@datagrok-libraries/bio 5.44.5 → 5.45.1

package/src/utils/cell-renderer-monomer-placer.d.ts.map

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

@@ -1,7 +1,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { SeqHandler } from './seq-handler';
+import { getSeqHelper } from './seq-helper';
 import { ALPHABET, NOTATION, TAGS as bioTAGS } from './macromolecule';
 import { CellRendererBackBase, getGridCellColTemp } from './cell-renderer-back-base';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
@@ -44,7 +44,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         this._processedMaxVisibleSeqLength = 0;
         this._monomerLengthMap = {}; // caches the lengths to save time on g.measureText
         this._monomerStructureMap = {}; // caches the atomic structures of monomers
-        this.monomerLib = null;
+        this.sysMonomerLib = null;
         this.padding = 5;
         this.props = this.propsProvider();
         this._processedRows = DG.BitSet.create(this.tableCol.length);
@@ -60,21 +60,29 @@ export class MonomerPlacer extends CellRendererBackBase {
                 if (df.currentRowIdx === -1) {
                     this.tableCol.temp["reference-sequence" /* tempTAGS.referenceSequence */] = null;
                     this.tableCol.temp["current-word" /* tempTAGS.currentWord */] = null;
-                    grid.invalidate();
+                    this.invalidateGrid();
                 }
             }));
         }
-        getMonomerLibHelper().then((libHelper) => {
-            if (this.destroyed)
-                return;
-            this.monomerLib = libHelper.getMonomerLib();
-            this.dirty = true;
-            this.gridCol?.grid?.invalidate();
-            this.subs.push(this.monomerLib.onChanged.subscribe(() => {
-                this.dirty = true;
-                this.gridCol?.grid?.invalidate();
-            }));
-        });
+    }
+    async init() {
+        await Promise.all([
+            (async () => {
+                this.seqHelper = await getSeqHelper();
+                this.invalidateGrid();
+            })(),
+            (async () => {
+                const libHelper = await getMonomerLibHelper();
+                this.sysMonomerLib = libHelper.getMonomerLib();
+            })(),
+        ]);
+        this.subs.push(this.sysMonomerLib.onChanged.subscribe(() => {
+            this.reset();
+        }));
+        this.reset();
+    }
+    getMonomerLib() {
+        return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary" /* MmcrTemps.overriddenLibrary */] ?? this.sysMonomerLib;
     }
     reset() {
         if (this.propsProvider)
@@ -84,10 +92,15 @@ export class MonomerPlacer extends CellRendererBackBase {
         this._monomerLengthMap = {};
         this._monomerStructureMap = {};
         super.reset();
+        this.invalidateGrid();
+    }
+    invalidateGrid() {
+        if (this.gridCol && this.gridCol.dart)
+            this.gridCol.grid?.invalidate();
     }
     /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
     getCellMonomerLengths(rowIdx, newWidth) {
-        const sh = SeqHandler.forColumn(this.tableCol);
+        const sh = this.seqHelper.getSeqHandler(this.tableCol);
         if (this.colWidth < newWidth) {
             this.colWidth = newWidth;
             this.dirty = true;
@@ -114,7 +127,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         // this.logger.debug(`${logPrefix}, start`);
         if (this._monomerLengthList === null)
             this._monomerLengthList = new Array(this.tableCol.length).fill(null);
-        const sh = SeqHandler.forColumn(this.tableCol);
+        const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
         const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
         const seqSS = sh.getSplitted(rowIdx);
@@ -167,7 +180,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
             if (this._processedRows.get(seqIdx) && maxVisibleSeqLength <= this._processedMaxVisibleSeqLength)
                 continue;
-            const seqSS = SeqHandler.forColumn(this.tableCol)
+            const seqSS = this.seqHelper.getSeqHandler(this.tableCol)
                 .getSplitted(seqIdx, maxVisibleSeqLength);
             const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
             if (visibleSeqLength > res.length)
@@ -189,7 +202,7 @@ export class MonomerPlacer extends CellRendererBackBase {
     /** Returns seq position for pointer x */
     getPosition(rowIdx, x, width) {
         const [_monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx, width);
-        const sh = SeqHandler.forColumn(this.tableCol);
+        const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const seqSS = sh.getSplitted(rowIdx);
         if (seqSS.length === 0)
             return null;
@@ -208,6 +221,8 @@ export class MonomerPlacer extends CellRendererBackBase {
         }
     }
     render(g, x, y, w, h, gridCell, _cellStyle) {
+        if (!this.seqHelper)
+            return;
         const gridCol = this.gridCol;
         const tableCol = this.tableCol;
         const dpr = window.devicePixelRatio;
@@ -223,7 +238,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         }
         g.save();
         try {
-            const sh = SeqHandler.forColumn(tableCol);
+            const sh = this.seqHelper.getSeqHandler(tableCol);
             if (tableCol.temp[".mm.cellRenderer.settingsChanged" /* MmcrTemps.rendererSettingsChanged */] === rendererSettingsChangedState.true ||
                 this.monomerLengthLimit != maxLengthOfMonomer) {
                 let gapLength = 0;
@@ -273,10 +288,11 @@ export class MonomerPlacer extends CellRendererBackBase {
                 const om = subParts.getOriginal(posIdx);
                 const cm = subParts.getCanonical(posIdx);
                 let color = undefinedColor;
-                if (this.monomerLib) {
+                const monomerLib = this.getMonomerLib();
+                if (monomerLib) {
                     const biotype = sh.defaultBiotype;
                     //this.logger.debug(`${logPrefix}, biotype: ${biotype}, amino: ${amino}`);
-                    color = this.monomerLib.getMonomerTextColor(biotype, cm);
+                    color = monomerLib.getMonomerTextColor(biotype, cm);
                 }
                 g.fillStyle = undefinedColor;
                 const last = posIdx === subParts.length - 1;
@@ -303,7 +319,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         }
     }
     onMouseMove(gridCell, e) {
-        if (gridCell.tableRowIndex == null)
+        if (!this.seqHelper || gridCell.tableRowIndex == null)
             return;
         // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
         //   return;
@@ -321,10 +337,9 @@ export class MonomerPlacer extends CellRendererBackBase {
         // const maxIndex = maxLengthWords.length;
         const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
         const left = seqColTemp.getPosition(gridCell.tableRowIndex, argsX, gridCellBounds.width);
-        const seqSS = SeqHandler.forColumn(tableCol)
-            .getSplitted(gridCell.tableRowIndex);
+        const sh = this.seqHelper.getSeqHandler(tableCol);
+        const seqSS = sh.getSplitted(gridCell.tableRowIndex);
         if (left !== null && left < seqSS.length) {
-            const sh = SeqHandler.forColumn(tableCol);
             const alphabet = sh.alphabet ?? ALPHABET.UN;
             const seqMonomer = {
                 position: left,
@@ -334,8 +349,9 @@ export class MonomerPlacer extends CellRendererBackBase {
             const tooltipElements = [];
             let monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol];
             if (!monomerDiv || true) {
+                const monomerLib = this.getMonomerLib();
                 monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol] = (() => {
-                    return this.monomerLib ? this.monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
+                    return monomerLib ? monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
                         ui.divText('Monomer library is not available');
                 })();
             }

package/src/utils/cell-renderer-monomer-placer.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,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"}
+{"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,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;gBAYzB,WAAW,EAAE,MAAM;CAIhC"}

package/src/utils/fasta-handler.js

@@ -1,5 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import { SeqHandler } from './seq-handler';
 import { NOTATION } from './macromolecule/consts';
 /** Class for parsing FASTA files */
 export class FastaFileHandler {
@@ -44,8 +43,6 @@ export class FastaFileHandler {
         const sequenceCol = DG.Column.fromStrings('sequence', this.sequencesArray);
         sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
         sequenceCol.meta.units = NOTATION.FASTA;
-        // here should go the code from units handler
-        const sh = SeqHandler.forColumn(sequenceCol);
         return [DG.DataFrame.fromColumns([
                 descriptionsArrayCol,
                 sequenceCol,

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

@@ -1 +1 @@
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package/src/utils/generator.d.ts

@@ -1,8 +1,9 @@
 import * as DG from 'datagrok-api/dg';
 import { ALPHABET, NOTATION } from './macromolecule';
+import { ISeqHelper } from './seq-helper';
 import { IMonomerLib } from '../types/index';
 export declare function generateManySequences(): DG.Column[];
 /** Generates the column 'MSA' with sequences length of order 10^6 and the 'Activity' float column. */
 export declare function generateLongSequence(length?: number): DG.Column[];
-export declare function generateLongSequence2(notation?: NOTATION, alphabet?: ALPHABET, separator?: string | undefined, monomerLib?: IMonomerLib | undefined, colName?: string, rowCount?: number, seqLength?: number): DG.Column;
+export declare function generateLongSequence2(seqHelper: ISeqHelper, notation?: NOTATION, alphabet?: ALPHABET, separator?: string | undefined, monomerLib?: IMonomerLib | undefined, colName?: string, rowCount?: number, seqLength?: number): DG.Column;
 //# sourceMappingURL=generator.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAe,QAAQ,EAAO,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAC,UAAU,EAAC,MAAM,cAAc,CAAC;AAExC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAI3C,wBAAgB,qBAAqB,IAAI,EAAE,CAAC,MAAM,EAAE,CAQnD;AAED,sGAAsG;AACtG,wBAAgB,oBAAoB,CAAC,MAAM,GAAE,MAAgB,GAAG,EAAE,CAAC,MAAM,EAAE,CAc1E;AAED,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,UAAU,EACzD,QAAQ,GAAE,QAA6B,EAAE,QAAQ,GAAE,QAAsB,EACzE,SAAS,GAAE,MAAM,GAAG,SAA+D,EACnF,UAAU,GAAE,WAAW,GAAG,SAAqB,EAC/C,OAAO,GAAE,MAAc,EAAE,QAAQ,GAAE,MAAY,EAAE,SAAS,GAAE,MAAgB,GAC3E,EAAE,CAAC,MAAM,CAqBX"}

package/src/utils/generator.js

@@ -1,7 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
-import { SeqHandler } from './seq-handler';
 import { StringListSeqSplitted } from './macromolecule/utils';
 import { GapOriginals } from './macromolecule/consts';
 export function generateManySequences() {
@@ -24,7 +23,7 @@ export function generateLongSequence(length = 10 ** 5) {
     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 = ALPHABET.PT, separator = (notation === NOTATION.SEPARATOR ? '-' : undefined), monomerLib = undefined, colName = 'seq', rowCount = 100, seqLength = 10 ** 6) {
+export function generateLongSequence2(seqHelper, 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;
@@ -34,7 +33,7 @@ export function generateLongSequence2(notation = NOTATION.SEPARATOR, alphabet =
     col.setTag(TAGS.alphabet, alphabet);
     if (notation == NOTATION.SEPARATOR)
         col.setTag(TAGS.separator, separator);
-    const sh = SeqHandler.forColumn(col);
+    const sh = seqHelper.getSeqHandler(col);
     for (let rowI = 0; rowI < rowCount; rowI++) {
         const seqMList = wu.count(0).take(seqLength)
             .map((i) => { return alphabetSet[Math.floor(Math.random() * alphabetSize)]; })

package/src/utils/generator.js.map

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

@@ -28,6 +28,7 @@ export declare enum TAGS {
     positionLabels = ".positionLabels",
     regions = ".regions"
 }
+export { TAGS as BioTags };
 export declare const positionSeparator: string;
 export declare const monomerRe: RegExp;
 export declare const helmRe: RegExp;

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

@@ -1 +1 @@
-{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;IACmB,MAAM,WAAW;CAClD;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;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAKxB,CAAC"}
+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;IACmB,MAAM,WAAW;CAClD;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,OAAO,EAAC,IAAI,IAAI,OAAO,EAAC,CAAC;AAEzB,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;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAKxB,CAAC"}

package/src/utils/macromolecule/consts.js

@@ -27,6 +27,7 @@ export var TAGS;
     TAGS["positionLabels"] = ".positionLabels";
     TAGS["regions"] = ".regions";
 })(TAGS || (TAGS = {}));
+export { TAGS as BioTags };
 export const positionSeparator = ', ';
 export const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
 export const helmRe = /(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g;

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

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

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { ISeqSplitted } from '../../utils/macromolecule/types';
+import { ISeqHelper } from '../seq-helper';
 export declare enum SCORE {
     IDENTITY = "identity",
     SIMILARITY = "similarity"
@@ -9,8 +10,9 @@ export declare enum SCORE {
  * @param {DG.Column<string>} col Sequences column to score. Must have Macromolecule semantic type.
  * @param {string} ref Reference sequence to score against.
  * @param {SCORE} scoring Scoring method.
+ * @param {ISeqHelper} seqHelper Helper for sequence operations.
  * @returns {DG.Column<number>} Scores column. */
-export declare function calculateScores(table: DG.DataFrame, col: DG.Column<string>, ref: string, scoring: SCORE): Promise<DG.Column<number>>;
+export declare function calculateScores(table: DG.DataFrame, col: DG.Column<string>, ref: string, scoring: SCORE, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
 /** Calculates identity scores as fraction of matching monomers on the same position.
  * @param {ISeqSplitted} reference Splitted reference sequence.
  * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
@@ -20,5 +22,5 @@ export declare function calculateIdentity(reference: ISeqSplitted, positionsDf:
  * @param {ISeqSplitted} reference Splitted reference sequence.
  * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
  * @return {DG.Column<number>} Scores column. */
-export declare function calculateSimilarity(reference: ISeqSplitted, positionsDf: DG.DataFrame): Promise<DG.Column<number>>;
+export declare function calculateSimilarity(reference: ISeqSplitted, positionsDf: DG.DataFrame, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
 //# sourceMappingURL=scoring.d.ts.map

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

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package/src/utils/macromolecule/scoring.js

@@ -1,7 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
 import { splitAlignedSequences } from '../splitter';
-import { SeqHandler } from '../seq-handler';
 import { GAP_SYMBOL } from './consts';
 export var SCORE;
 (function (SCORE) {
@@ -13,15 +12,16 @@ export var SCORE;
  * @param {DG.Column<string>} col Sequences column to score. Must have Macromolecule semantic type.
  * @param {string} ref Reference sequence to score against.
  * @param {SCORE} scoring Scoring method.
+ * @param {ISeqHelper} seqHelper Helper for sequence operations.
  * @returns {DG.Column<number>} Scores column. */
-export async function calculateScores(table, col, ref, scoring) {
-    const splitSeqDf = splitAlignedSequences(col);
-    const srcSh = SeqHandler.forColumn(col);
+export async function calculateScores(table, col, ref, scoring, seqHelper) {
+    const splitSeqDf = splitAlignedSequences(col, seqHelper);
+    const srcSh = seqHelper.getSeqHandler(col);
     const refCol = srcSh.getNewColumnFromList('ref', [ref]);
-    const refUh = SeqHandler.forColumn(refCol);
+    const refUh = seqHelper.getSeqHandler(refCol);
     const refSplitted = refUh.getSplitted(0); // ref is at 0
     const scoresCol = scoring === SCORE.IDENTITY ? calculateIdentity(refSplitted, splitSeqDf) :
-        scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf) : null;
+        scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf, seqHelper) : null;
     if (scoresCol === null)
         throw new Error(`In bio library: Unknown sequence scoring method: ${scoring}`);
     scoresCol.name = table.columns.getUnusedName(scoresCol.name);
@@ -62,9 +62,9 @@ export function calculateIdentity(reference, positionsDf) {
  * @param {ISeqSplitted} reference Splitted reference sequence.
  * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
  * @return {DG.Column<number>} Scores column. */
-export async function calculateSimilarity(reference, positionsDf) {
+export async function calculateSimilarity(reference, positionsDf, seqHelper) {
     const monomerColumns = positionsDf.columns.toList();
-    const scoresCol = await sequenceChemSimilarity(monomerColumns, reference);
+    const scoresCol = await sequenceChemSimilarity(monomerColumns, reference, seqHelper);
     return scoresCol;
 }
 //# sourceMappingURL=scoring.js.map

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+{"version":3,"file":"scoring.js","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,sBAAsB,EAAC,MAAM,mCAAmC,CAAC;AAEzE,OAAO,EAAC,qBAAqB,EAAC,MAAM,aAAa,CAAC;AAClD,OAAO,EAAC,UAAU,EAAC,MAAM,UAAU,CAAC;AAGpC,MAAM,CAAN,IAAY,KAGX;AAHD,WAAY,KAAK;IACf,8BAAqB,CAAA;IACrB,kCAAyB,CAAA;AAC3B,CAAC,EAHW,KAAK,KAAL,KAAK,QAGhB;AAED;;;;;;iDAMiD;AACjD,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,KAAmB,EAAE,GAAsB,EAAE,GAAW,EAAE,OAAc,EAAE,SAAqB;IAE/F,MAAM,UAAU,GAAG,qBAAqB,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC;IACzD,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC;IAC3C,MAAM,MAAM,GAAG,KAAK,CAAC,oBAAoB,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;IACxD,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc;IAExD,MAAM,SAAS,GAAG,OAAO,KAAK,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC;QACzF,OAAO,KAAK,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,mBAAmB,CAAC,WAAW,EAAE,UAAU,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACtG,IAAI,SAAS,KAAK,IAAI;QACpB,MAAM,IAAI,KAAK,CAAC,oDAAoD,OAAO,EAAE,CAAC,CAAC;IACjF,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IAC7D,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;IAC7B,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;iDAGiD;AACjD,MAAM,UAAU,iBAAiB,CAAC,SAAuB,EAAE,WAAyB;IAClF,MAAM,YAAY,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;IAChD,MAAM,YAAY,GAAkB,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAC5D,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAClE,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAElE,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,YAAY,EAAE,EAAE,MAAM,EAAE,CAAC;QACrD,MAAM,MAAM,GAAG,WAAW,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACnD,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,EAAiB,CAAC;QAC1D,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;QACpF,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACpE,CAAC;IAED,MAAM,iBAAiB,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,UAAU,EAAE,CAAC;IAC1D,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,WAAW,CAAC,QAAQ,EAAE,EAAE,QAAQ,EAAE,CAAC;QACnE,kBAAkB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;QACjC,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;YACzD,MAAM,WAAW,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC;YACzC,MAAM,aAAa,GAAW,WAAW,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC/E,IAAI,aAAa,KAAK,uBAAuB,CAAC,MAAM,CAAC;gBACnD,EAAE,kBAAkB,CAAC,QAAQ,CAAC,CAAC;QACnC,CAAC;QACD,kBAAkB,CAAC,QAAQ,CAAC,IAAI,SAAS,CAAC,MAAM,CAAC;IACnD,CAAC;IAED,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED;;;gDAGgD;AAChD,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,SAAuB,EAAE,WAAyB,EAAE,SAAqB;IAEzE,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,EAAyB,CAAC;IAC3E,MAAM,SAAS,GAAG,MAAM,sBAAsB,CAAC,cAAc,EAAE,SAAS,EAAE,SAAS,CAAC,CAAC;IACrF,OAAO,SAAS,CAAC;AACnB,CAAC"}

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

@@ -0,0 +1,47 @@
+import * as DG from 'datagrok-api/dg';
+import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import { ISeqSplitted, SeqColStats } from './types';
+import { NOTATION } from './consts';
+import { HelmType } from '../../helm/types';
+import { CellRendererBackBase } from '../cell-renderer-back-base';
+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;
+export interface ISeqHandler {
+    get alphabet(): string;
+    get notation(): NOTATION;
+    get separator(): string | undefined;
+    get aligned(): string;
+    get units(): string;
+    get defaultBiotype(): HelmType;
+    get maxLength(): number;
+    get length(): number;
+    get defaultGapOriginal(): string;
+    get stats(): SeqColStats;
+    get joiner(): JoinerFunc;
+    get posList(): string[];
+    isFasta(): boolean;
+    isMsa(): boolean;
+    isHelm(): boolean;
+    isSeparator(): boolean;
+    getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
+    getHelm(rowIdx: number, options?: any): Promise<DG.SemanticValue<string>>;
+    getAlphabetSize(): number;
+    getAlphabetIsMultichar(): boolean;
+    getNewColumnFromList(name: string, seqList: string[]): DG.Column<string>;
+    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string>;
+    convertHelmToFastaSeparator(srcSeq: string, tgtNotation: string, tgtSeparator?: string, tgtGapOriginal?: string): string;
+    getRegion(startIdx: number | null, endIdx: number | null, name: string): DG.Column<string>;
+    getJoiner(opts?: {
+        notation: NOTATION;
+        separator?: string;
+    }): JoinerFunc;
+    getDistanceFunctionName(): MmDistanceFunctionsNames;
+    getConverter(tgtUnits: NOTATION, tgtSeparator?: string): ConvertFunc;
+    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
+}
+//# sourceMappingURL=seq-handler.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"seq-handler.d.ts","sourceRoot":"","sources":["seq-handler.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,wBAAwB,EAAC,MAAM,6DAA6D,CAAC;AAErG,OAAO,EAAC,YAAY,EAAE,WAAW,EAAC,MAAM,SAAS,CAAC;AAClD,OAAO,EAAC,QAAQ,EAAC,MAAM,UAAU,CAAC;AAClC,OAAO,EAAC,QAAQ,EAAC,MAAM,kBAAkB,CAAC;AAC1C,OAAO,EAAC,oBAAoB,EAAC,MAAM,4BAA4B,CAAC;AAEhE,eAAO,MAAM,QAAQ;IACnB,sDAAsD;;;CAGrD,CAAC;AACJ,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;AAClD,MAAM,MAAM,UAAU,GAAG,CAAC,GAAG,EAAE,YAAY,KAAK,MAAM,CAAC;AAEvD,MAAM,WAAW,WAAW;IAC1B,IAAI,QAAQ,IAAI,MAAM,CAAC;IACvB,IAAI,QAAQ,IAAI,QAAQ,CAAC;IACzB,IAAI,SAAS,IAAI,MAAM,GAAG,SAAS,CAAC;IAEpC,IAAI,OAAO,IAAI,MAAM,CAAC;IACtB,IAAI,KAAK,IAAI,MAAM,CAAC;IACpB,IAAI,cAAc,IAAI,QAAQ,CAAC;IAC/B,IAAI,SAAS,IAAI,MAAM,CAAC;IACxB,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,kBAAkB,IAAI,MAAM,CAAC;IACjC,IAAI,KAAK,IAAI,WAAW,CAAC;IACzB,IAAI,MAAM,IAAI,UAAU,CAAC;IAEzB,IAAI,OAAO,IAAI,MAAM,EAAE,CAAC;IAExB,OAAO,IAAI,OAAO,CAAC;IACnB,KAAK,IAAI,OAAO,CAAC;IACjB,MAAM,IAAI,OAAO,CAAC;IAClB,WAAW,IAAI,OAAO,CAAC;IAGvB,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,GAAG,YAAY,CAAC;IAC1D,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC;IAE1E,eAAe,IAAI,MAAM,CAAC;IAC1B,sBAAsB,IAAI,OAAO,CAAC;IAClC,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACzE,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACzE,2BAA2B,CAAC,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAC7D,YAAY,CAAC,EAAE,MAAM,EAAE,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC1D,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,EAAE,IAAI,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAC3F,SAAS,CAAC,IAAI,CAAC,EAAE;QAAE,QAAQ,EAAE,QAAQ,CAAC;QAAC,SAAS,CAAC,EAAE,MAAM,CAAA;KAAE,GAAG,UAAU,CAAC;IAEzE,uBAAuB,IAAI,wBAAwB,CAAC;IACpD,YAAY,CAAC,QAAQ,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,WAAW,CAAC;IACrE,eAAe,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAAE,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;CAC3G"}

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

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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