"
     ],
     "brace-style": [
       "error",

package/CHANGELOG.md CHANGED Viewed

@@ -1,8 +1,13 @@
 # bio changelog
-## 5.35.0 (WIP)
+## 5.35.0 (2023-08-06)
-Add WebLogo property showPositionLabels
+Optimize with splitterAsFastaSimple returning ISeqSplitted allowing to speed up processing of
+single character alphabets.
+## Breaking changes
+* SplitterFunc now return type ISeqSplitted instead of string[]
 ### Features

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.34.2",
+  "version": "5.35.0",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.64",

package/src/monomer-works/monomer-utils.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/monomer-works/monomer-utils.js CHANGED Viewed

@@ -2,18 +2,17 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME } from '../utils/const';
-import { getSplitter } from '../utils/macromolecule/utils';
+import { UnitsHandler } from '../utils/units-handler';
 export function encodeMonomers(col) {
     let encodeSymbol = MONOMER_ENCODE_MIN;
     const monomerSymbolDict = {};
-    const units = col.tags[DG.TAGS.UNITS];
-    const sep = col.getTag("separator" /* TAGS.separator */);
-    const splitterFunc = getSplitter(units, sep);
+    const uh = UnitsHandler.getOrCreate(col);
+    const splitterFunc = uh.getSplitter();
     const encodedStringArray = [];
     for (let i = 0; i < col.length; ++i) {
         let encodedMonomerStr = '';
         const monomers = splitterFunc(col.get(i));
-        monomers.forEach((m) => {
+        for (const m of monomers) {
             if (!monomerSymbolDict[m]) {
                 if (encodeSymbol > MONOMER_ENCODE_MAX) {
                     grok.shell.error(`Not enough symbols to encode monomers`);
@@ -23,20 +22,19 @@ export function encodeMonomers(col) {
                 encodeSymbol++;
             }
             encodedMonomerStr += String.fromCodePoint(monomerSymbolDict[m]);
-        });
+        }
         encodedStringArray.push(encodedMonomerStr);
     }
     return DG.Column.fromStrings('encodedMolecules', encodedStringArray);
 }
 export function getMolfilesFromSeq(col, monomersLibObject) {
-    const units = col.tags[DG.TAGS.UNITS];
-    const sep = col.getTag('separator');
-    const splitterFunc = getSplitter(units, sep);
+    const uh = UnitsHandler.getOrCreate(col);
+    const splitter = uh.getSplitter();
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
     for (let i = 0; i < col.length; ++i) {
         const macroMolecule = col.get(i);
-        const monomers = splitterFunc(macroMolecule);
+        const monomers = splitter(macroMolecule);
         const molFilesForSeq = [];
         for (let j = 0; j < monomers.length; ++j) {
             if (monomers[j]) {
@@ -53,9 +51,8 @@ export function getMolfilesFromSeq(col, monomersLibObject) {
     return molFiles;
 }
 export function getMolfilesFromSingleSeq(cell, monomersLibObject) {
-    const units = cell.column.tags[DG.TAGS.UNITS];
-    const sep = cell.column.getTag('separator');
-    const splitterFunc = getSplitter(units, sep);
+    const uh = UnitsHandler.getOrCreate(cell.column);
+    const splitterFunc = uh.getSplitter();
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
     const macroMolecule = cell.value;

package/src/monomer-works/monomer-utils.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/src/monomer-works/to-atomic-level.d.ts CHANGED Viewed

@@ -7,7 +7,7 @@ import { Bonds, MolGraph } from './types';
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
-*/
+ */
 export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib): Promise<{
     col: DG.Column | null;
     warnings: string[];

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

	@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level.js CHANGED Viewed

@@ -1,20 +1,20 @@
 /* Do not change these import lines to match external modules in webpack configuration */
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import wu from 'wu';
+import { errorToConsole } from '@datagrok-libraries/utils';
 import { NOTATION } from '../utils/macromolecule/consts';
 import { NotationConverter } from '../utils/notation-converter';
 import { UnitsHandler } from '../utils/units-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
 import { monomerWorksConsts as C } from './consts';
-import { errorToConsole } from '@datagrok-libraries/utils';
-import { getSplitter } from '../utils/macromolecule';
 // todo: verify that all functions have return types
 /** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
-*/
+ */
 export async function _toAtomicLevel(df, seqCol, monomerLib) {
     // todo: remove this from the library
     if (DG.Func.find({ package: 'Chem', name: 'getRdKitModule' }).length === 0) {
@@ -70,13 +70,12 @@ export function getMonomerSequencesArray(macroMolCol) {
     const columnLength = macroMolCol.length;
     const result = new Array(columnLength);
     // split the string into monomers
-    const colUnits = macroMolCol.getTag(DG.TAGS.UNITS);
-    const separator = macroMolCol.getTag("separator" /* TAGS.separator */);
-    const splitterFunc = getSplitter(colUnits, separator);
+    const uh = UnitsHandler.getOrCreate(macroMolCol);
+    const splitter = uh.getSplitter();
     for (let row = 0; row < columnLength; ++row) {
         const macroMolecule = macroMolCol.get(row);
-        // todo: handle the exception case when macroMolecule is null
-        result[row] = macroMolecule ? splitterFunc(macroMolecule).filter((monomerCode) => monomerCode !== '') : [];
+        result[row] = macroMolecule ? wu(splitter(macroMolecule))
+            .filter((monomerCode) => monomerCode !== '').toArray() : [];
     }
     return result;
 }

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

	@@ -1 +1 @@
1	- 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package/src/utils/cell-renderer-monomer-placer.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.js CHANGED Viewed

@@ -1,5 +1,6 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import wu from 'wu';
 import { getSplitterForColumn } from './macromolecule';
 const polymerTypeMap = {
     ["DNA" /* ALPHABET.DNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
@@ -60,7 +61,7 @@ export class MonomerPlacer {
         if (res === null) {
             const seqMonList = this.getSeqMonList(rowIdx);
             res = this._monomerLengthList[rowIdx] = new Array(seqMonList.length);
-            for (const [seqMonI, seqMonLabel] of seqMonList.entries()) {
+            for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
                 const separatorWidth = this.props.unitsHandler.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
                 const seqMonWidth = separatorWidth + shortMon.length * this.props.monomerCharWidth;
@@ -86,7 +87,7 @@ export class MonomerPlacer {
             const seqMonList = this.getSeqMonList(seqIdx);
             if (seqMonList.length > res.length)
                 res.push(...new Array(seqMonList.length - res.length).fill(0));
-            for (const [seqMonI, seqMonLabel] of seqMonList.entries()) {
+            for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
                 const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.monomerCharWidth;
                 res[seqMonI] = Math.max(res[seqMonI] ?? 0, seqMonWidth);
@@ -99,7 +100,7 @@ export class MonomerPlacer {
     getPosition(rowIdx, x) {
         const [monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx);
         const seq = this.col.get(rowIdx);
-        const seqMonList = this._splitter(seq);
+        const seqMonList = wu(this._splitter(seq)).toArray();
         let iterationCount = 100;
         let left = null;
         let right = seqMonList.length;
@@ -112,12 +113,10 @@ export class MonomerPlacer {
                     left = mid;
                     found = true;
                 }
-                else if (x < monomerMaxLengthSumList[mid]) {
+                else if (x < monomerMaxLengthSumList[mid])
                     right = mid - 1;
-                }
-                else if (x > monomerMaxLengthSumList[mid + 1]) {
+                else if (x > monomerMaxLengthSumList[mid + 1])
                     left = mid + 1;
-                }
                 if (left == right)
                     found = true;
                 if (--iterationCount <= 0) {
@@ -130,7 +129,7 @@ export class MonomerPlacer {
     }
     getSeqMonList(rowIdx) {
         const seq = this.col.get(rowIdx);
-        return seq ? this._splitter(seq) : [];
+        return seq ? wu(this._splitter(seq)).toArray() : [];
     }
     getMonomer(symbol) {
         const alphabet = this.props.unitsHandler.alphabet ?? "UN" /* ALPHABET.UN */;

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package/src/utils/cell-renderer.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+import { ISeqSplitted } from './macromolecule/types';
 export declare enum DrawStyle {
     MSA = "MSA",
     classic = "classic"
@@ -20,11 +21,11 @@ export declare enum DrawStyle {
  * @param {number[]}maxWord {{[pos: number]: number}}  Max word lengths per position.
  * @param {number}wordIdx Is index of word we currently draw.
  * @param {DG.GridCell}gridCell Is grid cell.
- * @param {string[]}referenceSequence Is reference sequence for diff mode.
+ * @param {ISeqSplitted}referenceSequence Is reference sequence for diff mode.
  * @param {number}maxLengthOfMonomer Is max length of monomer.
  * @param {{[key: string]: TextMetrics}}monomerTextSizeMap Is map of monomer text sizes.
  * @return {number} x coordinate to start printing at.*/
-export declare function printLeftOrCentered(x: number, y: number, w: number, h: number, g: CanvasRenderingContext2D, s: string, color?: string, pivot?: number, left?: boolean, transparencyRate?: number, separator?: string, last?: boolean, drawStyle?: DrawStyle, maxWord?: number[], wordIdx?: number, gridCell?: DG.GridCell | null, referenceSequence?: string[], maxLengthOfMonomer?: number | null, monomerTextSizeMap?: {
+export declare function printLeftOrCentered(x: number, y: number, w: number, h: number, g: CanvasRenderingContext2D, s: string, color?: string, pivot?: number, left?: boolean, transparencyRate?: number, separator?: string, last?: boolean, drawStyle?: DrawStyle, maxWord?: number[], wordIdx?: number, gridCell?: DG.GridCell | null, referenceSequence?: ISeqSplitted, maxLengthOfMonomer?: number | null, monomerTextSizeMap?: {
     [key: string]: TextMetrics;
 }): number;
 //# sourceMappingURL=cell-renderer.d.ts.map

package/src/utils/cell-renderer.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer.js CHANGED Viewed

@@ -25,7 +25,7 @@ export var DrawStyle;
  * @param {number[]}maxWord {{[pos: number]: number}}  Max word lengths per position.
  * @param {number}wordIdx Is index of word we currently draw.
  * @param {DG.GridCell}gridCell Is grid cell.
- * @param {string[]}referenceSequence Is reference sequence for diff mode.
+ * @param {ISeqSplitted}referenceSequence Is reference sequence for diff mode.
  * @param {number}maxLengthOfMonomer Is max length of monomer.
  * @param {{[key: string]: TextMetrics}}monomerTextSizeMap Is map of monomer text sizes.
  * @return {number} x coordinate to start printing at.*/

package/src/utils/cell-renderer.js.map CHANGED Viewed

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

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

@@ -6,7 +6,7 @@ export var NOTATION;
     NOTATION["SEPARATOR"] = "separator";
     NOTATION["HELM"] = "helm";
 })(NOTATION || (NOTATION = {}));
-export const monomerRe = /(\[[A-Za-z0-9-_]+\]|.)/g;
+export const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
 export const Alphabets = new class {
     constructor() {
         this.fasta = {

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

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package/src/utils/macromolecule/index.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
 export { SplitterFunc, } from './types';
 export { TAGS, NOTATION, ALPHABET, ALIGNMENT, } from './consts';
-export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, MonomerToShortFunc, getSplitterForColumn } from './utils';
+export { splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, MonomerToShortFunc, getSplitterForColumn } from './utils';
 //# sourceMappingURL=index.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EACL,YAAY,GAEb,MAAM,SAAS,CAAC;AAEjB,OAAO,EACL,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,SAAS,GACV,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAChB,kBAAkB,EAClB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}

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

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

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EAEL,QAAQ,GAGT,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEhB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/types.d.ts CHANGED Viewed

@@ -1,8 +1,12 @@
+export interface ISeqSplitted extends Iterable<string> {
+    [jPos: number]: string;
+    length: number;
+}
 export type SeqColStats = {
     freq: MonomerFreqs;
     sameLength: boolean;
 };
-export type SplitterFunc = (seq: string) => string[];
+export type SplitterFunc = (seq: string) => ISeqSplitted;
 export type MonomerFreqs = {
     [m: string]: number;
 };

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

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

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

@@ -14,6 +14,7 @@ export declare function getStatsForCol(seqCol: DG.Column, minLength: number, spl
  * @return {string[]} array of monomers
  */
 export declare function splitterAsFasta(seq: any): string[];
+export declare function splitterAsFastaSimple(seq: any): string[];
 /** Gets method to split sequence by separator
  * @param {string} separator
  * @param limit
@@ -28,13 +29,6 @@ export declare function getSplitterWithSeparator(separator: string, limit?: numb
 export declare function splitterAsHelm(seq: any): string[];
 /** Func type to shorten a {@link monomerLabel} with length {@link limit} */
 export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string;
-/** Get splitter method to split sequences to monomers
- * @param {string} units
- * @param {string} separator
- * @param limit
- * @return {SplitterFunc}
- */
-export declare function getSplitter(units: string, separator: string, limit?: number | undefined): SplitterFunc;
 /** Generate splitter function for sequence column
  * @param {DG.Column} col
  * @return {SplitterFunc} Splitter function
@@ -60,5 +54,5 @@ export declare function detectAlphabet(freq: MonomerFreqs, candidates: Candidate
  */
 export declare function pickUpPalette(seqCol: DG.Column, minLength?: number): SeqPalette;
 export declare function getPaletteByType(paletteType: string): SeqPalette;
-export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column | null;
+export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column<string> | null;
 //# sourceMappingURL=utils.d.ts.map

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

	@@ -1 +1 @@
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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 } from './types';
-import { Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
+import { Alphabets, candidateAlphabets, monomerRe } from './consts';
 import { UnitsHandler } from '../units-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
 import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
@@ -44,14 +44,21 @@ function getStats(splitted, minLength) {
  * @return {string[]} array of monomers
  */
 export function splitterAsFasta(seq) {
-    return seq.toString().replace(monomerRe, '.$1').slice(1).split('.').map((monomer) => {
-        if (monomer.startsWith('[') && monomer.endsWith(']'))
-            return monomer.slice(1, -1);
-        else if (monomer === '-')
-            return '';
-        else
-            return monomer;
-    });
+    // return seq.toString().replace(monomerRe, '.$1').slice(1).split('.').map((monomer: string) => {
+    //   if (monomer.startsWith('[') && monomer.endsWith(']'))
+    //     return monomer.slice(1, -1);
+    //   else if (monomer === '-')
+    //     return '';
+    //   else
+    //     return monomer;
+    // });
+    return wu(seq.toString().matchAll(monomerRe))
+        .map((ma) => {
+        return ma[2] ?? ma[1]; // preserve '-' as gap symbol for compatibility with simpleAsFastaSimple
+    }).toArray();
+}
+export function splitterAsFastaSimple(seq) {
+    return !seq ? [] : seq;
 }
 /** Gets method to split sequence by separator
  * @param {string} separator
@@ -85,33 +92,13 @@ export function splitterAsHelm(seq) {
     const mmList = inSeq ? inSeq.split('.') : [];
     return mmList.map(mmPostProcess);
 }
-/** Get splitter method to split sequences to monomers
- * @param {string} units
- * @param {string} separator
- * @param limit
- * @return {SplitterFunc}
- */
-export function getSplitter(units, separator, limit = undefined) {
-    if (units.toLowerCase().startsWith(NOTATION.FASTA))
-        return splitterAsFasta;
-    else if (units.toLowerCase().startsWith(NOTATION.SEPARATOR))
-        return getSplitterWithSeparator(separator, limit);
-    else if (units.toLowerCase().startsWith(NOTATION.HELM))
-        return splitterAsHelm;
-    else
-        throw new Error(`Unexpected units ${units} .`);
-    // TODO: Splitter for HELM
-}
 /** Generate splitter function for sequence column
  * @param {DG.Column} col
  * @return {SplitterFunc} Splitter function
  */
 export function getSplitterForColumn(col) {
-    if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
-        throw new Error(`Get splitter for semType "${DG.SEMTYPE.MACROMOLECULE}" only.`);
-    const units = col.getTag(DG.TAGS.UNITS);
-    const separator = col.getTag("separator" /* TAGS.separator */);
-    return getSplitter(units, separator);
+    const uh = UnitsHandler.getOrCreate(col);
+    return uh.getSplitter();
 }
 const longMonomerPartRe = /([^\W_]+)/g;
 /** Convert long monomer names to short ones */

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

	@@ -1 +1 @@
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1	+ 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package/src/utils/notation-converter.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAa,YAAY,EAAC,MAAM,iBAAiB,CAAC;AACzD,OAAO,~~EAAC~~,YAAY,EAAC,MAAM,uBAAuB,CAAC;~~AACnD~~,OAAO,EAAC,QAAQ,~~EAAO~~,MAAM,wBAAwB,CAAC;~~AAGtD~~,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;AAElD,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;~~IAgCT~~;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM;~~gBAUpD~~,GAAG,EAAE,EAAE,CAAC,MAAM;IAI1B,YAAY,CAAC,QAAQ,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,WAAW;CAczF"}
1	+ {"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAa,YAAY,EAAC,MAAM,iBAAiB,CAAC;AACzD,OAAO,EAAe,YAAY,EAAC,MAAM,uBAAuB,CAAC;AACjE,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAGhD,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;AAElD,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;IA+BT;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM;gBASpD,GAAG,EAAE,EAAE,CAAC,MAAM;IAI1B,YAAY,CAAC,QAAQ,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,WAAW;CAczF"}

package/src/utils/notation-converter.js CHANGED Viewed

@@ -39,17 +39,15 @@ export class NotationConverter extends UnitsHandler {
             let item = helmItemsArray[i];
             if (isNucleotide)
                 item = item.replace(helmWrappersRe, '');
-            if (item === GapSymbols[NOTATION.HELM]) {
+            if (item === GapSymbols[NOTATION.HELM])
                 tgtMonomersArray.push(tgtGapSymbol);
-            }
             else if (this.toFasta(tgtNotation) && item.length > 1) {
                 // the case of a multi-character monomer converted to FASTA
                 const monomer = '[' + item + ']';
                 tgtMonomersArray.push(monomer);
             }
-            else {
+            else
                 tgtMonomersArray.push(item);
-            }
         }
         return tgtMonomersArray.join(tgtSeparator);
     }
@@ -117,8 +115,8 @@ function convertToHelm(srcUh, src) {
     const isDna = src.startsWith('DNA');
     const isRna = src.startsWith('RNA');
     const [prefix, leftWrapper, rightWrapper, postfix] = srcUh.getHelmWrappers();
-    const srcMList = srcUh.getSplitter()(src);
-    const tgtMList = srcMList.map((srcM) => {
+    const srcS = srcUh.getSplitter()(src);
+    const tgtMList = wu(srcS).map((srcM) => {
         let m = srcM;
         if (srcUh.isGap(m))
             m = GapSymbols[NOTATION.HELM];
@@ -127,7 +125,7 @@ function convertToHelm(srcUh, src) {
         else
             m = srcM.length == 1 ? `${leftWrapper}${srcM}${rightWrapper}` : `${leftWrapper}[${srcM}]${rightWrapper}`;
         return m;
-    });
+    }).toArray();
     return `${prefix}${tgtMList.join('.')}${postfix}`;
 }
 /** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */

package/src/utils/notation-converter.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/utils/splitter.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;~~AAKtC~~,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,SAAS,CA0BrF"}
1	+ {"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,SAAS,CA0BrF"}

package/src/utils/splitter.js CHANGED Viewed

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+import wu from 'wu';
 import { getSplitterForColumn } from './macromolecule/utils';
 export function splitAlignedSequences(sequenceColumn) {
     const splitter = getSplitterForColumn(sequenceColumn);
@@ -16,10 +17,10 @@ export function splitAlignedSequences(sequenceColumn) {
         if (sequence == null)
             continue;
         const currentMonomerList = splitter(sequence);
-        currentMonomerList.forEach((monomer, positionIndex) => {
+        for (const [monomer, positionIndex] of wu.enumerate(currentMonomerList)) {
             const col = getCol(positionIndex) || createCol(positionIndex);
             col.set(rowIndex, monomer || '-', false);
-        });
+        }
     }
     return resultDf;
 }

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

	@@ -1 +1 @@
1	- {"version":3,"file":"splitter.js","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,oBAAoB,EAAC,MAAM,uBAAuB,CAAC;AAG3D,MAAM,UAAU,qBAAqB,CAAC,cAAiC;IACrE,MAAM,QAAQ,GAAG,oBAAoB,CAAC,cAAc,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,CAAC,KAAa,EAA4B,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC;IACtF,MAAM,SAAS,GAAG,CAAC,KAAa,EAAqB,EAAE;QACrD,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC1E,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;QAC7B,OAAO,WAAW,CAAC;IACrB,CAAC,CAAC;IAEF,MAAM,UAAU,GAAwB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,CAAC;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;IAE/C,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,EAAE,QAAQ,EAAE;QACtD,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9C,IAAI,QAAQ,IAAI,IAAI;YAClB,SAAS;QAEX,MAAM,kBAAkB,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAC9C,~~kBAAkB~~,CAAC,OAAO,~~CAAC~~,CAAC,~~OAAO~~,EAAE,~~aAAa~~,~~EAAE~~,EAAE;~~YACpD~~,MAAM,GAAG,GAAG,MAAM,CAAC,aAAa,CAAC,IAAI,SAAS,CAAC,aAAa,CAAC,CAAC;YAC9D,GAAG,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,IAAI,GAAG,EAAE,KAAK,CAAC,CAAC;~~QAC3C,CAAC,CAAC,CAAC~~;~~KACJ~~;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}
1	+ {"version":3,"file":"splitter.js","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,oBAAoB,EAAC,MAAM,uBAAuB,CAAC;AAG3D,MAAM,UAAU,qBAAqB,CAAC,cAAiC;IACrE,MAAM,QAAQ,GAAG,oBAAoB,CAAC,cAAc,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,CAAC,KAAa,EAA4B,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC;IACtF,MAAM,SAAS,GAAG,CAAC,KAAa,EAAqB,EAAE;QACrD,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC1E,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;QAC7B,OAAO,WAAW,CAAC;IACrB,CAAC,CAAC;IAEF,MAAM,UAAU,GAAwB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,CAAC;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;IAE/C,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,EAAE,QAAQ,EAAE;QACtD,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9C,IAAI,QAAQ,IAAI,IAAI;YAClB,SAAS;QAEX,MAAM,kBAAkB,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAC9C,KAAK,MAAM,CAAC,OAAO,EAAE,aAAa,CAAC,IAAI,EAAE,CAAC,SAAS,CAAC,kBAAkB,CAAC,EAAE;YACvE,MAAM,GAAG,GAAG,MAAM,CAAC,aAAa,CAAC,IAAI,SAAS,CAAC,aAAa,CAAC,CAAC;YAC9D,GAAG,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,IAAI,GAAG,EAAE,KAAK,CAAC,CAAC;SAC1C;KACF;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/src/utils/units-handler.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { NOTATION } from './macromolecule/consts';
-import { SeqColStats, SplitterFunc } from './macromolecule/types';
+import { ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
 export declare const Tags: {
@@ -34,7 +34,7 @@ export declare class UnitsHandler {
     getAlphabetIsMultichar(): boolean;
     private _splitted;
     /** */
-    get splitted(): string[][];
+    get splitted(): ISeqSplitted[];
     private _stats;
     get stats(): SeqColStats;
     isFasta(): boolean;
@@ -92,7 +92,7 @@ export declare class UnitsHandler {
      */
     static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
     /** Gets function to split seq value to monomers */
-    getSplitter(): SplitterFunc;
+    getSplitter(limit?: number): SplitterFunc;
     getDistanceFunctionName(): MmDistanceFunctionsNames;
     getDistanceFunction(): mmDistanceFunctionType;
     checkHelmCompatibility(): Promise<boolean>;

package/src/utils/units-handler.d.ts.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { candidateAlphabets, NOTATION } from './macromolecule/consts';
-import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator } from './macromolecule/utils';
+import { detectAlphabet, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, splitterAsFastaSimple } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 export const Tags = new class {
@@ -90,9 +90,8 @@ export class UnitsHandler {
         if (this.notation == NOTATION.HELM || this.alphabet == "UN" /* ALPHABET.UN */) {
             const alphabetSizeStr = this.column.getTag(".alphabetSize" /* TAGS.alphabetSize */);
             let alphabetSize;
-            if (alphabetSizeStr) {
+            if (alphabetSizeStr)
                 alphabetSize = parseInt(alphabetSizeStr);
-            }
             else {
                 // calculate alphabetSize on demand
                 const stats = this.stats;
@@ -167,8 +166,8 @@ export class UnitsHandler {
     isMsa() { return this.aligned ? this.aligned.toUpperCase().includes('MSA') : false; }
     isHelmCompatible() { return this.helmCompatible === 'true'; }
     isGap(m) {
-        return !m || (this.units === NOTATION.FASTA && m === GapSymbols.FASTA) ||
-            (this.units === NOTATION.HELM && m === GapSymbols.HELM);
+        return !m || (this.units === NOTATION.FASTA && m === GapSymbols[NOTATION.FASTA]) ||
+            (this.units === NOTATION.HELM && m === GapSymbols[NOTATION.HELM]);
     }
     /** Associate notation types with the corresponding units */
     /**
@@ -224,13 +223,13 @@ export class UnitsHandler {
         if (srcAligned)
             newColumn.setTag("aligned" /* TAGS.aligned */, srcAligned);
         const srcAlphabet = col.getTag("alphabet" /* TAGS.alphabet */);
-        if (srcAlphabet)
+        if (srcAlphabet != null)
             newColumn.setTag("alphabet" /* TAGS.alphabet */, srcAlphabet);
         let srcAlphabetSize = col.getTag(".alphabetSize" /* TAGS.alphabetSize */);
-        if (srcAlphabetSize)
+        if (srcAlphabet != null && srcAlphabetSize)
             newColumn.setTag(".alphabetSize" /* TAGS.alphabetSize */, srcAlphabetSize);
         const srcAlphabetIsMultichar = col.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */);
-        if (srcAlphabetIsMultichar !== undefined)
+        if (srcAlphabet != null && srcAlphabetIsMultichar !== undefined)
             newColumn.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, srcAlphabetIsMultichar);
         if (tgtNotation == NOTATION.HELM) {
             srcAlphabetSize = this.getAlphabetSize().toString();
@@ -284,8 +283,21 @@ export class UnitsHandler {
         return newColumn;
     }
     /** Gets function to split seq value to monomers */
-    getSplitter() {
-        return getSplitterForColumn(this._column);
+    getSplitter(limit) {
+        if (this.units.toLowerCase().startsWith(NOTATION.FASTA)) {
+            const alphabet = this.column.getTag("alphabet" /* TAGS.alphabet */);
+            if (alphabet !== null && !this.getAlphabetIsMultichar())
+                return splitterAsFastaSimple;
+            else
+                return splitterAsFasta;
+        }
+        else if (this.units.toLowerCase().startsWith(NOTATION.SEPARATOR))
+            return getSplitterWithSeparator(this.separator, limit);
+        else if (this.units.toLowerCase().startsWith(NOTATION.HELM))
+            return splitterAsHelm;
+        else
+            throw new Error(`Unexpected units ${this.units} .`);
+        // TODO: Splitter for HELM
     }
     getDistanceFunctionName() {
         // TODO add support for helm and separator notation
@@ -357,19 +369,16 @@ export class UnitsHandler {
             (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) && !this.isHelm() && this.alphabet === "UN" /* ALPHABET.UN */)) {
             // The following detectors and setters are to be called because the column is likely
             // as the UnitsHandler constructor was called on the column.
-            if (this.isFasta()) {
+            if (this.isFasta())
                 UnitsHandler.setUnitsToFastaColumn(this);
-            }
             else if (this.isSeparator()) {
                 const separator = col.getTag("separator" /* TAGS.separator */);
                 UnitsHandler.setUnitsToSeparatorColumn(this, separator);
             }
-            else if (this.isHelm()) {
+            else if (this.isHelm())
                 UnitsHandler.setUnitsToHelmColumn(this);
-            }
-            else {
+            else
                 throw new Error(`Unexpected units '${this.column.getTag(DG.TAGS.UNITS)}'.`);
-            }
         }
         // if (!this.column.tags.has(TAGS.alphabetSize)) {
         //   if (this.isHelm())
@@ -380,9 +389,8 @@ export class UnitsHandler {
         //       `tag '${TAGS.alphabetSize}' is mandatory.`);
         // }
         if (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */)) {
-            if (this.isHelm()) {
+            if (this.isHelm())
                 this.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, 'true');
-            }
             else if (['UN'].includes(this.alphabet)) {
                 throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' ` +
                     `tag '${".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */}' is mandatory.`);

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

	@@ -1 +1 @@
1	- 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