@datagrok/bio 2.16.0 → 2.16.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.16.0",
+  "version": "2.16.2",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,7 +37,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.45.0",
+    "@datagrok-libraries/bio": "^5.45.2",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.1",
     "@datagrok-libraries/ml": "^6.7.4",
@@ -55,7 +55,7 @@
     "rxjs": "^6.5.5",
     "style-loader": "^3.3.1",
     "umap-js": "^1.3.3",
-    "wu": "latest"
+    "wu": "^2.1.0"
   },
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.12",
@@ -64,18 +64,18 @@
     "@datagrok/dendrogram": "^1.2.33",
     "@datagrok/helm": "^2.5.3",
     "@types/node": "^17.0.24",
-    "@types/wu": "latest",
-    "@typescript-eslint/eslint-plugin": "latest",
-    "@typescript-eslint/parser": "latest",
+    "@types/wu": "^2.1.44",
+    "@typescript-eslint/eslint-plugin": "^8.8.1",
+    "@typescript-eslint/parser": "^8.8.1",
     "datagrok-tools": "latest",
-    "eslint": "latest",
-    "eslint-config-google": "latest",
-    "eslint-plugin-rxjs": "latest",
-    "source-map-loader": "latest",
+    "eslint": "^9.12.0",
+    "eslint-config-google": "^0.14.0",
+    "eslint-plugin-rxjs": "^5.0.3",
+    "source-map-loader": "^5.0.0",
     "ts-loader": "^9.5.1",
     "typescript": "^5.5.3",
     "webpack": "^5.92.1",
-    "webpack-bundle-analyzer": "latest",
+    "webpack-bundle-analyzer": "^4.10.2",
     "webpack-cli": "^5.1.4"
   },
   "scripts": {

package/src/analysis/sequence-activity-cliffs.ts

@@ -6,13 +6,15 @@ import wu from 'wu';
 
 import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {getSimilarityFromDistance} from '@datagrok-libraries/ml/src/distance-metrics-methods';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {AvailableMetrics, DistanceMetricsSubjects, StringMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
-import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
-import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
 import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 
+import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
+import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
+
 import {_package} from '../package';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
@@ -46,11 +48,11 @@ export async function getSimilaritiesMatrix(
   return simArr;
 }
 
-export async function getChemSimilaritiesMatrix(dim: number, seqCol: DG.Column,
+export async function getChemSimilaritiesMatrix(dim: number, seqCol: DG.Column, seqHelper: ISeqHelper,
   df: DG.DataFrame, colName: string, simArr: (DG.Column | null)[])
   : Promise<(DG.Column | null)[]> {
   if (seqCol.version !== seqCol.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
-    await invalidateMols(seqCol, false);
+    await invalidateMols(seqCol, seqHelper, false);
   const fpDf = DG.DataFrame.create(seqCol.length);
   fpDf.columns.addNewString(colName).init((i) => seqCol.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS].get(i));
   const res = await grok.functions.call('Chem:getChemSimilaritiesMatrix', {

package/src/analysis/sequence-diversity-viewer.ts

@@ -50,7 +50,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   }
 
   private async computeByChem() {
-    const monomericMols = await getMonomericMols(this.moleculeColumn!);
+    const monomericMols = await getMonomericMols(this.moleculeColumn!, this.seqHelper);
     //need to create df to calculate fingerprints
     const _monomericMolsDf = DG.DataFrame.fromColumns([monomericMols]);
     this.renderMolIds = await grok.functions.call('Chem:callChemDiversitySearch', {

package/src/analysis/sequence-similarity-viewer.ts

@@ -86,7 +86,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   }
 
   private async computeByChem() {
-    const monomericMols = await getMonomericMols(this.moleculeColumn!);
+    const monomericMols = await getMonomericMols(this.moleculeColumn!, this.seqHelper);
     //need to create df to calculate fingerprints
     const _monomericMolsDf = DG.DataFrame.fromColumns([monomericMols]);
     const df = await grok.functions.call('Chem:callChemSimilaritySearch', {

package/src/calculations/monomerLevelMols.ts

@@ -6,19 +6,18 @@ import wu from 'wu';
 
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
-
-import {_package, getHelmMonomers} from '../package';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 const V2000_ATOM_NAME_POS = 31;
 
 export async function getMonomericMols(
-  mcol: DG.Column<string>, pattern: boolean = false, monomersDict?: Map<string, string>
+  mcol: DG.Column<string>, seqHelper: ISeqHelper, pattern: boolean = false, monomersDict?: Map<string, string>
 ): Promise<DG.Column> {
-  const sh = _package.seqHelper.getSeqHandler(mcol);
+  const sh = seqHelper.getSeqHandler(mcol);
   let molV3000Array;
   monomersDict ??= new Map();
   const monomers = sh.isHelm() ?
-    getHelmMonomers(mcol) : Object.keys(sh.stats.freq).filter((it) => it !== '');
+    seqHelper.getSeqMonomers(mcol) : Object.keys(sh.stats.freq).filter((it) => it !== '');
 
   for (let i = 0; i < monomers.length; i++) {
     if (!monomersDict.has(monomers[i]))

package/src/package-types.ts

@@ -7,7 +7,6 @@ import {Observable, Subject} from 'rxjs';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import {SeqHelper} from './utils/seq-helper';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {IMonomerLib, IMonomerLibBase, IMonomerSet} from '@datagrok-libraries/bio/src/types';
 

package/src/package.ts

@@ -562,7 +562,7 @@ export async function macromoleculePreprocessingFunction(
 export async function helmPreprocessingFunction(
   col: DG.Column<string>, _metric: BitArrayMetrics): Promise<PreprocessFunctionReturnType> {
   if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
-    await invalidateMols(col, false);
+    await invalidateMols(col, _package.seqHelper, false);
   const molCol = col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS];
   const fingerPrints: DG.Column<DG.BitSet | null> =
     await grok.functions.call('Chem:getMorganFingerprints', {molColumn: molCol});
@@ -858,9 +858,7 @@ export async function splitToMonomersTopMenu(table: DG.DataFrame, sequence: DG.C
 //input: column sequence {semType: Macromolecule}
 //output: object result
 export function getHelmMonomers(sequence: DG.Column<string>): string[] {
-  const sh = _package.seqHelper.getSeqHandler(sequence);
-  const stats = sh.stats;
-  return Object.keys(stats.freq);
+  return _package.seqHelper.getSeqMonomers(sequence);
 }
 
 
@@ -908,7 +906,7 @@ export function searchSubsequenceEditor(call: DG.FuncCall) {
   if (columns.length === 1)
     call.func.prepare({macromolecules: columns[0]}).call(true);
   else
-    new SubstructureSearchDialog(columns);
+    new SubstructureSearchDialog(columns, _package.seqHelper);
 }
 
 //top-menu: Bio | Search | Subsequence Search ...
@@ -980,7 +978,7 @@ export function saveAsFasta() {
 //output: filter result
 //meta.semType: Macromolecule
 export function bioSubstructureFilter(): BioSubstructureFilter {
-  return new BioSubstructureFilter();
+  return new BioSubstructureFilter(_package.seqHelper, _package.logger);
 }
 
 // -- Test apps --

package/src/substructure-search/substructure-search.ts

@@ -2,10 +2,12 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {getMonomericMols} from '../calculations/monomerLevelMols';
-import {updateDivInnerHTML} from '../utils/ui-utils';
 import {delay} from '@datagrok-libraries/utils/src/test';
 import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+
+import {getMonomericMols} from '../calculations/monomerLevelMols';
+import {updateDivInnerHTML} from '../utils/ui-utils';
 
 export const MONOMER_MOLS_COL = 'monomeric-mols';
 
@@ -29,7 +31,9 @@ export class SubstructureSearchDialog {
   col: DG.Column;
   dialog: DG.Dialog;
 
-  constructor(columns: DG.Column<string>[]) {
+  constructor(columns: DG.Column<string>[],
+    private readonly seqHelper: ISeqHelper
+  ) {
     this.col = columns[0];
     this.createUI();
   }
@@ -96,7 +100,7 @@ export class SubstructureSearchDialog {
           substructure = substructure.replaceAll(this.separatorInput.value, this.separator);
         let matches: DG.BitSet;
         if (this.units === NOTATION.HELM)
-          matches = await helmSubstructureSearch(substructure, this.col);
+          matches = await helmSubstructureSearch(substructure, this.col, this.seqHelper);
         else
           matches = linearSubstructureSearch(substructure, this.col);
         this.col.dataFrame.filter.and(matches);
@@ -129,14 +133,16 @@ function prepareSubstructureRegex(substructure: string, separator: string) {
   return re;
 }
 
-export async function helmSubstructureSearch(substructure: string, col: DG.Column<string>): Promise<DG.BitSet> {
+export async function helmSubstructureSearch(
+  substructure: string, col: DG.Column<string>, seqHelper: ISeqHelper
+): Promise<DG.BitSet> {
   if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
-    await invalidateMols(col, true);
+    await invalidateMols(col, seqHelper, true);
   const substructureCol: DG.Column<string> = DG.Column.string('helm', 1).init((_i) => substructure);
   substructureCol.semType = DG.SEMTYPE.MACROMOLECULE;
   substructureCol.meta.units = NOTATION.HELM;
   const substructureMolsCol =
-    await getMonomericMols(substructureCol, true, col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT]);
+    await getMonomericMols(substructureCol, seqHelper, true, col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT]);
   const matchesCol = await grok.functions.call('Chem:searchSubstructure', {
     molStringsColumn: col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS],
     molString: substructureMolsCol.get(0),
@@ -145,12 +151,12 @@ export async function helmSubstructureSearch(substructure: string, col: DG.Colum
   return matchesCol.get(0);
 }
 
-export async function invalidateMols(col: DG.Column<string>, pattern: boolean) {
+export async function invalidateMols(col: DG.Column<string>, seqHelper: ISeqHelper, pattern: boolean): Promise<void> {
   const progressBar = DG.TaskBarProgressIndicator.create(`Invalidating molfiles for ${col.name}`);
   try {
     await delay(10);
     const monomersDict = new Map();
-    const monomericMolsCol = await getMonomericMols(col, pattern, monomersDict);
+    const monomericMolsCol = await getMonomericMols(col, seqHelper, pattern, monomersDict);
     col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS] = monomericMolsCol;
     col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT] = monomersDict;
     col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION] = col.version;

package/src/tests/substructure-filters-tests.ts

@@ -11,7 +11,7 @@ import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {getSeqHelper, ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {awaitGrid, readDataframe} from './utils';
 
@@ -24,13 +24,13 @@ import {HelmBioFilter} from '../widgets/bio-substructure-filter-helm';
 import {_package} from '../package-test';
 
 category('bio-substructure-filters', async () => {
-  let helmHelper: IHelmHelper;
+  let seqHelper: ISeqHelper;
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
   let userLibSettings: UserLibSettings;
 
   before(async () => {
-    helmHelper = await getHelmHelper(); // init Helm package
+    seqHelper = await getSeqHelper();
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
 
@@ -51,7 +51,7 @@ category('bio-substructure-filters', async () => {
     const fSubStr: string = 'MD';
     const fTrueCount: number = 3;
 
-    const filter = await createBioSubstructureFilter();
+    const filter = new BioSubstructureFilter(seqHelper, _package.logger);
     filter.attach(df);
     await filter.awaitRendered();
     try {
@@ -68,11 +68,11 @@ category('bio-substructure-filters', async () => {
       filter.detach();
     }
     await filter.awaitRendered();
-  }, {skipReason: 'GROK-16782'});
+  });
 
   test('separator', async () => {
     const msa = await readDataframe('tests/filter_MSA.csv');
-    const filter = await createBioSubstructureFilter();
+    const filter = new BioSubstructureFilter(seqHelper, _package.logger);
     await grok.data.detectSemanticTypes(msa);
     filter.attach(msa);
     await filter.awaitRendered();
@@ -101,7 +101,7 @@ category('bio-substructure-filters', async () => {
       filter.detach();
     }
     await filter.awaitRendered();
-  }, {skipReason: 'GROK-16782'});
+  });
 
   // test('helm', async () => {
   //   const df = await readDataframe('tests/filter_HELM.csv');
@@ -156,7 +156,7 @@ category('bio-substructure-filters', async () => {
     const view = grok.shell.addTableView(df);
 
     _package.logger.debug(`${logPrefix}, filter attaching.`);
-    const filter = await createBioSubstructureFilter();
+    const filter = new BioSubstructureFilter(seqHelper, _package.logger);
     filter.attach(df);
     const dlg = ui.dialog('Test filters').add(filter.root).show(); // to waitForElementInDom
     await filter.awaitRendered();
@@ -187,7 +187,7 @@ category('bio-substructure-filters', async () => {
     }
     await filter.awaitRendered();
     await delay(3000); //TODO: await for grid.onLookChanged
-  }, {skipReason: 'GROK-16782'});
+  });
 
   // Generates unhandled exception accessing isFiltering before bioFilter created
   test('helm-view', async () => {
@@ -234,7 +234,7 @@ category('bio-substructure-filters', async () => {
       f2.detach();
     }
     await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
-  }, {skipReason: 'GROK-16782'});
+  });
 
   // MSA filter has the second input field for separator
   test('sync-msa', async () => {
@@ -268,7 +268,7 @@ category('bio-substructure-filters', async () => {
       f2.detach();
     }
     await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
-  }, {skipReason: 'GROK-16782'});
+  });
 
   test('sync-helm', async () => {
     const df = await _package.files.readCsv('tests/filter_HELM.csv');
@@ -311,7 +311,7 @@ category('bio-substructure-filters', async () => {
     await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
     await awaitGrid(view.grid);
     await delay(3000); //TODO: await for grid.onLookChanged
-  }, {skipReason: 'GROK-16782'});
+  });
 
   // two seq columns
 
@@ -449,24 +449,20 @@ category('bio-substructure-filters', async () => {
     await delay(100);
     await awaitGrid(view.grid);
   });
+
+  async function createFilter(colName: string, df: DG.DataFrame): Promise<BioSubstructureFilter> {
+    if (!df.columns.names().includes(colName)) {
+      throw new Error(`The column '${colName}' not found. ` +
+        `Available in data frame are ${JSON.stringify(df.columns.names())}`);
+    }
+
+    const filter = new BioSubstructureFilter(seqHelper, _package.logger);
+    filter.attach(df);
+    filter.applyState({columnName: colName});
+    filter.column = df.col(colName);
+    filter.columnName = colName;
+    //filter.tableName = df.name;
+    return filter;
+  };
 });
 
-async function createFilter(colName: string, df: DG.DataFrame): Promise<BioSubstructureFilter> {
-  if (!df.columns.names().includes(colName)) {
-    throw new Error(`The column '${colName}' not found. ` +
-      `Available in data frame are ${JSON.stringify(df.columns.names())}`);
-  }
-
-  const filter = await createBioSubstructureFilter();
-  filter.attach(df);
-  filter.applyState({columnName: colName});
-  filter.column = df.col(colName);
-  filter.columnName = colName;
-  //filter.tableName = df.name;
-  return filter;
-};
-
-async function createBioSubstructureFilter(): Promise<BioSubstructureFilter> {
-  const filter = await grok.functions.call('Bio:bioSubstructureFilter');
-  return filter.dart.jsFilter as BioSubstructureFilter;
-}

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

@@ -16,6 +16,8 @@ import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 import {ISeqHandler, ConvertFunc, JoinerFunc, SeqTemps} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
+import {SeqHelper} from './seq-helper';
+
 /* eslint-enable max-len */
 
 /** Class for handling notation units in Macromolecule columns and
@@ -30,7 +32,9 @@ export class SeqHandler implements ISeqHandler {
 
   private _splitter: SplitterFunc | null = null;
 
-  protected constructor(col: DG.Column<string>) {
+  protected constructor(col: DG.Column<string>,
+    private readonly seqHelper: SeqHelper,
+  ) {
     if (col.type !== DG.TYPE.STRING)
       throw new Error(`Unexpected column type '${col.type}', must be '${DG.TYPE.STRING}'.`);
     this._column = col;
@@ -50,12 +54,12 @@ export class SeqHandler implements ISeqHandler {
       // 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())
-        SeqHandler.setUnitsToFastaColumn(this);
+        this.seqHelper.setUnitsToFastaColumn(this);
       else if (this.isSeparator()) {
         const separator = col.getTag(TAGS.separator);
-        SeqHandler.setUnitsToSeparatorColumn(this, separator);
+        this.seqHelper.setUnitsToSeparatorColumn(this, separator);
       } else if (this.isHelm())
-        SeqHandler.setUnitsToHelmColumn(this);
+        this.seqHelper.setUnitsToHelmColumn(this);
       else
         throw new Error(`Unexpected units '${this.column.meta.units}'.`);
     }
@@ -85,33 +89,6 @@ export class SeqHandler implements ISeqHandler {
     this.columnVersion = this.column.version;
   }
 
-  public static setUnitsToFastaColumn(uh: SeqHandler) {
-    if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.meta.units !== NOTATION.FASTA)
-      throw new Error(`The column of notation '${NOTATION.FASTA}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
-
-    uh.column.meta.units = NOTATION.FASTA;
-    SeqHandler.setTags(uh);
-  }
-
-  public static setUnitsToSeparatorColumn(uh: SeqHandler, separator?: string) {
-    if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.meta.units !== NOTATION.SEPARATOR)
-      throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
-    if (!separator)
-      throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must have the separator tag.`);
-
-    uh.column.meta.units = NOTATION.SEPARATOR;
-    uh.column.setTag(TAGS.separator, separator);
-    SeqHandler.setTags(uh);
-  }
-
-  public static setUnitsToHelmColumn(uh: SeqHandler) {
-    if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE)
-      throw new Error(`The column of notation '${NOTATION.HELM}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
-
-    uh.column.meta.units = NOTATION.HELM;
-    SeqHandler.setTags(uh);
-  }
-
   /** From detectMacromolecule */
   public static setTags(uh: SeqHandler): void {
     const units = uh.column.meta.units as NOTATION;
@@ -141,7 +118,7 @@ export class SeqHandler implements ISeqHandler {
     }
   }
 
-  protected get column(): DG.Column { return this._column; }
+  get column(): DG.Column { return this._column; }
 
   public get length(): number { return this._column.length; }
 
@@ -741,11 +718,11 @@ export class SeqHandler implements ISeqHandler {
   }
 
   /** Gets a column's UnitsHandler object from temp slot or creates a new and stores it to the temp slot. */
-  public static forColumn(col: DG.Column<string>): SeqHandler {
+  public static forColumn(col: DG.Column<string>, seqHelper: SeqHelper): SeqHandler {
     // TODO: Invalidate col.temp[Temps.uh] checking column's metadata
     let res = col.temp[SeqTemps.seqHandler];
     if (!res || res.columnVersion !== col.version)
-      res = col.temp[SeqTemps.seqHandler] = new SeqHandler(col);
+      res = col.temp[SeqTemps.seqHandler] = new SeqHandler(col, seqHelper);
     return res;
   }
 

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

@@ -17,6 +17,8 @@ import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
 import {HelmToMolfileConverter} from '../helm-to-molfile/converter';
 import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 import {SeqHandler} from './seq-handler';
+import {Column} from 'datagrok-api/dg';
+import {NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 type SeqHelperWindowType = Window & { $seqHelperPromise?: Promise<SeqHelper> };
 declare const window: SeqHelperWindowType;
@@ -28,7 +30,12 @@ export class SeqHelper implements ISeqHelper {
   ) {}
 
   getSeqHandler(seqCol: DG.Column<string>): ISeqHandler {
-    return SeqHandler.forColumn(seqCol);
+    return SeqHandler.forColumn(seqCol, this);
+  }
+
+  getSeqMonomers(seqCol: Column<string>): string[] {
+    const sh = this.getSeqHandler(seqCol);
+    return Object.keys(sh.stats.freq);
   }
 
   // TODO: Move to the Helm package
@@ -89,4 +96,31 @@ export class SeqHelper implements ISeqHelper {
 
     return {molCol: molCol, warnings: []};
   }
+
+  public setUnitsToFastaColumn(uh: SeqHandler) {
+    if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.meta.units !== NOTATION.FASTA)
+      throw new Error(`The column of notation '${NOTATION.FASTA}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
+
+    uh.column.meta.units = NOTATION.FASTA;
+    SeqHandler.setTags(uh);
+  }
+
+  public setUnitsToSeparatorColumn(uh: SeqHandler, separator?: string) {
+    if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.meta.units !== NOTATION.SEPARATOR)
+      throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
+    if (!separator)
+      throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must have the separator tag.`);
+
+    uh.column.meta.units = NOTATION.SEPARATOR;
+    uh.column.setTag(TAGS.separator, separator);
+    SeqHandler.setTags(uh);
+  }
+
+  public setUnitsToHelmColumn(uh: SeqHandler) {
+    if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE)
+      throw new Error(`The column of notation '${NOTATION.HELM}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
+
+    uh.column.meta.units = NOTATION.HELM;
+    SeqHandler.setTags(uh);
+  }
 }

package/src/widgets/bio-substructure-filter-helm.ts

@@ -10,6 +10,7 @@ import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {delay} from '@datagrok-libraries/utils/src/test';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {helmSubstructureSearch} from '../substructure-search/substructure-search';
@@ -32,7 +33,9 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
 
   get type(): string { return 'HelmBioFilter'; }
 
-  constructor() {
+  constructor(
+    private readonly seqHelper: ISeqHelper,
+  ) {
     super();
     this.logger = _package.logger;
   }
@@ -138,7 +141,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
     _package.logger.debug(`${logPrefix}, start`);
     try {
       await delay(10);
-      const res = await helmSubstructureSearch(this.props.substructure, column);
+      const res = await helmSubstructureSearch(this.props.substructure, column, this.seqHelper);
       return res;
     } finally {
       _package.logger.debug(`${logPrefix}, end`);