npm - @datagrok-libraries/bio - Versions diffs - 5.31.0 → 5.32.1 - Mend

@datagrok-libraries/bio 5.31.0 → 5.32.1

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 (21) hide show

package/package.json +3 -3
package/src/monomer-works/to-atomic-level.js +2 -2
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/fasta-handler.d.ts.map +1 -1
package/src/utils/fasta-handler.js +1 -1
package/src/utils/fasta-handler.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/utils.d.ts +1 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +11 -6
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 +3 -4
package/src/utils/notation-converter.js.map +1 -1
package/src/utils/units-handler.d.ts +20 -7
package/src/utils/units-handler.d.ts.map +1 -1
package/src/utils/units-handler.js +79 -27
package/src/utils/units-handler.js.map +1 -1

package/package.json CHANGED Viewed

@@ -8,10 +8,10 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.31.0",
+  "version": "5.32.1",
   "description": "",
   "dependencies": {
-    "@datagrok-libraries/gridext": "^1.3.22",
+    "@datagrok-libraries/gridext": "^1.3.54",
     "@datagrok-libraries/utils": "^2.5.0",
     "@datagrok-libraries/ml": "^6.3.28",
     "@deck.gl/core": "8.8.12",
@@ -36,7 +36,7 @@
     "link": "npm link",
     "link-api": "npm link datagrok-api",
     "link-utils": "npm link @datagrok-libraries/utils",
-    "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/gridext",
+    "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/gridext @datagrok-libraries/ml",
     "build-bio": "git clean -f -X -d ./src && tsc",
     "build": "git clean -f -X -d ./src && tsc",
     "lint": "eslint \"./src/**/*.ts\"",

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

@@ -57,14 +57,14 @@ export function _toAtomicLevel(df, seqCol, monomerLib) {
             return { col: null, warnings: [msg] };
         }
         let srcCol = seqCol;
-        const seqUh = new UnitsHandler(seqCol);
+        const seqUh = UnitsHandler.getOrCreate(seqCol);
         // convert 'helm' to 'separator' units
         if (seqUh.isHelm()) {
             const converter = new NotationConverter(seqCol);
             srcCol = converter.convert("separator" /* NOTATION.SEPARATOR */, '.');
             srcCol.name = seqCol.name; // Replace converted col name 'separator(<original>)' to '<original>';
         }
-        const srcUh = new UnitsHandler(srcCol);
+        const srcUh = UnitsHandler.getOrCreate(srcCol);
         const alphabet = srcUh.alphabet;
         // determine the polymer type according to HELM specifications
         let polymerType;

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

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,oCAAoC;AACpC,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,kBAAkB,CAAgB;IAC1C,OAAO,CAAC,eAAe,CAAgB;IAGvC,IAAW,iBAAiB,IAAI,MAAM,EAAE,CAAoC;IAE5E,IAAW,cAAc,IAAI,MAAM,EAAE,CAAiC;IAEtE;;;;;;;OAOG;IACH,OAAO,CAAC,kBAAkB;IAS1B,2DAA2D;IAC3D,OAAO,CAAC,YAAY;IAiBpB;;;;OAIG;IACI,WAAW,IAAI,EAAE,CAAC,SAAS,EAAG;gBAezB,WAAW,EAAE,MAAM;CAIhC"}

package/src/utils/fasta-handler.js CHANGED Viewed

@@ -44,7 +44,7 @@ export class FastaFileHandler {
         sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
         sequenceCol.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
         // here should go the code from units handler
-        UnitsHandler.setUnitsToFastaColumn(sequenceCol);
+        const uh = UnitsHandler.getOrCreate(sequenceCol);
         return [DG.DataFrame.fromColumns([
                 descriptionsArrayCol,
                 sequenceCol,

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

	@@ -1 +1 @@
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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, getStats, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, } from './utils';
+export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, } 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,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,GACjB,MAAM,SAAS,CAAC"}

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

@@ -1,2 +1,2 @@
-export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getStats, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, } from './utils';
+export { getSplitter, 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 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAgBA,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,GACjB,MAAM,SAAS,CAAC"}

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

@@ -8,7 +8,7 @@ import { SeqPalette } from '../../seq-palettes';
  * @param {SplitterFunc} splitter
  * @return { SeqColStats }, sameLength: boolean } stats of column sequences
  */
-export declare function getStats(seqCol: DG.Column, minLength: number, splitter: SplitterFunc): SeqColStats;
+export declare function getStatsForCol(seqCol: DG.Column, minLength: number, splitter: SplitterFunc): SeqColStats;
 /** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol.
  * @param {any} seq object with sequence
  * @return {string[]} array of monomers

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

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

@@ -14,12 +14,17 @@ import { UnknownSeqPalettes } from '../../unknown';
  * @param {SplitterFunc} splitter
  * @return { SeqColStats }, sameLength: boolean } stats of column sequences
  */
-export function getStats(seqCol, minLength, splitter) {
+export function getStatsForCol(seqCol, minLength, splitter) {
+    const cats = seqCol.categories;
+    const splitted = wu(seqCol.getRawData())
+        .map((catI) => splitter(seqCol.categories[catI]));
+    return getStats(splitted, minLength);
+}
+function getStats(splitted, minLength) {
     const freq = {};
     let sameLength = true;
     let firstLength = null;
-    for (const seq of seqCol.categories) {
-        const mSeq = splitter(seq);
+    for (const mSeq of splitted) {
         if (firstLength == null)
             firstLength = mSeq.length;
         else if (mSeq.length !== firstLength)
@@ -42,7 +47,7 @@ export function splitterAsFasta(seq) {
     return wu(seq.toString().matchAll(monomerRe))
         .map((ma) => {
         const m = ma[0];
-        const mRes = m.length > 1 ? ma[1] : m;
+        const mRes = m === '-' ? '' : m.length > 1 ? ma[1] : m;
         return mRes;
     }).toArray();
 }
@@ -173,11 +178,11 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
 export function pickUpPalette(seqCol, minLength = 5) {
     let alphabet;
     if (seqCol.semType == DG.SEMTYPE.MACROMOLECULE) {
-        const uh = new UnitsHandler(seqCol);
+        const uh = UnitsHandler.getOrCreate(seqCol);
         alphabet = uh.alphabet;
     }
     else {
-        const stats = getStats(seqCol, minLength, splitterAsFasta);
+        const stats = getStatsForCol(seqCol, minLength, splitterAsFasta);
         alphabet = detectAlphabet(stats.freq, candidateAlphabets);
     }
     const res = getPaletteByType(alphabet);

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

	@@ -1 +1 @@
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":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAc,YAAY,EAAC,MAAM,uBAAuB,CAAC;AAChE,OAAO,EAAC,QAAQ,EAAO,MAAM,wBAAwB,CAAC;AAGtD,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;;;;;;OAMG;IACH,OAAO,CAAC,uBAAuB;IAmB/B;;;;;OAKG;IACH,OAAO,CAAC,eAAe;IAiBvB,OAAO,CAAC,mBAAmB;IAkB3B;;;;;;;OAOG;IACI,mBAAmB,CACxB,aAAa,EAAE,MAAM,EACrB,eAAe,GAAE,MAAM,GAAG,IAAW,GACpC,MAAM;IAOT;;;;;OAKG;IACH,OAAO,CAAC,aAAa;IAgBrB;;;;;OAKG;IACH,OAAO,CAAC,uBAAuB;IA6B/B;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;IAgCT;;;;;;;;OAQG;IACH,OAAO,CAAC,WAAW;~~IAsBnB~~,OAAO,CAAC,sBAAsB;IAK9B;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,EAAE,CAAC,MAAM;gBAsBjE,GAAG,EAAE,EAAE,CAAC,MAAM;CAGlC"}
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package/src/utils/notation-converter.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { UnitsHandler } from './units-handler';
-import { getSplitterForColumn, getStats } from './macromolecule/utils';
+import { getSplitterForColumn } from './macromolecule/utils';
 /** Class for handling conversion of notation systems in Macromolecule columns */
 export class NotationConverter extends UnitsHandler {
     get splitter() {
@@ -58,7 +58,7 @@ export class NotationConverter extends UnitsHandler {
     convertToHelmHelper(sourcePolymer, sourceGapSymbol, prefix, leftWrapper, rightWrapper, postfix) {
         const monomerArray = this.splitter(sourcePolymer);
         const monomerHelmArray = monomerArray.map((mm) => {
-            if (mm === sourceGapSymbol)
+            if (!mm || mm === sourceGapSymbol)
                 return UnitsHandler._defaultGapSymbolsDict.HELM;
             else
                 return `${leftWrapper}${mm}${rightWrapper}`;
@@ -198,8 +198,7 @@ export class NotationConverter extends UnitsHandler {
         });
         // TAGS.aligned is mandatory for columns of NOTATION.FASTA and NOTATION.SEPARATOR
         const splitter = getSplitterForColumn(newColumn);
-        const stats = getStats(newColumn, 5, splitter);
-        const aligned = stats.sameLength ? 'SEQ.MSA' : 'SEQ';
+        const aligned = this.stats.sameLength ? 'SEQ.MSA' : 'SEQ';
         newColumn.setTag("aligned" /* TAGS.aligned */, aligned);
         return newColumn;
     }

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

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

@@ -1,8 +1,12 @@
 import * as DG from 'datagrok-api/dg';
 import { NOTATION } from './macromolecule/consts';
-import { SplitterFunc } from './macromolecule/types';
+import { 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: {
+    /** Column's temp slot name for a UnitsHandler object */
+    uhTemp: string;
+};
 /** Class for handling notation units in Macromolecule columns */
 export declare class UnitsHandler {
     protected readonly _column: DG.Column;
@@ -14,12 +18,12 @@ export declare class UnitsHandler {
         SEPARATOR: string;
         FASTA: string;
     };
-    static setUnitsToFastaColumn(col: DG.Column): void;
-    static setUnitsToSeparatorColumn(col: DG.Column, separator?: string): void;
-    static setUnitsToHelmColumn(col: DG.Column): void;
+    static setUnitsToFastaColumn(uh: UnitsHandler): void;
+    static setUnitsToSeparatorColumn(uh: UnitsHandler, separator?: string): void;
+    static setUnitsToHelmColumn(uh: UnitsHandler): void;
     /** From detectMacromolecule */
-    static setTags(col: DG.Column, splitter: SplitterFunc): void;
-    protected get units(): string;
+    static setTags(uh: UnitsHandler): void;
+    get units(): string;
     protected get column(): DG.Column;
     get notation(): NOTATION;
     get defaultGapSymbol(): string;
@@ -30,6 +34,11 @@ export declare class UnitsHandler {
     protected get helmCompatible(): string | undefined;
     getAlphabetSize(): number;
     getAlphabetIsMultichar(): boolean;
+    private _splitted;
+    /** */
+    get splitted(): string[][];
+    private _stats;
+    get stats(): SeqColStats;
     isFasta(): boolean;
     isSeparator(): boolean;
     isHelm(): boolean;
@@ -76,9 +85,13 @@ export declare class UnitsHandler {
      * @return {DG.Column}
      */
     static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
+    /** Gets function to split seq value to monomers */
+    getSplitter(): SplitterFunc;
     getDistanceFunctionName(): MmDistanceFunctionsNames;
     getDistanceFunction(): mmDistanceFunctionType;
     checkHelmCompatibility(): Promise<boolean>;
-    constructor(col: DG.Column);
+    protected constructor(col: DG.Column<string>);
+    /** Gets a column's UnitsHandler object from temp slot or creates a new and stores it to the temp slot. */
+    static getOrCreate(col: DG.Column<string>): UnitsHandler;
 }
 //# sourceMappingURL=units-handler.d.ts.map

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

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

@@ -9,50 +9,56 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
 };
 import * as DG from 'datagrok-api/dg';
 import { candidateAlphabets } from './macromolecule/consts';
-import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator, getStats, splitterAsFasta, splitterAsHelm } from './macromolecule/utils';
+import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator } 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 {
+    constructor() {
+        /** Column's temp slot name for a UnitsHandler object */
+        this.uhTemp = `units-handler.${DG.SEMTYPE.MACROMOLECULE}`;
+    }
+}();
 /** Class for handling notation units in Macromolecule columns */
 export class UnitsHandler {
-    static setUnitsToFastaColumn(col) {
-        if (col.semType !== DG.SEMTYPE.MACROMOLECULE || col.getTag(DG.TAGS.UNITS) !== "fasta" /* NOTATION.FASTA */)
+    static setUnitsToFastaColumn(uh) {
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== "fasta" /* NOTATION.FASTA */)
             throw new Error(`The column of notation '${"fasta" /* NOTATION.FASTA */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
-        col.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
-        UnitsHandler.setTags(col, splitterAsFasta);
+        uh.column.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
+        UnitsHandler.setTags(uh);
     }
-    static setUnitsToSeparatorColumn(col, separator) {
-        if (col.semType !== DG.SEMTYPE.MACROMOLECULE || col.getTag(DG.TAGS.UNITS) !== "separator" /* NOTATION.SEPARATOR */)
+    static setUnitsToSeparatorColumn(uh, separator) {
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== "separator" /* NOTATION.SEPARATOR */)
             throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
         if (!separator)
             throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must have the separator tag.`);
-        col.setTag(DG.TAGS.UNITS, "separator" /* NOTATION.SEPARATOR */);
-        col.setTag("separator" /* TAGS.separator */, separator);
-        UnitsHandler.setTags(col, getSplitterWithSeparator(separator));
+        uh.column.setTag(DG.TAGS.UNITS, "separator" /* NOTATION.SEPARATOR */);
+        uh.column.setTag("separator" /* TAGS.separator */, separator);
+        UnitsHandler.setTags(uh);
     }
-    static setUnitsToHelmColumn(col) {
-        if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
+    static setUnitsToHelmColumn(uh) {
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE)
             throw new Error(`The column of notation '${"helm" /* NOTATION.HELM */}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
-        col.setTag(DG.TAGS.UNITS, "helm" /* NOTATION.HELM */);
-        UnitsHandler.setTags(col, splitterAsHelm);
+        uh.column.setTag(DG.TAGS.UNITS, "helm" /* NOTATION.HELM */);
+        UnitsHandler.setTags(uh);
     }
     /** From detectMacromolecule */
-    static setTags(col, splitter) {
-        const units = col.getTag(DG.TAGS.UNITS);
-        const stats = getStats(col, 5, splitter);
+    static setTags(uh) {
+        const units = uh.column.getTag(DG.TAGS.UNITS);
+        const stats = uh.stats;
         const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
         if (["fasta" /* NOTATION.FASTA */, "separator" /* NOTATION.SEPARATOR */].includes(units)) {
             // Empty monomer alphabet is not allowed
             if (Object.keys(stats.freq).length === 0)
                 throw new Error('Alphabet is empty');
             const aligned = stats.sameLength ? "SEQ.MSA" /* ALIGNMENT.SEQ_MSA */ : "SEQ" /* ALIGNMENT.SEQ */;
-            col.setTag("aligned" /* TAGS.aligned */, aligned);
+            uh.column.setTag("aligned" /* TAGS.aligned */, aligned);
             const alphabet = detectAlphabet(stats.freq, candidateAlphabets);
-            col.setTag("alphabet" /* TAGS.alphabet */, alphabet);
+            uh.column.setTag("alphabet" /* TAGS.alphabet */, alphabet);
             if (alphabet === "UN" /* ALPHABET.UN */) {
                 const alphabetSize = Object.keys(stats.freq).length;
                 const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
-                col.setTag(".alphabetSize" /* TAGS.alphabetSize */, alphabetSize.toString());
-                col.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, alphabetIsMultichar ? 'true' : 'false');
+                uh.column.setTag(".alphabetSize" /* TAGS.alphabetSize */, alphabetSize.toString());
+                uh.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, alphabetIsMultichar ? 'true' : 'false');
             }
         }
     }
@@ -94,8 +100,7 @@ export class UnitsHandler {
             }
             else {
                 // calculate alphabetSize on demand
-                const splitter = getSplitterForColumn(this.column);
-                const stats = getStats(this.column, 1, splitter);
+                const stats = this.stats;
                 alphabetSize = Object.keys(stats.freq).length;
             }
             return alphabetSize;
@@ -123,6 +128,41 @@ export class UnitsHandler {
         else
             return this.column.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) === 'true';
     }
+    /** */
+    get splitted() {
+        if (this._splitted === null) {
+            const splitter = this.getSplitter();
+            const colLength = this._column.length;
+            this._splitted = new Array(colLength);
+            const catIdxList = this._column.getRawData();
+            const catList = this._column.categories;
+            for (let rowI = 0; rowI < colLength; rowI++) {
+                const seq = catList[catIdxList[rowI]];
+                this._splitted[rowI] = splitter(seq);
+            }
+        }
+        return this._splitted;
+    }
+    get stats() {
+        if (this._stats === null) {
+            const freq = {};
+            let sameLength = true;
+            let firstLength = null;
+            for (const mSeq of this.splitted) {
+                if (firstLength == null)
+                    firstLength = mSeq.length;
+                else if (mSeq.length !== firstLength)
+                    sameLength = false;
+                for (const m of mSeq) {
+                    if (!(m in freq))
+                        freq[m] = 0;
+                    freq[m] += 1;
+                }
+            }
+            this._stats = { freq: freq, sameLength: sameLength };
+        }
+        return this._stats;
+    }
     isFasta() { return this.notation === "fasta" /* NOTATION.FASTA */; }
     isSeparator() { return this.notation === "separator" /* NOTATION.SEPARATOR */; }
     isHelm() { return this.notation === "helm" /* NOTATION.HELM */; }
@@ -192,7 +232,7 @@ export class UnitsHandler {
      * @return {DG.Column}
      */
     static getNewColumn(templateCol) {
-        const col = new UnitsHandler(templateCol);
+        const col = UnitsHandler.getOrCreate(templateCol);
         const targetNotation = col.notation;
         return col.getNewColumn(targetNotation);
     }
@@ -229,6 +269,10 @@ export class UnitsHandler {
         newColumn.setTag(DG.TAGS.UNITS, units);
         return newColumn;
     }
+    /** Gets function to split seq value to monomers */
+    getSplitter() {
+        return getSplitterForColumn(this._column);
+    }
     getDistanceFunctionName() {
         // TODO add support for helm and separator notation
         if (!this.isFasta())
@@ -283,6 +327,8 @@ export class UnitsHandler {
         });
     }
     constructor(col) {
+        this._splitted = null;
+        this._stats = null;
         this._column = col;
         const units = this._column.getTag(DG.TAGS.UNITS);
         if (units !== null && units !== undefined)
@@ -298,14 +344,14 @@ export class UnitsHandler {
             // 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()) {
-                UnitsHandler.setUnitsToFastaColumn(this.column);
+                UnitsHandler.setUnitsToFastaColumn(this);
             }
             else if (this.isSeparator()) {
                 const separator = col.getTag("separator" /* TAGS.separator */);
-                UnitsHandler.setUnitsToSeparatorColumn(this.column, separator);
+                UnitsHandler.setUnitsToSeparatorColumn(this, separator);
             }
             else if (this.isHelm()) {
-                UnitsHandler.setUnitsToHelmColumn(this.column);
+                UnitsHandler.setUnitsToHelmColumn(this);
             }
             else {
                 throw new Error(`Unexpected units '${this.column.getTag(DG.TAGS.UNITS)}'.`);
@@ -329,6 +375,12 @@ export class UnitsHandler {
             }
         }
     }
+    /** Gets a column's UnitsHandler object from temp slot or creates a new and stores it to the temp slot. */
+    static getOrCreate(col) {
+        if (!(Tags.uhTemp in col.temp))
+            col.temp[Tags.uhTemp] = new UnitsHandler(col);
+        return col.temp[Tags.uhTemp];
+    }
 }
 UnitsHandler._defaultGapSymbolsDict = {
     HELM: '*',

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

	@@ -1 +1 @@
1	- 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