@datagrok-libraries/bio 5.44.4 → 5.45.0

package/src/utils/macromolecule/seq-handler.js

@@ -0,0 +1,8 @@
+export const SeqTemps = new class {
+    constructor() {
+        /** Column's temp slot name for a SeqHandler object */
+        this.seqHandler = `seq-handler`;
+        this.notationProvider = `seq-handler.notation-provider`;
+    }
+}();
+//# sourceMappingURL=seq-handler.js.map

package/src/utils/macromolecule/seq-handler.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seq-handler.js","sourceRoot":"","sources":["seq-handler.ts"],"names":[],"mappings":"AAWA,MAAM,CAAC,MAAM,QAAQ,GAAG,IAAI;IAAA;QAC1B,sDAAsD;QACtD,eAAU,GAAG,aAAa,CAAC;QAC3B,qBAAgB,GAAG,+BAA+B,CAAC;IACrD,CAAC;CAAA,EAAE,CAAC"}

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

@@ -11,7 +11,8 @@ export interface ISeqSplitted {
 }
 export interface INotationProvider {
     get splitter(): SplitterFunc;
-    getHelm(seqCol: DG.Column<string>, options?: any): Promise<DG.Column<string>>;
+    /** Any Macromolecule can be presented as Helm notation */
+    getHelm(seq: string, options: any): Promise<DG.SemanticValue<string>>;
     createCellRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
 }
 export type SeqColStats = {

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

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,oBAAoB,EAAC,MAAM,4BAA4B,CAAC;AAEhE,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEpC,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,0DAA0D;IAC1D,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC;IAEtE,sBAAsB,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAAE,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;CAClH;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}

package/src/utils/macromolecule/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAgCA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAiCA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}

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

@@ -2,6 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import { CandidateType, ISeqSplitted, MonomerFreqs, SeqColStats, SeqSplittedBase, SplitterFunc } from './types';
 import { ALPHABET } from './consts';
 import { SeqPalette } from '../../seq-palettes';
+import { ISeqHelper } from '../seq-helper';
 export declare class StringListSeqSplitted implements ISeqSplitted {
     private readonly mList;
     private readonly gapOriginalMonomer;
@@ -73,7 +74,7 @@ export declare function detectAlphabet(freq: MonomerFreqs, candidates: Candidate
  * @param {number}  minLength minimum length of sequence to detect palette (empty strings are allowed)
  * @return {SeqPalette} Palette corresponding to the alphabet of the sequences in the column
  */
-export declare function pickUpPalette(seqCol: DG.Column, minLength?: number): SeqPalette;
+export declare function pickUpPalette(seqCol: DG.Column, seqHelper: ISeqHelper, minLength?: number): SeqPalette;
 export declare function getPaletteByType(paletteType: string): SeqPalette;
 export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column<string> | null;
 //# sourceMappingURL=utils.d.ts.map

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

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

@@ -1,10 +1,9 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { CandidateSimType } from './types';
-import { ALPHABET, Alphabets, candidateAlphabets, GAP_SYMBOL, GapOriginals, monomerRe, NOTATION } from './consts';
-import { SeqHandler } from '../seq-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
 import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
+import { CandidateSimType } from './types';
+import { ALPHABET, Alphabets, candidateAlphabets, GAP_SYMBOL, GapOriginals, monomerRe, NOTATION } from './consts';
 import { AminoacidsPalettes } from '../../aminoacids';
 import { NucleotidesPalettes } from '../../nucleotides';
 import { UnknownSeqPalettes } from '../../unknown';
@@ -234,10 +233,10 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
  * @param {number}  minLength minimum length of sequence to detect palette (empty strings are allowed)
  * @return {SeqPalette} Palette corresponding to the alphabet of the sequences in the column
  */
-export function pickUpPalette(seqCol, minLength = 5) {
+export function pickUpPalette(seqCol, seqHelper, minLength = 5) {
     let alphabet;
     if (seqCol.semType == DG.SEMTYPE.MACROMOLECULE) {
-        const sh = SeqHandler.forColumn(seqCol);
+        const sh = seqHelper.getSeqHandler(seqCol);
         alphabet = sh.alphabet;
     }
     else {

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

@@ -1 +1 @@
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package/src/utils/seq-helper.d.ts

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { IMonomerLibBase } from '../types';
+import { ISeqHandler } from './macromolecule/seq-handler';
 export type ToAtomicLevelRes = {
     molCol: DG.Column<string> | null;
     warnings: string[];
@@ -12,6 +13,7 @@ export interface ISeqHelper {
      * @param overrideMonomerLib {IMonomerLibBase} [null] Override monomer library for monomers from reactions
      **/
     helmToAtomicLevel(helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean, overrideMonomerLib?: IMonomerLibBase): Promise<ToAtomicLevelRes>;
+    getSeqHandler(seqCol: DG.Column<string>): ISeqHandler;
 }
 export declare function getSeqHelper(): Promise<ISeqHelper>;
 //# sourceMappingURL=seq-helper.d.ts.map

package/src/utils/seq-helper.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"seq-helper.d.ts","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,EAAC,eAAe,EAAC,MAAM,UAAU,CAAC;AAEzC,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,IAAI,CAAC;IACjC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB,CAAA;AAED,MAAM,WAAW,UAAU;IACzB;;;;;QAKI;IACJ,iBAAiB,CACf,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,EAAE,OAAO,EAAE,SAAS,CAAC,EAAE,OAAO,EAAE,kBAAkB,CAAC,EAAE,eAAe,GAC/G,OAAO,CAAC,gBAAgB,CAAC,CAAC;CAC9B;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,UAAU,CAAC,CAOxD"}
+{"version":3,"file":"seq-helper.d.ts","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,eAAe,EAAC,MAAM,UAAU,CAAC;AAEzC,OAAO,EAAC,WAAW,EAAC,MAAM,6BAA6B,CAAC;AAExD,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,IAAI,CAAC;IACjC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB,CAAA;AAED,MAAM,WAAW,UAAU;IACzB;;;;;QAKI;IACJ,iBAAiB,CACf,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,EAAE,OAAO,EAAE,SAAS,CAAC,EAAE,OAAO,EAAE,kBAAkB,CAAC,EAAE,eAAe,GAC/G,OAAO,CAAC,gBAAgB,CAAC,CAAC;IAE7B,aAAa,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,WAAW,CAAC;CACvD;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,UAAU,CAAC,CAOxD"}

package/src/utils/seq-helper.js.map

@@ -1 +1 @@
-{"version":3,"file":"seq-helper.js","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAoBtC,MAAM,CAAC,KAAK,UAAU,YAAY;IAChC,MAAM,WAAW,GAAG,KAAK,CAAC;IAC1B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,cAAc,EAAC,CAAC,CAAC;IAC5E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,oCAAoC,CAAC,CAAC;IAC/E,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAgB,CAAC;IACrF,OAAO,GAAG,CAAC;AACb,CAAC"}
+{"version":3,"file":"seq-helper.js","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAyBtC,MAAM,CAAC,KAAK,UAAU,YAAY;IAChC,MAAM,WAAW,GAAG,KAAK,CAAC;IAC1B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,cAAc,EAAC,CAAC,CAAC;IAC5E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,oCAAoC,CAAC,CAAC;IAC/E,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAgB,CAAC;IACrF,OAAO,GAAG,CAAC;AACb,CAAC"}

package/src/utils/splitter.d.ts

@@ -1,3 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-export declare function splitAlignedSequences(sequenceColumn: DG.Column<string>): DG.DataFrame;
+import { ISeqHelper } from './seq-helper';
+export declare function splitAlignedSequences(sequenceColumn: DG.Column<string>, seqHelper: ISeqHelper): DG.DataFrame;
 //# sourceMappingURL=splitter.d.ts.map

package/src/utils/splitter.d.ts.map

@@ -1 +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,CAuBrF"}
+{"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,UAAU,EAAC,MAAM,cAAc,CAAC;AAGxC,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,SAAS,EAAE,UAAU,GAAG,EAAE,CAAC,SAAS,CAuB5G"}

package/src/utils/splitter.js

@@ -1,6 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import { SeqHandler } from './seq-handler';
-export function splitAlignedSequences(sequenceColumn) {
+export function splitAlignedSequences(sequenceColumn, seqHelper) {
     const getCol = (index) => columnList[index] ?? null;
     const createCol = (index) => {
         const positionCol = resultDf.columns.addNewString((index + 1).toString());
@@ -10,7 +9,7 @@ export function splitAlignedSequences(sequenceColumn) {
     const columnList = [];
     const rowCount = sequenceColumn.length;
     const resultDf = DG.DataFrame.create(rowCount);
-    const uh = SeqHandler.forColumn(sequenceColumn);
+    const uh = seqHelper.getSeqHandler(sequenceColumn);
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         const currentMonomerList = uh.getSplitted(rowIdx);
         for (let posIdx = 0; posIdx < currentMonomerList.length; ++posIdx) {

package/src/utils/splitter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"splitter.js","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,MAAM,UAAU,qBAAqB,CAAC,cAAiC,EAAE,SAAqB;IAC5F,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,MAAM,EAAE,GAAG,SAAS,CAAC,aAAa,CAAC,cAAc,CAAC,CAAC;IACnD,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC;QACjD,MAAM,kBAAkB,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAClD,KAAK,IAAI,MAAM,GAAW,CAAC,EAAE,MAAM,GAAG,kBAAkB,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;YAC1E,MAAM,EAAE,GAAW,kBAAkB,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC;YAC3D,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,SAAS,CAAC,MAAM,CAAC,CAAC;YAChD,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,EAAE,EAAE,KAAK,CAAC,CAAC;QAC7B,CAAC;IACH,CAAC;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/src/viewers/helm-service.d.ts

@@ -1,9 +1,11 @@
 import * as DG from 'datagrok-api/dg';
 import { HelmType, Mol } from '../helm/types';
 import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
+import { IMonomerLibBase } from '../types/index';
 export declare class HelmProps extends PropsBase {
     readonly helm: string;
-    constructor(helm: string, backColor: number, width: number, height: number);
+    readonly monomerLib: IMonomerLibBase;
+    constructor(helm: string, monomerLib: IMonomerLibBase, backColor: number, width: number, height: number);
 }
 export type HelmAux = {
     /** The molecule made of atoms (monomers) and bonds */ mol: Mol<HelmType>;

package/src/viewers/helm-service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"helm-service.d.ts","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,QAAQ,EAAE,GAAG,EAAC,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,qBAAa,SAAU,SAAQ,SAAS;aAEpB,IAAI,EAAE,MAAM;gBAAZ,IAAI,EAAE,MAAM,EAC5B,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAInD;AAED,MAAM,MAAM,OAAO,GAAG;IACpB,sDAAsD,CAAC,GAAG,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAC;IAC1E,uBAAuB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;IACtC,4BAA4B,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;CAC5C,CAAA;AAED,8BAAsB,eAAgB,SAAQ,iBAAiB,CAAC,SAAS,EAAE,OAAO,CAAC;CAAG;AAEtF,wBAAsB,cAAc,IAAI,OAAO,CAAC,eAAe,CAAC,CAO/D"}
+{"version":3,"file":"helm-service.d.ts","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,QAAQ,EAAE,GAAG,EAAC,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAC/E,OAAO,EAAC,eAAe,EAAC,MAAM,gBAAgB,CAAC;AAE/C,qBAAa,SAAU,SAAQ,SAAS;aAEpB,IAAI,EAAE,MAAM;aACZ,UAAU,EAAE,eAAe;gBAD3B,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,eAAe,EAC3C,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAInD;AAED,MAAM,MAAM,OAAO,GAAG;IACpB,sDAAsD,CAAC,GAAG,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAC;IAC1E,uBAAuB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;IACtC,4BAA4B,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;CAC5C,CAAA;AAED,8BAAsB,eAAgB,SAAQ,iBAAiB,CAAC,SAAS,EAAE,OAAO,CAAC;CAAG;AAEtF,wBAAsB,cAAc,IAAI,OAAO,CAAC,eAAe,CAAC,CAO/D"}

package/src/viewers/helm-service.js

@@ -1,9 +1,10 @@
 import * as DG from 'datagrok-api/dg';
 import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
 export class HelmProps extends PropsBase {
-    constructor(helm, backColor, width, height) {
+    constructor(helm, monomerLib, backColor, width, height) {
         super(backColor, width, height);
         this.helm = helm;
+        this.monomerLib = monomerLib;
     }
 }
 export class HelmServiceBase extends RenderServiceBase {

package/src/viewers/helm-service.js.map

@@ -1 +1 @@
-{"version":3,"file":"helm-service.js","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,MAAM,OAAO,SAAU,SAAQ,SAAS;IACtC,YACkB,IAAY,EAC5B,SAAiB,EAAE,KAAa,EAAE,MAAc;QAEhD,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;QAHhB,SAAI,GAAJ,IAAI,CAAQ;IAI9B,CAAC;CACF;AAQD,MAAM,OAAgB,eAAgB,SAAQ,iBAAqC;CAAG;AAEtF,MAAM,CAAC,KAAK,UAAU,cAAc;IAClC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACzE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IAEzE,MAAM,GAAG,GAAoB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAqB,CAAC;IAC3G,OAAO,GAAG,CAAC;AACb,CAAC"}
+{"version":3,"file":"helm-service.js","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAG/E,MAAM,OAAO,SAAU,SAAQ,SAAS;IACtC,YACkB,IAAY,EACZ,UAA2B,EAC3C,SAAiB,EAAE,KAAa,EAAE,MAAc;QAEhD,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;QAJhB,SAAI,GAAJ,IAAI,CAAQ;QACZ,eAAU,GAAV,UAAU,CAAiB;IAI7C,CAAC;CACF;AAQD,MAAM,OAAgB,eAAgB,SAAQ,iBAAqC;CAAG;AAEtF,MAAM,CAAC,KAAK,UAAU,cAAc;IAClC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACzE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IAEzE,MAAM,GAAG,GAAoB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAqB,CAAC;IAC3G,OAAO,GAAG,CAAC;AACb,CAAC"}

package/src/utils/seq-handler.d.ts

@@ -1,167 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-import { NOTATION } from './macromolecule';
-import { INotationProvider, 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';
-import { CellRendererBackBase } from './cell-renderer-back-base';
-import { HelmType } from '../helm/types';
-export declare const SeqTemps: {
-    /** Column's temp slot name for a SeqHandler object */
-    seqHandler: string;
-    notationProvider: string;
-};
-export type ConvertFunc = (src: string) => string;
-export type JoinerFunc = (src: ISeqSplitted) => string;
-/** Class for handling notation units in Macromolecule columns and
- * conversion of notation systems in Macromolecule columns
- */
-export declare class SeqHandler {
-    protected readonly _column: DG.Column;
-    protected readonly _units: string;
-    protected readonly _notation: NOTATION;
-    protected readonly _defaultGapOriginal: string;
-    protected readonly notationProvider: INotationProvider | null;
-    private _splitter;
-    protected constructor(col: DG.Column<string>);
-    static setUnitsToFastaColumn(uh: SeqHandler): void;
-    static setUnitsToSeparatorColumn(uh: SeqHandler, separator?: string): void;
-    static setUnitsToHelmColumn(uh: SeqHandler): void;
-    /** From detectMacromolecule */
-    static setTags(uh: SeqHandler): void;
-    protected get column(): DG.Column;
-    get length(): number;
-    get units(): string;
-    get notation(): NOTATION;
-    get defaultGapOriginal(): string;
-    get separator(): string | undefined;
-    get aligned(): string;
-    /** Alphabet name (upper case) */
-    get alphabet(): string;
-    get defaultBiotype(): HelmType;
-    protected get helmCompatible(): string | undefined;
-    getAlphabetSize(): number;
-    getAlphabetIsMultichar(): boolean;
-    private cached;
-    private _splitted;
-    private columnVersion;
-    getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
-    /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
-    getHelm(rowIdx: number, options?: any): Promise<string>;
-    private _stats;
-    get stats(): SeqColStats;
-    private _maxLength;
-    get maxLength(): number;
-    private _posList;
-    get posList(): string[];
-    isFasta(): boolean;
-    isSeparator(): boolean;
-    isHelm(): boolean;
-    isRna(): boolean;
-    isDna(): boolean;
-    isPeptide(): boolean;
-    isMsa(): boolean;
-    isHelmCompatible(): boolean;
-    /** Checks {@link om} for being a gap
-     * @param {string} om Original monomer of sequence symbol
-     * @return {boolean}
-     */
-    isGap(om: string): boolean;
-    /** Associate notation types with the corresponding units */
-    /**
-     * @return {NOTATION}     Notation associated with the units type
-     */
-    protected getNotation(): NOTATION;
-    /**
-     * Get the wrapper strings for HELM, depending on the type of the
-     * macromolecule (peptide, DNA, RNA)
-     *
-     * @return {string[]} Array of wrappers
-     */
-    getHelmWrappers(): string[];
-    /**
-     * Create a new empty column of the specified notation type and the same
-     * length as column
-     *
-     * @param {NOTATION} tgtNotation
-     * @return {DG.Column}
-     */
-    protected getNewColumn(tgtNotation: NOTATION, tgtSeparator?: string, colName?: string, data?: string[]): DG.Column<string>;
-    /** Creates a new column on data of {@link seqList} with the same tags */
-    getNewColumnFromList(name: string, seqList: string[]): DG.Column<string>;
-    /**
-     * Create a new empty column using templateCol as a template
-     *
-     * @param {DG.Column} templateCol  the properties and units of this column are used as a
-     * template to build the new one
-     * @return {DG.Column}
-     */
-    static getNewColumn(templateCol: DG.Column): DG.Column;
-    /**
-     * A helper function checking the validity of the 'units' string
-     *
-     * @param {string} units  the string to be validated
-     * @return {boolean}
-     */
-    static unitsStringIsValid(units: string): boolean;
-    /**
-     * Construct a new column of semantic type MACROMOLECULE from the list of
-     * specified parameters
-     *
-     * @param {number}    len  the length of the new column
-     * @param {string}    name  the name of the new column
-     * @param {string}    units  the units of the new column
-     * @return {DG.Column}
-     */
-    static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
-    /** Gets function to split seq value to monomers */
-    protected getSplitter(limit?: number): SplitterFunc;
-    split(seq: string): ISeqSplitted;
-    getDistanceFunctionName(): MmDistanceFunctionsNames;
-    getDistanceFunction(): mmDistanceFunctionType;
-    checkHelmCompatibility(): Promise<boolean>;
-    protected get splitter(): SplitterFunc;
-    toFasta(targetNotation: NOTATION): boolean;
-    toSeparator(targetNotation: NOTATION): boolean;
-    toHelm(targetNotation: NOTATION): boolean;
-    /**
-     *  Convert HELM string to FASTA/SEPARATOR
-     *
-     * @param {string} srcSeq    A string to be converted
-     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
-     * @param {string} tgtSeparator   Optional target separator (for HELM ->
-     * @param {string | null} tgtGapOriginal   Optional target gap symbol
-     * SEPARATOR)
-     * @return {string} Converted string
-     */
-    convertHelmToFastaSeparator(srcSeq: string, tgtNotation: string, tgtSeparator?: string, tgtGapOriginal?: string): string;
-    /** Dispatcher method for notation conversion
-     *
-     * @param {NOTATION} tgtNotation   Notation we want to convert to
-     * @param {string | null} tgtSeparator   Possible separator
-     * @return {DG.Column}                Converted column
-     */
-    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string>;
-    /**
-     * @param name
-     * @param startIdx Start position index of the region (0-based)
-     * @param endIdx   End position index of the region (0-based, inclusive)
-     */
-    getRegion(startIdx: number | null, endIdx: number | null, name: string): DG.Column<string>;
-    private _joiner?;
-    get joiner(): JoinerFunc;
-    getJoiner(opts?: {
-        notation: NOTATION;
-        separator?: string;
-    }): JoinerFunc;
-    getConverter(tgtUnits: NOTATION, tgtSeparator?: string | undefined): ConvertFunc;
-    /** Gets a column's UnitsHandler object from temp slot or creates a new and stores it to the temp slot. */
-    static forColumn(col: DG.Column<string>): SeqHandler;
-    private joinToFasta;
-    private convertToFasta;
-    private convertToSeparator;
-    private convertToHelm;
-    /** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
-    private splitterAsHelmNucl;
-    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
-}
-//# sourceMappingURL=seq-handler.d.ts.map

package/src/utils/seq-handler.d.ts.map

@@ -1 +0,0 @@
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