@datagrok/helm 2.5.3 → 2.5.5

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.5.3",
+  "version": "2.5.5",
   "author": {
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
@@ -16,33 +16,35 @@
     "css/helm.css"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.44.2",
+    "@datagrok-libraries/bio": "^5.45.0",
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/utils": "^4.3.4",
+    "@datagrok-libraries/utils": "^4.3.6",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.21.1",
     "dayjs": "^1.10.6",
+    "lru-cache": "^10.4.3",
     "rxjs": "^6.5.5",
-    "wu": "latest"
+    "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.11",
-    "@datagrok-libraries/js-draw-lite": "^0.0.8",
-    "@datagrok/bio": "^2.15.6",
-    "@datagrok/chem": "^1.12.1",
+    "@datagrok-libraries/helm-web-editor": "^1.1.12",
+    "@datagrok-libraries/js-draw-lite": "^0.0.9",
+    "@datagrok/bio": "^2.16.0",
+    "@datagrok/chem": "^1.12.3",
     "@types/node": "17.0.45",
     "@types/webpack-env": "^1.18.5",
-    "@types/wu": "latest",
+    "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^7.16.0",
     "@typescript-eslint/parser": "^7.16.0",
     "datagrok-tools": "latest",
-    "eslint": "^8.18.0",
+    "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
+    "eslint-plugin-deprecation": "^3.0.0",
     "eslint-plugin-rxjs": "^5.0.3",
     "path": "^0.12.7",
-    "source-map-loader": "^4.0.1",
-    "ts-loader": "^9.2.6",
-    "typescript": "^4.8.4",
+    "source-map-loader": "^5.0.0",
+    "ts-loader": "^9.5.1",
+    "typescript": "^5.6.3",
     "webpack": "^5.76.3",
     "webpack-cli": "^4.9.1"
   },
@@ -77,4 +79,4 @@
     "directory": "packages/Helm"
   },
   "category": "Bioinformatics"
-}
+}

package/src/helm-helper.ts

@@ -4,12 +4,13 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 
+/* eslint-disable max-len */
 import {
   App, Point, HelmAtom, HelmBond, HelmMol, HelmType, GetMonomerFunc, GetMonomerResType,
   MonomerExplorer, TabDescType, MonomersFuncs, MonomerSetType, ISeqMonomer, PolymerType, MonomerType,
-  DojoType, JSDraw2ModuleType,
+  DojoType, JSDraw2ModuleType, IHelmEditorOptions, IHelmDrawOptions
 } from '@datagrok-libraries/bio/src/helm/types';
-import {HelmTypes, MonomerTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
+import {HelmTabKeys, HelmTypes, MonomerTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {
@@ -17,13 +18,13 @@ import {
 } from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
 import {IMonomerLib, IMonomerLibBase, IMonomerLinkData, IMonomerSetPlaceholder} from '@datagrok-libraries/bio/src/types/index';
-import {HelmTabKeys, IHelmDrawOptions} from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 import {GAP_SYMBOL, GapOriginals, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
 import {HelmWebEditor} from './helm-web-editor';
 import {OrgHelmModule, ScilModule} from './types';
 import {HelmInput} from './widgets/helm-input';
 import {getHoveredMonomerFromEditorMol} from './utils/get-hovered';
+/* eslint-enable max-len */
 
 import {_package} from './package';
 
@@ -47,7 +48,7 @@ export class HelmHelper implements IHelmHelper {
 
   createHelmInput(name?: string, options?: IHelmInputInitOptions): HelmInputBase {
     try {
-      const monomerLib: IMonomerLibBase = _package.libHelper!.getMonomerLib();
+      const monomerLib: IMonomerLibBase = _package._libHelper!.getMonomerLib();
       return HelmInput.create(this, monomerLib, name, options);
     } catch (err: any) {
       const [errMsg, errStack] = errInfo(err);
@@ -56,8 +57,8 @@ export class HelmHelper implements IHelmHelper {
     }
   }
 
-  createHelmWebEditor(host?: HTMLDivElement, drawOptions?: Partial<IHelmDrawOptions>): IHelmWebEditor {
-    return new HelmWebEditor(host, drawOptions);
+  createHelmWebEditor(host?: HTMLDivElement, options?: Partial<IHelmEditorOptions>): IHelmWebEditor {
+    return new HelmWebEditor(host, options);
   }
 
   createWebEditorApp(host: HTMLDivElement, helm: string): App {
@@ -146,7 +147,7 @@ export class HelmHelper implements IHelmHelper {
   }
 
   public onShowTabPlaceholdersSets(mex: MonomerExplorer, div: HTMLDivElement): void {
-    const monomerSets = _package.libHelper!.getMonomerSets();
+    const monomerSets = _package._libHelper!.getMonomerSets();
 
     const phSet: { [polymerType: string]: { [helmType: string]: IMonomerSetPlaceholder[] } } = {};
     for (const ph of monomerSets.placeholders) {
@@ -260,7 +261,8 @@ export class HelmHelper implements IHelmHelper {
         const logPrefixInt = `${logPrefix}, org.helm.webeditor.Monomers.getMonomer()`;
         try {
           // logger.debug(`${logPrefixInt}, a: ${JSON.stringify(a, helmJsonReplacer)}, name: '${name}'`);
-
+          if (name?.startsWith('[') && name.endsWith(']'))
+            name = name.substring(1, name.length - 1);
           // Creates monomers in lib
           const dgWem = monomerLib.getWebEditorMonomer(a, name);
 
@@ -340,7 +342,7 @@ export class HelmHelper implements IHelmHelper {
   }
 
   public parse(helm: string, origin?: Point): HelmMol {
-    const molHandler = new JSDraw2.MolHandler<HelmType>();
+    const molHandler = new JSDraw2.MolHandler<HelmType, IHelmEditorOptions>();
     const plugin = new org.helm.webeditor.Plugin(molHandler);
     org.helm.webeditor.IO.parseHelm(plugin, helm, origin ?? new JSDraw2.Point(0, 0));
     return plugin.jsd.m;

package/src/helm-web-editor.ts

@@ -6,7 +6,7 @@ import {Unsubscribable} from 'rxjs';
 
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {
-  App, Editor, HelmType, IHelmWebEditor, HelmEditor, IHelmDrawOptions
+  App, Editor, HelmType, IHelmWebEditor, HelmEditor, IHelmEditorOptions
 } from '@datagrok-libraries/bio/src/helm/types';
 
 import {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
@@ -27,16 +27,17 @@ export class HelmWebEditor implements IHelmWebEditor {
 
   constructor(
     host?: HTMLDivElement,
-    drawOptions?: Partial<IHelmDrawOptions>,
+    options?: Partial<IHelmEditorOptions>,
     private logger: ILogger = _package.logger
   ) {
     this.host = host ?? ui.div([], {style: {width: `${this.w}px`, height: `${this.h}px`}});
 
-    const styleBackup = {width: this.host.style.width, height: this.host.style.height, overflow: this.host.style.overflow};
-    this.editor = new JSDraw2.Editor(this.host, {
-      width: this.w, height: this.h, viewonly: true,
-      drawOptions: drawOptions
-    });
+    const styleBackup = {
+      width: this.host.style.width, height: this.host.style.height,
+      overflow: this.host.style.overflow
+    };
+    this.editor = new JSDraw2.Editor(this.host,
+      Object.assign({width: this.w, height: this.h, viewonly: true}, options));
     this.host.style.width = styleBackup.width;
     this.host.style.height = styleBackup.height;
     this.host.style.overflow = styleBackup.overflow;

package/src/package-test.ts

@@ -5,7 +5,7 @@ import * as grok from 'datagrok-api/grok';
 // import {JSDraw2ModuleType} from '@datagrok/js-draw-lite/src/types/jsdraw2';
 // import {HelmType, OrgHelmModuleType} from '@datagrok/helm-web-editor/src/types/org-helm';
 
-import {runTests, tests, TestContext, initAutoTests as initTests } from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/utils/src/test';
 
 import './tests/_first-tests';
 import './tests/helm-tests';

package/src/package-utils.ts

@@ -13,9 +13,10 @@ import {
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
+import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
-import {HelmHelper} from './helm-helper';
 import {HelmService} from './utils/helm-service';
 import {OrgHelmModule, ScilModule} from './types';
 import {rewriteLibraries} from './utils/get-monomer';
@@ -38,14 +39,15 @@ type DojoConfigWindowType = {
   },
 };
 type HelmWindowType = {
-  $helmService?: HelmServiceBase,
+  $helmServicePromise?: Promise<HelmServiceBase>,
   require: any,
 };
 declare const window: Window & DojoConfigWindowType & DojoWindowType & HweWindow & HelmWindowType;
 
-export function _getHelmService(): HelmServiceBase {
-  let res = window.$helmService;
-  if (!res) res = window.$helmService = new HelmService();
+export async function _getHelmService(): Promise<HelmServiceBase> {
+  let res = window.$helmServicePromise;
+  if (!res)
+    res = window.$helmServicePromise = Promise.resolve(new HelmService());
   return res;
 }
 
@@ -57,7 +59,8 @@ export async function initHelmLoadAndPatchDojo(): Promise<void> {
   try {
     const requireBackup = window.require;
 
-    // dojo.window','dojo.io.script','dojo.io.iframe','dojo.dom','dojox.gfx','dojox.gfx.svg','dojox.gfx.shape','dojox.charting'
+    // 'dojo.window','dojo.io.script','dojo.io.iframe','dojo.dom',
+    // 'dojox.gfx','dojox.gfx.svg','dojox.gfx.shape','dojox.charting'
     const dojoTargetList: { name: string, checker: () => boolean }[] = [
       {name: 'dojo.window', checker: () => !!(window.dojo?.window)},
       {name: 'dojo.ready', checker: () => !!(window.dojo?.ready)},
@@ -120,14 +123,16 @@ export async function initHelmLoadAndPatchDojo(): Promise<void> {
         const cmp = dojoRequire == requireBackup;
         try {
           await new Promise<void>((resolve, reject) => {
-            dojoRequire(['dojo/window', 'dojo/dom', 'dojo/io/script', 'dojo/io/iframe',
+            /* eslint-disable indent */
+            dojoRequire([
+                'dojo/window', 'dojo/dom', 'dojo/io/script', 'dojo/io/iframe',
                 'dojox/gfx', 'dojox/gfx/svg', 'dojox/gfx/shape',
                 'dojox/storage/Provider', 'dojox/storage/LocalStorageProvider',
                 'dijit/_base', 'dijit/Tooltip', 'dijit/form/_FormValueWidget',
                 'dijit/form/DropDownButton', 'dijit/layout/AccordionContainer', 'dijit/form/ComboButton',
-                'dijit/layout/StackController', 'dijit/layout/StackContainer',
-              ],
+                'dijit/layout/StackController', 'dijit/layout/StackContainer',],
               (...args: any[]) => { resolve(); });
+            /* eslint-enable indent */
           });
         } finally {
           // TODO: Check interference with NGL
@@ -142,7 +147,8 @@ export async function initHelmLoadAndPatchDojo(): Promise<void> {
           const dojoProgress = dojoTargetList.length - dojoNotReadyList.length;
           pi.update(Math.round(100 * dojoProgress / dojoTargetList.length),
             `Loading Helm Web Editor ${dojoProgress}/${dojoTargetList.length}`);
-          _package.logger.debug(`${logPrefix}, dojo loading ... ${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
+          _package.logger.debug(`${logPrefix}, dojo loading ... ` +
+            `${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
           await delay(100);
         }
         _package.logger.debug(`${logPrefix}, dojo ready all modules`);
@@ -199,15 +205,27 @@ export const helmJsonReplacer = (key: string, value: any): any => {
 
 export class HelmPackage extends DG.Package {
   public alertOriginal: ((s: string) => void) | null = null;
-  public readonly helmHelper: HelmHelper;
-  public libHelper!: IMonomerLibHelper;
+
+  private _seqHelper: ISeqHelper;
+  public get seqHelper(): ISeqHelper {
+    if (!this._seqHelper)
+      throw new Error('Package Helm .seqHelper is not initialized');
+    return this._seqHelper;
+  }
+
+  private _helmHelper: IHelmHelper;
+  public get helmHelper(): IHelmHelper {
+    if (!this._helmHelper)
+      throw new Error('Package Helm .helmHelper is not initialized');
+    return this._helmHelper;
+  };
+
+  public _libHelper!: IMonomerLibHelper;
 
   constructor(opts: { debug: boolean } = {debug: false}) {
     super();
     // @ts-ignore
     super._logger = new LoggerWrapper(super.logger, opts.debug);
-
-    this.helmHelper = new HelmHelper(this.logger);
   }
 
   // -- Init --
@@ -299,16 +317,20 @@ export class HelmPackage extends DG.Package {
   // -- MonomerLib --
 
   public get monomerLib(): IMonomerLib {
-    if (!this.libHelper)
+    if (!this._libHelper)
       throw new Error(`Helm: _package.libHelper is not initialized yet`);
-    return this.libHelper.getMonomerLib();
+    return this._libHelper.getMonomerLib();
   }
 
   private _monomerLibSub?: Unsubscribable;
 
+  private _initialized: boolean = false;
+
   /** Requires both Bio & HELMWebEditor initialized */
-  initMonomerLib(libHelper: IMonomerLibHelper): void {
-    this.libHelper = libHelper;
+  completeInit(seqHelper: ISeqHelper, helmHelper: IHelmHelper, libHelper: IMonomerLibHelper): void {
+    this._seqHelper = seqHelper;
+    this._helmHelper = helmHelper;
+    this._libHelper = libHelper;
 
     const lib = this.monomerLib;
     rewriteLibraries(lib); // initHelm()
@@ -316,6 +338,7 @@ export class HelmPackage extends DG.Package {
       .subscribe(this.monomerLibOnChangedHandler.bind(this));
 
     this.initHelmPatchPistoia();
+    this._initialized = true;
   }
 
   monomerLibOnChangedHandler(): void {

package/src/package.ts

@@ -8,15 +8,16 @@ import $ from 'cash-dom';
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {App, Editor, HelmMol, HelmType, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
+import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {App, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
 import {HelmInputBase, IHelmHelper, IHelmInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {getPropertiesWidget} from './widgets/properties-widget';
 import {HelmGridCellRenderer, HelmGridCellRendererBack} from './utils/helm-grid-cell-renderer';
-import {_getHelmService, HelmPackage, initHelmLoadAndPatchDojo} from './package-utils';
+import {_getHelmService, HelmPackage} from './package-utils';
+import {HelmHelper} from './helm-helper';
 
 // Do not import anything than types from @datagrok/helm-web-editor/src/types
 import type {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
@@ -40,10 +41,9 @@ let initHelmPromise: Promise<void> | null = null;
 
 //tags: init
 export async function initHelm(): Promise<void> {
-  if (initHelmPromise === null) {
+  if (initHelmPromise === null)
     initHelmPromise = initHelmInt();
-  }
-  await initHelmPromise;
+  return initHelmPromise;
 }
 
 async function initHelmInt(): Promise<void> {
@@ -51,13 +51,15 @@ async function initHelmInt(): Promise<void> {
   _package.logger.debug(`${logPrefix}, start`);
 
   try {
-    const [_, libHelper] = await Promise.all([
+    const helmHelper: IHelmHelper = new HelmHelper(_package.logger);
+    const [_, seqHelper, libHelper] = await Promise.all([
       _package.initHELMWebEditor(),
+      getSeqHelper(),
       getMonomerLibHelper(),
     ]);
 
     _package.logger.debug(`${logPrefix}, lib loaded`);
-    _package.initMonomerLib(libHelper);
+    _package.completeInit(seqHelper, helmHelper, libHelper);
   } catch (err: any) {
     const [errMsg, errStack] = errInfo(err);
     // const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Exception \'undefined\'';
@@ -72,8 +74,9 @@ async function initHelmInt(): Promise<void> {
 }
 
 //name: getHelmService
+//description: Helm renderer service
 //output: object result
-export function getHelmService(): HelmServiceBase {
+export async function getHelmService(): Promise<HelmServiceBase> {
   return _getHelmService();
 }
 
@@ -108,7 +111,7 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 export function openEditor(mol: string): void {
   const df = grok.shell.tv.grid.dataFrame;
   const col = df.columns.bySemType('Macromolecule')! as DG.Column<string>;
-  const colSh = SeqHandler.forColumn(col);
+  const colSh = _package.seqHelper.getSeqHandler(col);
   const colUnits = col.meta.units;
   if (df.currentRowIdx === -1)
     return;
@@ -133,7 +136,7 @@ function openWebEditor(cell: DG.GridCell, value?: string, units?: string) {
   // const df = grok.shell.tv.grid.dataFrame;
   // const col = df.columns.bySemType('Macromolecule')!
   const col = cell.cell.column as DG.Column<string>;
-  const sh = SeqHandler.forColumn(col);
+  const sh = _package.seqHelper.getSeqHandler(col);
   const app: App =
     _package.helmHelper.createWebEditorApp(view, !!cell && units === undefined ? cell.cell.value : value!);
   const dlg = ui.dialog({showHeader: false, showFooter: true});
@@ -184,7 +187,7 @@ export function helmInput(name: string, options: IHelmInputInitOptions): HelmInp
 
 //name: getHelmHelper
 //output: object result
-export async function getHelmHelper(): Promise<IHelmHelper> {
+export function getHelmHelper(): IHelmHelper {
   return _package.helmHelper;
 }
 
@@ -224,7 +227,6 @@ export async function measureCellRenderer(): Promise<void> {
 // -- Test apps --
 
 //name: Highlight Monomers
-//tags: app
 //output: view result
 export async function highlightMonomers(): Promise<void> {
   const pi = DG.TaskBarProgressIndicator.create('Test app highlight monomers');

package/src/tests/get-monomer-tests.ts

@@ -92,16 +92,11 @@ category('getMonomer', ()=>{
     const monomerLib = monomerLibHelper.getMonomerLib();
     rewriteLibraries(monomerLib);
 
-    // const overriddenMonomersFuncs = helmHelper.revertOriginalMonomersFuncs();
-    // try {
-      const helmHelper: IHelmHelper = await getHelmHelper();
-      expect(helmHelper != null, true);
-      const getMonomerFunc: GetMonomerFunc = helmHelper.originalMonomersFuncs!.getMonomer!;
-
-      return _testAll('original', getMonomerFunc);
-    // } finally {
-    //   helmHelper.overrideMonomersFuncs(overriddenMonomersFuncs);
-    // }
+    const helmHelper: IHelmHelper = await getHelmHelper();
+    expect(helmHelper != null, true);
+    const getMonomerFunc: GetMonomerFunc = helmHelper.originalMonomersFuncs!.getMonomer!;
+
+    return _testAll('original', getMonomerFunc);
   }, {isAggregated: true});
 
   test('monomerLib', async () =>{

package/src/tests/helm-helper-tests.ts

@@ -2,14 +2,16 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+/* eslint-disable max-len */
 import {after, before, category, delay, expect, expectArray, test, testEvent} from '@datagrok-libraries/utils/src/test';
 import {HelmNotSupportedError, HelmNotSupportedErrorType, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+/* eslint-enable max-len */
 
 import {_package} from '../package-test';
 
 type TestSrcType = { helm: string };
-type TestTgtType = { helm: string | null, map: [number, number][] };
+type TestTgtType = { helm: string | null, map: [number, number][], errType?: string };
 
 category('HelmHelper: removeGaps', () => {
   let helmHelper: IHelmHelper;
@@ -63,7 +65,7 @@ category('HelmHelper: removeGaps', () => {
     },
     'single-cycle-gap-at-connection': {
       src: {helm: 'PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0'},
-      tgt: {helm: null, map: []}
+      tgt: {helm: null, map: [], errType: HelmNotSupportedErrorType}
     }
   };
 
@@ -78,8 +80,8 @@ category('HelmHelper: removeGaps', () => {
         resErr = err;
       }
 
-      expect(resErr?.type == HelmNotSupportedErrorType, testData.tgt.helm === null,
-        'HelmNotSupportedError thrown expected');
+      if (testData.tgt.errType)
+        expect(resErr?.type, testData.tgt.errType, 'HelmNotSupportedError thrown expected');
     });
   }
 });

package/src/tests/helm-service-tests.ts

@@ -64,6 +64,7 @@ category('HelmService', () => {
     const logPrefix: string = `Helm: tests: HelmService: helm`;
     _package.logger.debug(`${logPrefix}, start`);
     const helmStr: string = 'PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$';
+    const monomerLib = monomerLibHelper.getMonomerLib();
     let consumerId: number | null = null;
     let taskAux: HelmAux | null = null;
     const event = new Subject<void>();
@@ -74,7 +75,7 @@ category('HelmService', () => {
         const task: RenderTask<HelmProps, HelmAux> = {
           name: 'test1',
           props: {
-            helm: helmStr,
+            helm: helmStr, monomerLib: monomerLib,
             backColor: DG.Color.fromHtml('#FFFFFF'),
             width: 300, height: 100,
           },

package/src/tests/parse-helm-tests.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 
 import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/utils/src/test';
-import {HelmType, IHelmDrawOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmType, IHelmEditorOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
@@ -50,8 +50,7 @@ category('parseHelm', () => {
 
     libHelper = await getMonomerLibHelper();
 
-    await timeout(async () => { userLibSettings = await getUserLibSettings(); }, 5000,
-      'get user lib settings for backup');
+    userLibSettings = await getUserLibSettings();
 
     // parseHelm is dependent on monomers RGroups available, test requires default monomer library
     await libHelper.loadMonomerLibForTests();
@@ -71,7 +70,7 @@ category('parseHelm', () => {
   for (const [testName, {src, tgt}] of Object.entries(testData)) {
     test(`woDOM-${testName}`, async () => {
       _testParseHelmWithoutDOM(src, tgt);
-    }, testName == 'RNA' ? {skipReason: 'GROK-16721'} : undefined);
+    });
   }
 });
 
@@ -79,7 +78,7 @@ function _testParseHelmWithEditor(src: string, tgt: TestTgtType): void {
   const io = org.helm.webeditor.IO;
 
   const editorHost = ui.div();
-  const editor = new JSDraw2.Editor<HelmType, IHelmDrawOptions>(editorHost, {viewonly: true});
+  const editor = new JSDraw2.Editor<HelmType, IHelmEditorOptions>(editorHost, {viewonly: true});
 
   const plugin = new org.helm.webeditor.Plugin(editor);
   const origin = new JSDraw2.Point(0, 0);
@@ -93,7 +92,7 @@ function _testParseHelmWithEditor(src: string, tgt: TestTgtType): void {
 function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
   const io = org.helm.webeditor.IO;
 
-  const molHandler = new JSDraw2.MolHandler<HelmType>();
+  const molHandler = new JSDraw2.MolHandler<HelmType, IHelmEditorOptions>();
 
   const plugin = new org.helm.webeditor.Plugin(molHandler);
   const origin = new JSDraw2.Point(0, 0);
@@ -104,4 +103,5 @@ function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
   expect(m.atoms.length, tgt.atomCount);
   expect(m.bonds.length, tgt.bondCount);
   expect(resHelm, tgt.helm);
+  expect(m.atoms.every((a) => !a.elem.startsWith('[') && !a.elem.endsWith(']')), true, 'Atoms should not contain square braces.');
 }

package/src/tests/properties-widget-tests.ts

@@ -4,12 +4,12 @@ import * as grok from 'datagrok-api/grok';
 
 import {after, before, category, expect, expectObject, test, timeout} from '@datagrok-libraries/utils/src/test';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {generateLongSequence} from '@datagrok-libraries/bio/src/utils/generator';
+import {getSeqHelper, ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {initHelmMainPackage} from './utils';
 import {getPropertiesDict, SeqPropertiesError} from '../widgets/properties-widget';
@@ -72,12 +72,14 @@ const TestsData: {
 };
 
 category('properties-widget', () => {
+  let seqHelper: ISeqHelper;
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
   let userLibSettings: any = null;
 
   before(async () => {
     await initHelmMainPackage();
+    seqHelper = await getSeqHelper();
 
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = getUserLibSettings();
@@ -101,7 +103,7 @@ category('properties-widget', () => {
     const df = DG.DataFrame.fromColumns(colList);
     const col = df.getCol('MSA');
 
-    const sh = SeqHandler.forColumn(col);
+    const sh = seqHelper.getSeqHandler(col);
     let errCatched = true;
     try {
       const _actPropDict = getPropertiesDict(col.get(0), sh);
@@ -111,17 +113,17 @@ category('properties-widget', () => {
     }
     expect(errCatched, true);
   });
-});
 
-function testPropertiesDict(
-  seq: string, units: NOTATION, separator: string | undefined, alphabet: ALPHABET | undefined, expPropDict: {}
-) {
-  const col = DG.Column.fromStrings('seq', [seq]) as DG.Column<string>;
-  col.semType = DG.SEMTYPE.MACROMOLECULE;
-  col.meta.units = units;
-  if (separator) col.setTag(bioTAGS.separator, separator);
-  if (alphabet) col.setTag(bioTAGS.alphabet, alphabet);
-  const sh = SeqHandler.forColumn(col);
-  const actPropDict = getPropertiesDict(seq, sh);
-  expectObject(actPropDict, expPropDict);
-}
+  function testPropertiesDict(
+    seq: string, units: NOTATION, separator: string | undefined, alphabet: ALPHABET | undefined, expPropDict: {}
+  ) {
+    const col = DG.Column.fromStrings('seq', [seq]) as DG.Column<string>;
+    col.semType = DG.SEMTYPE.MACROMOLECULE;
+    col.meta.units = units;
+    if (separator) col.setTag(bioTAGS.separator, separator);
+    if (alphabet) col.setTag(bioTAGS.alphabet, alphabet);
+    const sh = seqHelper.getSeqHandler(col);
+    const actPropDict = getPropertiesDict(seq, sh);
+    expectObject(actPropDict, expPropDict);
+  }
+});

package/src/utils/get-hovered.ts

@@ -85,9 +85,8 @@ export function getHoveredMonomerFallback(
 }
 
 export function getSeqMonomerFromHelmAtom(atom: HelmAtom): ISeqMonomer {
-  const polymerType = helmTypeToPolymerType(atom.bio!.type);
   const canonicalSymbol = atom.elem === GapOriginals[NOTATION.HELM] ? GAP_SYMBOL : atom.elem;
-  return {position: parseInt(atom.bio!.continuousId as string) - 1, symbol: atom.elem, biotype: atom.bio!.type};
+  return {position: parseInt(atom.bio!.continuousId as string) - 1, symbol: canonicalSymbol, biotype: atom.bio!.type};
 }
 
 /** Linear