@datagrok/bio 2.15.13 → 2.16.0

package/src/utils/cell-renderer-custom.ts

@@ -3,11 +3,14 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {getGridCellColTemp, CellRendererBackBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {GridCell} from 'datagrok-api/dg';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+
+import {_package} from '../package';
 
 export class MacromoleculeCustomCellRenderer extends DG.GridCellRenderer {
+  private readonly seqHelper: ISeqHelper;
+
   get name(): string { return 'sequence'; }
 
   get cellType(): string { return 'sequence'; }
@@ -16,18 +19,26 @@ export class MacromoleculeCustomCellRenderer extends DG.GridCellRenderer {
 
   get defaultWidth(): number | null { return 230; }
 
-  getRendererBack(gridCell: DG.GridCell): CellRendererBackBase<string> {
-    const [gridCol, tableCol, temp] = getGridCellColTemp<string, any>(gridCell);
-    const sh = SeqHandler.forColumn(tableCol);
-    if (sh.notation !== NOTATION.CUSTOM)
-      throw new Error(`Unexpected notation: '${sh.notation}'.`);
-    const back = sh.getRendererBack(gridCol, tableCol);
+  constructor() {
+    super();
+    this.seqHelper = _package.seqHelper;
+  }
+
+  getRendererBack(gridCell: DG.GridCell): CellRendererBackBase<string> | null {
+    const [gridCol, tableCol, _temp] = getGridCellColTemp<string, any>(gridCell);
+    let back: CellRendererBackBase<string> | null = null;
+    if (this.seqHelper) {
+      const sh = this.seqHelper.getSeqHandler(tableCol);
+      if (sh.notation !== NOTATION.CUSTOM)
+        throw new Error(`Unexpected notation: '${sh.notation}'.`);
+      back = sh.getRendererBack(gridCol, tableCol);
+    }
     return back;
   }
 
-  override onMouseEnter(gridCell: GridCell, e: MouseEvent) {
+  override onMouseEnter(gridCell: DG.GridCell, e: MouseEvent) {
     const back = this.getRendererBack(gridCell);
-    back.onMouseEnter(gridCell, e);
+    back?.onMouseEnter(gridCell, e);
   }
 
   override onMouseLeave(gridCell: DG.GridCell, e: MouseEvent) {
@@ -39,32 +50,31 @@ export class MacromoleculeCustomCellRenderer extends DG.GridCellRenderer {
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent) {
     const back = this.getRendererBack(gridCell);
-    back.onMouseMove(gridCell, e);
+    back?.onMouseMove(gridCell, e);
   }
 
   override onClick(gridCell: DG.GridCell, e: MouseEvent) {
     const back = this.getRendererBack(gridCell);
-    back.onClick(gridCell, e);
+    back?.onClick(gridCell, e);
   }
 
   override onDoubleClick(gridCell: DG.GridCell, e: MouseEvent) {
     const back = this.getRendererBack(gridCell);
-    back.onDoubleClick(gridCell, e);
+    back?.onDoubleClick(gridCell, e);
   }
 
   override onKeyDown(gridCell: DG.GridCell, e: KeyboardEvent) {
     const back = this.getRendererBack(gridCell);
-    back.onKeyDown(gridCell, e);
+    back?.onKeyDown(gridCell, e);
   }
 
   override onKeyPress(gridCell: DG.GridCell, e: KeyboardEvent) {
     const back = this.getRendererBack(gridCell);
-    back.onKeyPress(gridCell, e);
+    back?.onKeyPress(gridCell, e);
   }
 
   override render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, cellStyle: DG.GridCellStyle) {
     const back = this.getRendererBack(gridCell);
-    back.render(g, x, y, w, h, gridCell, cellStyle);
+    back?.render(g, x, y, w, h, gridCell, cellStyle);
   }
 }
-

package/src/utils/cell-renderer.ts

@@ -17,21 +17,19 @@ import {
   TAGS as bioTAGS,
   ALPHABET,
 } from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
-import {IMonomerLib, IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
-import {ISeqMonomer} from '@datagrok-libraries/bio/src/helm/types';
 import {execMonomerHoverLinks} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
-import {CellRendererBackBase, getGridCellColTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
+import {getGridCellColTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {MmcrTemps, rendererSettingsChangedState, tempTAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+
+import {CellRendererWithMonomerLibBackBase} from './monomer-cell-renderer-base';
 import * as C from './constants';
 
 import {_package} from '../package';
-import {CellRendererWithMonomerLibBackBase} from './monomer-cell-renderer-base';
-import {timeout} from 'rxjs/operators';
 
 type TempType = { [tagName: string]: any };
 
@@ -60,6 +58,8 @@ type RendererGridCellTemp = {
 }
 
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
+  private readonly seqHelper: ISeqHelper;
+
   get name(): string { return 'sequence'; }
 
   get cellType(): string { return 'sequence'; }
@@ -68,6 +68,11 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
   get defaultWidth(): number | null { return 230; }
 
+  constructor() {
+    super();
+    this.seqHelper = _package.seqHelper;
+  }
+
   onClick(gridCell: DG.GridCell, _e: MouseEvent): void {
     const colTemp: TempType = gridCell.cell.column.temp;
     colTemp[tempTAGS.currentWord] = gridCell.cell.value;
@@ -106,7 +111,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       getGridCellColTemp<string, MonomerPlacer>(gridCell);
     if (!tableCol) return;
     const tableColTemp: TempType = tableCol.temp;
-    const sh = SeqHandler.forColumn(tableCol);
+    const sh = this.seqHelper.getSeqHandler(tableCol);
 
     let gapLength = 0;
     const msaGapLength = 8;
@@ -132,6 +137,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
           };
         });
       tableCol.temp[MmcrTemps.rendererSettingsChanged] === rendererSettingsChangedState.true;
+      seqColTemp.init().then(() => {});
     }
 
     seqColTemp.render(g, x, y, w, h, gridCell, _cellStyle);

package/src/utils/check-input-column.ts

@@ -2,7 +2,9 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+
+import {_package} from '../package';
 
 /**
  * Checks if the column is suitable for the analysis.
@@ -13,9 +15,11 @@ import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
  * @param {boolean} notify show warning message if the column is not suitable for the analysis
  * @return {boolean} True if the column is suitable for the analysis.
  */
-export function checkInputColumnUI(col: DG.Column, name: string, allowedNotations: string[] = [],
-  allowedAlphabets: string[] = [], notify: boolean = true): boolean {
-  const [res, msg]: [boolean, string] = checkInputColumn(col, name, allowedNotations, allowedAlphabets);
+export function checkInputColumnUI(col: DG.Column, name: string,
+  allowedNotations: string[] = [], allowedAlphabets: string[] = [], notify: boolean = true
+): boolean {
+  const seqHelper = _package.seqHelper;
+  const [res, msg]: [boolean, string] = checkInputColumn(col, name, seqHelper, allowedNotations, allowedAlphabets);
   if (notify && !res)
     grok.shell.warning(msg);
   return res;
@@ -23,23 +27,23 @@ export function checkInputColumnUI(col: DG.Column, name: string, allowedNotation
 
 /**
  * Checks if the column is suitable for the analysis.
- * @param {DG.Column} col macromolecule coulumn.
- * @param {string} name column name
+ * @param {DG.Column} col macromolecule column.
+ * @param {string} name Analysis name
  * @param {string[]} allowedNotations allowed notations
  * @param {string[]} allowedAlphabets allowed alphabets
  * @return {[boolean, string]} [True if the column is suitable for the analysis, warning message].
  */
-export function checkInputColumn(
-  col: DG.Column, name: string, allowedNotations: string[] = [], allowedAlphabets: string[] = [],
+export function checkInputColumn(col: DG.Column, name: string, seqHelper: ISeqHelper,
+  allowedNotations: string[] = [], allowedAlphabets: string[] = [],
 ): [boolean, string] {
   let res: boolean = true;
   let msg: string = '';
 
-  const sh = SeqHandler.forColumn(col);
   if (col.semType !== DG.SEMTYPE.MACROMOLECULE) {
     grok.shell.warning(name + ' analysis is allowed for Macromolecules semantic type');
     res = false;
   } else {
+    const sh = seqHelper.getSeqHandler(col);
     const notation: string = sh.notation;
     if (allowedNotations.length > 0 &&
       !allowedNotations.some((n) => notation.toUpperCase() == (n.toUpperCase()))

package/src/utils/context-menu.ts

@@ -2,21 +2,21 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {_package} from '../package';
 
 
-export function addCopyMenuUI(cell: DG.Cell, menu: DG.Menu): void {
-  const sh = SeqHandler.forColumn(cell.column);
+export function addCopyMenuUI(cell: DG.Cell, menu: DG.Menu, seqHelper: ISeqHelper): void {
+  const sh = seqHelper.getSeqHandler(cell.column);
   const tgtNotationList: string[] = Object.values(NOTATION).filter((v) => v !== sh.units);
 
   menu.group('Copy')
     .items(tgtNotationList, (tgtNotation) => {
       const srcCol = cell.column;
       const srcRowIdx = cell.rowIndex;
-      const srcSh = SeqHandler.forColumn(srcCol);
+      const srcSh = seqHelper.getSeqHandler(srcCol);
       const separator = tgtNotation === NOTATION.SEPARATOR ? _package.properties.defaultSeparator : undefined;
       const joiner = srcSh.getJoiner({notation: tgtNotation as NOTATION, separator});
       const srcSS = srcSh.getSplitted(srcRowIdx);

package/src/utils/convert.ts

@@ -6,7 +6,7 @@ import $ from 'cash-dom';
 import {Subscription} from 'rxjs';
 
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 
 let convertDialog: DG.Dialog | null = null;
@@ -15,13 +15,14 @@ let convertDialogSubs: Subscription[] = [];
 /**
  * Converts notations of a Macromolecule column
  *
- * @param {DG.column} col Column with 'Macromolecule' semantic type
+ * @param {DG.Column<string>} col Column with 'Macromolecule' semantic type
+ * @param {ISeqHelper} seqHelper
  */
-export function convert(col?: DG.Column): void {
+export function convert(col: DG.Column<string> | undefined, seqHelper: ISeqHelper): void {
   let srcCol = col ?? grok.shell.t.columns.bySemType('Macromolecule')!;
   if (!srcCol)
     throw new Error('No column with Macromolecule semantic type found');
-  let converterSh = SeqHandler.forColumn(srcCol);
+  let converterSh = seqHelper.getSeqHandler(srcCol);
   let currentNotation: NOTATION = converterSh.notation;
   const dialogHeader = ui.divText(
     'Current notation: ' + currentNotation,
@@ -46,14 +47,16 @@ export function convert(col?: DG.Column): void {
     }
 
     srcCol = newCol;
-    converterSh = SeqHandler.forColumn(srcCol);
+    converterSh = seqHelper.getSeqHandler(srcCol);
     currentNotation = converterSh.notation;
     if (currentNotation === NOTATION.HELM)
       separatorInput.value = '/'; // helm monomers can have - in the name like D-aThr;
     dialogHeader.textContent = 'Current notation: ' + currentNotation;
     filteredNotations = notations.filter((e) => e !== currentNotation);
-    targetNotationInput = ui.input.choice('Convert to', {value: filteredNotations[0], items: filteredNotations,
-      onValueChanged: toggleSeparator});
+    targetNotationInput = ui.input.choice('Convert to', {
+      value: filteredNotations[0], items: filteredNotations,
+      onValueChanged: toggleSeparator
+    });
     toggleSeparator();
     convertDialog?.clear();
     convertDialog?.add(ui.div([
@@ -64,8 +67,10 @@ export function convert(col?: DG.Column): void {
     ]));
   };
 
-  const targetColumnInput = ui.input.column('Column', {table: grok.shell.t, value: srcCol,
-    onValueChanged: (value) => toggleColumn(value)});
+  const targetColumnInput = ui.input.column('Column', {
+    table: grok.shell.t, value: srcCol,
+    onValueChanged: (value) => toggleColumn(value)
+  });
 
   const separatorArray = ['-', '.', '/'];
   let filteredNotations = notations.filter((e) => e !== currentNotation);
@@ -79,8 +84,10 @@ export function convert(col?: DG.Column): void {
     else
       $(separatorInput.root).show();
   };
-  let targetNotationInput = ui.input.choice('Convert to', {value: filteredNotations[0], items: filteredNotations,
-    onValueChanged: toggleSeparator});
+  let targetNotationInput = ui.input.choice('Convert to', {
+    value: filteredNotations[0], items: filteredNotations,
+    onValueChanged: toggleSeparator
+  });
 
   // set correct visibility on init
   toggleSeparator();
@@ -101,7 +108,7 @@ export function convert(col?: DG.Column): void {
         const targetNotation = targetNotationInput.value as NOTATION;
         const separator: string | undefined = targetNotation === NOTATION.SEPARATOR ? separatorInput.value! : undefined;
 
-        await convertDo(srcCol, targetNotation, separator);
+        await convertDo(srcCol, seqHelper, targetNotation, separator);
       })
       .show({x: 350, y: 100});
 
@@ -118,8 +125,8 @@ export function convert(col?: DG.Column): void {
  * @param {NOTATION} targetNotation Target notation
  * @param {string | null} separator Separator for SEPARATOR notation
  */
-export async function convertDo(srcCol: DG.Column, targetNotation: NOTATION, separator?: string): Promise<DG.Column> {
-  const converterSh = SeqHandler.forColumn(srcCol);
+export async function convertDo(srcCol: DG.Column, seqHelper: ISeqHelper, targetNotation: NOTATION, separator?: string): Promise<DG.Column> {
+  const converterSh = seqHelper.getSeqHandler(srcCol);
   const newColumn = converterSh.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);
 

package/src/utils/get-region-func-editor.ts

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {_package} from '../package';
 
@@ -33,12 +33,14 @@ export class GetRegionFuncEditor {
   }();
 
   constructor(
-    private readonly call: DG.FuncCall
+    private readonly call: DG.FuncCall,
+    private readonly seqHelper: ISeqHelper,
   ) {
     const getDesc = (paramName: string) => this.call.inputParams[paramName].property.description;
 
     this.inputs.table = ui.input.table('Table', {value: this.call.inputParams['table'].value ?? grok.shell.tv.dataFrame});
 
+    //@formatter:off
     const seqColValue = this.call.inputParams['sequence'].value ??
       this.inputs.table.value!.columns.bySemType(DG.SEMTYPE.MACROMOLECULE);
     this.inputs.sequence = ui.input.column('Sequence', {table: grok.shell.tv.dataFrame, value: seqColValue,
@@ -52,6 +54,7 @@ export class GetRegionFuncEditor {
     this.inputs.name = ui.input.string('Column name', {value: this.getDefaultName(),
       onValueChanged: this.nameInputChanged.bind(this), clearIcon: true});
     this.inputs.name.onInput.subscribe(() => this.nameInputInput.bind(this)); // To catch clear event
+    //@formatter:on
 
     // tooltips
     for (const paramName in this.call.inputParams) {
@@ -65,7 +68,7 @@ export class GetRegionFuncEditor {
 
   private sequenceInputChanged(): void {
     const seqCol = this.inputs.sequence.value;
-    const sh = seqCol ? SeqHandler.forColumn(seqCol) : null;
+    const sh = seqCol ? this.seqHelper.getSeqHandler(seqCol) : null;
     this.updateRegionItems();
     this.updateStartEndInputItems();
     this.updateRegion(true);
@@ -84,7 +87,7 @@ export class GetRegionFuncEditor {
         this.inputs.start.value = reg?.start;
         this.inputs.end.value = reg?.end;
       } else {
-        const sh = SeqHandler.forColumn(this.inputs.sequence.value!);
+        const sh = this.seqHelper.getSeqHandler(this.inputs.sequence.value!);
         this.inputs.start.value = sh.posList[0];
         this.inputs.end.value = sh.posList[sh.posList.length - 1];
       }
@@ -117,7 +120,7 @@ export class GetRegionFuncEditor {
 
   private updateStartEndInputItems(): void {
     const seqCol = this.inputs.sequence.value;
-    const sh = seqCol ? SeqHandler.forColumn(seqCol) : null;
+    const sh = seqCol ? this.seqHelper.getSeqHandler(seqCol) : null;
 
     const startSE = (this.inputs.start.input as HTMLSelectElement);
     const endSE = (this.inputs.end.input as HTMLSelectElement);

package/src/utils/get-region.ts

@@ -2,11 +2,10 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {TaskBarProgressIndicator} from 'datagrok-api/dg';
+import {_package} from '../package';
 
 export function getRegionUI(col: DG.Column<string>): void {
-  const sh = SeqHandler.forColumn(col);
+  const sh = _package.seqHelper.getSeqHandler(col);
 
   const nameInput = ui.input.string('Name', {value: ''});
   const startPositionInput = ui.input.choice('Start Position', {value: sh.posList[0], items: sh.posList,
@@ -23,7 +22,7 @@ export function getRegionUI(col: DG.Column<string>): void {
     startPositionInput,
     endPositionInput,
   ])).onOK(() => {
-    const pi = TaskBarProgressIndicator.create('Getting region...');
+    const pi = DG.TaskBarProgressIndicator.create('Getting region...');
     try {
       const name: string = nameInput.value ?? getDefaultName();
       const regCol = getRegionDo(col, name, startPositionInput.value, endPositionInput.value);
@@ -39,7 +38,7 @@ export function getRegionUI(col: DG.Column<string>): void {
 export function getRegionDo(
   col: DG.Column<string>, startPosName: string | null, endPosName: string | null, name: string | null
 ): DG.Column<string> {
-  const sh = SeqHandler.forColumn(col);
+  const sh = _package.seqHelper.getSeqHandler(col);
 
   let startPosIdx: number | null = null;
   let endPosIdx: number | null = null;

package/src/utils/helm-to-molfile/converter/helm.ts

@@ -21,8 +21,8 @@ export class Helm {
    * complex polymer scope) */
   readonly bondData: Bond[][];
 
-  private simplePolymers: SimplePolymer[];
-  private connectionList?: ConnectionList;
+  public readonly simplePolymers: SimplePolymer[];
+  public readonly connectionList?: ConnectionList;
 
   /** Maps global monomer index to r-group ids (starting from 1) participating
    * in connection */
@@ -74,8 +74,8 @@ export class Helm {
     });
   }
 
-  private getMonomerIdxShifts(): {[simplePolymerId: string]: number} {
-    const result: {[simplePolymerId: string]: number} = {};
+  private getMonomerIdxShifts(): { [simplePolymerId: string]: number } {
+    const result: { [simplePolymerId: string]: number } = {};
     let shift = 0;
     this.simplePolymers.forEach((simplePolymer) => {
       result[simplePolymer.id] = shift;

package/src/utils/helm-to-molfile/utils.ts

@@ -6,14 +6,14 @@ import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
 
 import {SeqHelper} from '../seq-helper';
 
-import {_package, getMonomerLib} from '../../package';
+import {_package} from '../../package';
 
 /** Translate HELM column into molfile column and append to the dataframe */
 export async function getMolColumnFromHelm(
   df: DG.DataFrame, helmCol: DG.Column<string>, chiralityEngine: boolean = true, monomerLib: IMonomerLibBase
 ): Promise<DG.Column<string>> {
-  const seqHelper = await SeqHelper.getInstance();
-  const converter = seqHelper.getHelmToMolfileConverter(monomerLib);
+  const seqHelper: SeqHelper = _package.seqHelper as SeqHelper;
+  const converter = await seqHelper.getHelmToMolfileConverter(monomerLib);
   const molCol = converter.convertToRdKitBeautifiedMolfileColumn(helmCol, chiralityEngine, _package.rdKitModule, monomerLib);
   molCol.semType = DG.SEMTYPE.MOLECULE;
   return molCol;
@@ -22,9 +22,8 @@ export async function getMolColumnFromHelm(
 export async function getSmilesColumnFromHelm(
   helmCol: DG.Column<string>
 ): Promise<DG.Column<string>> {
-  const seqHelper = await SeqHelper.getInstance();
-  const monomerLib = getMonomerLib();
-  const converter = seqHelper.getHelmToMolfileConverter(monomerLib);
+  const seqHelper: SeqHelper = _package.seqHelper as SeqHelper;
+  const converter = await seqHelper.getHelmToMolfileConverter(_package.monomerLib);
   const smilesCol = converter.convertToSmiles(helmCol);
   smilesCol.semType = DG.SEMTYPE.MOLECULE;
   return smilesCol;

package/src/utils/macromolecule-column-widget.ts

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {TAGS as wlTAGS} from '@datagrok-libraries/bio/src/viewers/web-logo';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {WebLogoViewer} from '../viewers/web-logo-viewer';
 
@@ -13,18 +13,17 @@ import {_package} from '../package';
 export class MacromoleculeColumnWidget extends DG.Widget {
   private viewed: boolean = false;
 
-  private readonly seqCol: DG.Column<string>;
-
   private wlViewer: WebLogoViewer | null = null;
 
-  constructor(seqCol: DG.Column<string>) {
+  constructor(
+    private readonly seqCol: DG.Column<string>,
+    private readonly seqHelper: ISeqHelper,
+  ) {
     super(ui.divV([]));
-
-    this.seqCol = seqCol;
   }
 
   async init(): Promise<void> {
-    const sh = SeqHandler.forColumn(this.seqCol);
+    const sh = this.seqHelper.getSeqHandler(this.seqCol);
     const pkgTooltipWebLogo = _package.properties.tooltipWebLogo;
     const colTooltipWebLogo = this.seqCol.getTag(wlTAGS.tooltipWebLogo);
 

package/src/utils/monomer-cell-renderer-base.ts

@@ -5,13 +5,15 @@ import * as ui from 'datagrok-api/ui';
 import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {CellRendererBackBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {ISeqHelper, getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {_package} from '../package';
 
 export abstract class CellRendererWithMonomerLibBackBase extends CellRendererBackBase<string> {
   protected monomerLib: IMonomerLibBase | null = null;
+  protected seqHelper: ISeqHelper | null = null;
 
-  constructor(
+  protected constructor(
     gridCol: DG.GridColumn | null,
     tableCol: DG.Column<string>,
   ) {
@@ -26,5 +28,10 @@ export abstract class CellRendererWithMonomerLibBackBase extends CellRendererBac
         this.gridCol?.grid?.invalidate();
       }));
     });
+    getSeqHelper().then((seqHelper) => {
+      this.seqHelper = seqHelper;
+      this.dirty = true;
+      this.gridCol?.grid?.invalidate();
+    });
   }
 }

package/src/utils/monomer-lib/lib-manager.ts

@@ -35,7 +35,8 @@ export class MonomerLibManager implements IMonomerLibHelper {
 
   public get eventManager(): IMonomerLibFileEventManager { return this._eventManager; }
 
-  public async awaitLoaded(timeout: number = 5000): Promise<void> {
+  public async awaitLoaded(timeout: number = Infinity): Promise<void> {
+    timeout = timeout === Infinity ? 1 * 60000 : timeout; // Limit the max lib loaded timeout
     return await Promise.race([
       (async () => {
         const fileManager = await this.getFileManager();
@@ -273,7 +274,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
   /** Changes userLibSettings set only HELMCoreLibrary.json, polytool-lib.json */
   async loadMonomerLibForTests(): Promise<void> {
     await setUserLibSettings(LIB_SETTINGS_FOR_TESTS);
-    await this.awaitLoaded();
+    await this.awaitLoaded(10000);
     await this.loadMonomerLib(true); // load default libraries
   }
 

package/src/utils/monomer-lib/monomer-colors.ts

@@ -8,20 +8,20 @@ import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 export const naturalMonomerColors = {
   [HelmTypes.BASE]: {
     // Chromatogram palette  // HELMWebEditor monomerColors
-    A: "green",              // "#A0A0FF",
-    G: "black",              // "#FF7070",
-    T: "red",                // "#A0FFA0",
-    C: "blue",               // "#FF8C4B",
-    U: "red",                // "#FF8080"
+    A: "#20E040",            // "#A0A0FF",
+    G: "#040404",            // "#FF7070",
+    T: "#FF8080",            // "#A0FFA0",
+    C: "#2060FF",            // "#FF8C4B",
+    U: "#FF8080",            // "#FF8080"
   },
 
   [HelmTypes.NUCLEOTIDE]: {
     // Chromatogram palette  // HELMWebEditor monomerColors
-    A: "green",              // "#A0A0FF",
-    G: "black",              // "#FF7070",
-    T: "red",                // "#A0FFA0",
-    C: "blue",               // "#FF8C4B",
-    U: "red",                // "#FF8080"
+    A: "#20E040",            // "#A0A0FF",
+    G: "#040404",            // "#FF7070",
+    T: "#FF8080",            // "#A0FFA0",
+    C: "#2060FF",            // "#FF8C4B",
+    U: "#FF8080",            // "#FF8080"
   },
 
   [HelmTypes.LINKER]: {

package/src/utils/monomer-lib/monomer-lib-base.ts

@@ -42,11 +42,16 @@ export class MonomerLibBase implements IMonomerLibBase {
 
   constructor(
     protected _monomers: MonomerLibDataType,
+    public readonly source: string,
   ) {
     this._isEmpty = !this._monomers || Object.keys(this._monomers).length === 0 ||
       Object.entries(this._monomers).every(([_, ptMonomers]) => Object.keys(ptMonomers).length === 0);
   }
 
+  getMonomerSymbolsByType(polymerType: PolymerType): string[] {
+    return Object.keys(this._monomers[polymerType]);
+  }
+
   /** Creates missing {@link Monomer} */
   addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer {
     let mSet = this._monomers[polymerType];
@@ -212,7 +217,7 @@ export class MonomerLibBase implements IMonomerLibBase {
       if (rgbM)
         return [parseInt(rgbM[1]), parseInt(rgbM[2]), parseInt(rgbM[3])];
 
-      const n = DG.Color.fromHtml(colors.textcolor!);
+      const n = DG.Color.fromHtml(html);
       return [DG.Color.r(n), DG.Color.g(n), DG.Color.b(n)];
     };