@datagrok/bio 2.12.16 → 2.12.18

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.12.16",
+  "version": "2.12.18",
   "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",
@@ -34,12 +34,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.40.8",
+    "@datagrok-libraries/bio": "^5.41.2",
     "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/math": "^1.1.5",
     "@datagrok-libraries/ml": "^6.6.5",
     "@datagrok-libraries/tutorials": "^1.3.12",
-    "@datagrok-libraries/utils": "^4.2.0",
+    "@datagrok-libraries/utils": "^4.2.5",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -55,9 +55,9 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok/chem": "^1.9.0",
-    "@datagrok/dendrogram": "^1.2.27",
-    "@datagrok/helm": "^2.1.30",
+    "@datagrok/chem": "^1.9.2",
+    "@datagrok/dendrogram": "^1.2.29",
+    "@datagrok/helm": "^2.1.34",
     "@types/node": "^17.0.24",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",

package/src/package-test.ts

@@ -23,7 +23,7 @@ import './tests/WebLogo-project-tests';
 import './tests/WebLogo-layout-tests';
 import './tests/checkInputColumn-tests';
 import './tests/similarity-diversity-tests';
-import './tests/substructure-filters-tests';
+// import './tests/substructure-filters-tests';
 import './tests/pepsea-tests';
 import './tests/viewers';
 import './tests/seq-handler-tests';

package/src/package.ts

@@ -3,6 +3,8 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import '@datagrok-libraries/bio/src/types/helm';
+
 import {Options} from '@datagrok-libraries/utils/src/type-declarations';
 import {DimReductionBaseEditor, PreprocessFunctionReturnType}
   from '@datagrok-libraries/ml/src/functionEditors/dimensionality-reduction-editor';
@@ -55,13 +57,9 @@ import {SplitToMonomersFunctionEditor} from './function-edtiors/split-to-monomer
 import {splitToMonomersUI} from './utils/split-to-monomers';
 import {MonomerCellRenderer} from './utils/monomer-cell-renderer';
 import {BioPackage, BioPackageProperties} from './package-types';
-// import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
 import {getCompositionAnalysisWidget} from './widgets/composition-analysis-widget';
 import {MacromoleculeColumnWidget} from './utils/macromolecule-column-widget';
 import {addCopyMenuUI} from './utils/context-menu';
-import {getPolyToolDialog} from './utils/poly-tool/ui';
-import {PolyToolCsvLibHandler} from './utils/poly-tool/csv-to-json-monomer-lib-converter';
-import {_setPeptideColumn} from './utils/poly-tool/utils';
 import {getRegionDo} from './utils/get-region';
 import {GetRegionApp} from './apps/get-region-app';
 import {GetRegionFuncEditor} from './utils/get-region-func-editor';
@@ -77,7 +75,8 @@ import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimen
 import {
   ITSNEOptions, IUMAPOptions
 } from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/multi-column-dim-reducer';
-import {CyclizedNotationProvider} from './utils/poly-tool/cyclized';
+import {CyclizedNotationProvider} from './utils/cyclized';
+import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
 
 export const _package = new BioPackage();
 
@@ -87,8 +86,8 @@ export const _package = new BioPackage();
 //name: getMonomerLibHelper
 //description:
 //output: object result
-export function getMonomerLibHelper(): IMonomerLibHelper {
-  return MonomerLibManager.instance;
+export async function getMonomerLibHelper(): Promise<IMonomerLibHelper> {
+  return await MonomerLibManager.getInstance();
 }
 
 export let hydrophobPalette: SeqPaletteCustom | null = null;
@@ -105,12 +104,20 @@ export class SeqPaletteCustom implements SeqPalette {
   }
 }
 
+let monomerLib: IMonomerLib | null = null;
+
 //tags: init
 export async function initBio() {
-  _package.logger.debug('Bio: initBio(), started');
+  const logPrefix = 'Bio: initBio()';
+  _package.logger.debug(`${logPrefix}, start`);
   const module = await grok.functions.call('Chem:getRdKitModule');
+  const t1: number = window.performance.now();
   await Promise.all([
-    (async () => { await MonomerLibManager.instance.loadLibraries(); })(),
+    (async () => {
+      const monomerLibManager = await MonomerLibManager.getInstance();
+      await monomerLibManager.loadLibraries();
+      monomerLib = monomerLibManager.getBioLib();
+    })(),
     (async () => {
       const pkgProps = await _package.getProperties();
       const bioPkgProps = new BioPackageProperties(pkgProps);
@@ -118,9 +125,10 @@ export async function initBio() {
     })(),
   ]).finally(() => {
     _package.completeInit();
+    const t2: number = window.performance.now();
+    _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
   });
 
-  const monomerLib = MonomerLibManager.instance.getBioLib();
   const monomers: string[] = [];
   const logPs: number[] = [];
 
@@ -160,10 +168,16 @@ export function sequenceTooltip(col: DG.Column): DG.Widget<any> {
   return resWidget;
 }
 
+// Keep for backward compatibility
 //name: getBioLib
 //output: object monomerLib
 export function getBioLib(): IMonomerLib {
-  return MonomerLibManager.instance.getBioLib();
+  return monomerLib!;
+}
+
+// For sync internal use, on initialized package
+export function getMonomerLib(): IMonomerLib | null {
+  return monomerLib!;
 }
 
 //name: getSeqHandler
@@ -572,7 +586,8 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
 export async function toAtomicLevel(table: DG.DataFrame, seqCol: DG.Column, nonlinear: boolean): Promise<void> {
   const pi = DG.TaskBarProgressIndicator.create('Converting to atomic level ...');
   try {
-    await sequenceToMolfile(table, seqCol, nonlinear);
+    const monomerLib = (await getMonomerLibHelper()).getBioLib();
+    await sequenceToMolfile(table, seqCol, nonlinear, monomerLib);
   } finally {
     pi.close();
   }
@@ -685,19 +700,6 @@ export function convertDialog() {
   convert(col);
 }
 
-//top-menu: Bio | Convert | PolyTool
-//name: polyTool
-//description: Perform cyclization of polymers
-export async function polyTool(): Promise<void> {
-  let dialog: DG.Dialog;
-  try {
-    dialog = await getPolyToolDialog();
-    dialog.show();
-  } catch (err: any) {
-    grok.shell.warning('To run PolyTool, open a dataframe with macromolecules');
-  }
-}
-
 //name: monomerCellRenderer
 //tags: cellRenderer
 //meta.cellType: Monomer
@@ -1010,25 +1012,6 @@ export async function demoBioHelmMsaSequenceSpace(): Promise<void> {
   await demoBio05UI();
 }
 
-//name: polyToolColumnChoice
-//input: dataframe df [Input data table]
-//input: column macroMolecule
-export async function polyToolColumnChoice(df: DG.DataFrame, macroMolecule: DG.Column): Promise<void> {
-  _setPeptideColumn(macroMolecule);
-  await grok.data.detectSemanticTypes(df);
-}
-
-//name: createMonomerLibraryForPolyTool
-//input: file file
-export async function createMonomerLibraryForPolyTool(file: DG.FileInfo) {
-  const fileContent = await file.readAsString();
-  const libHandler = new PolyToolCsvLibHandler(file.fileName, fileContent);
-  const libObject = await libHandler.getJson();
-  const jsonFileName = file.fileName.replace(/\.csv$/, '.json');
-  const jsonFileContent = JSON.stringify(libObject, null, 2);
-  DG.Utils.download(jsonFileName, jsonFileContent);
-}
-
 //name: SDF to JSON Library
 //input: dataframe table
 export async function sdfToJsonLib(table: DG.DataFrame) {
@@ -1048,6 +1031,17 @@ export async function detectMacromoleculeProbe(file: DG.FileInfo, colName: strin
   await detectMacromoleculeProbeDo(csv, colName, probeCount);
 }
 
+//name: getMolFromHelm
+//input: dataframe df
+//input: column helmCol
+//input: bool chiralityEngine
+//output: column result
+export async function getMolFromHelm(
+  df: DG.DataFrame, helmCol: DG.Column<string>, chiralityEngine?: boolean
+): Promise<DG.Column<string>> {
+  return getMolColumnFromHelm(df, helmCol, chiralityEngine);
+}
+
 // -- Custom notation providers --
 
 //name: applyNotationProviderForCyclized

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

@@ -8,8 +8,6 @@ import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/sr
 import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
-import {MonomerLibFileManager} from '../utils/monomer-lib/library-file-manager/file-manager';
-import {MonomerLibFileEventManager} from '../utils/monomer-lib/library-file-manager/event-manager';
 
 
 category('monomerLibraries', () => {
@@ -51,8 +49,7 @@ category('monomerLibraries', () => {
   test('empty', async () => {
     // exclude all monomer libraries for empty set
     const libSettings = await getUserLibSettings();
-    const libFileEventManager = MonomerLibFileEventManager.getInstance();
-    const libFileManager = await MonomerLibFileManager.getInstance(libFileEventManager);
+    const libFileManager = await monomerLibHelper.getFileManager();
 
     let libFnList = libFileManager.getValidLibraryPaths();
     if (libFnList.length === 0)

package/src/tests/renderers-monomer-placer-tests.ts

@@ -8,8 +8,7 @@ import {category, test} from '@datagrok-libraries/utils/src/test';
 import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-
-import {MonomerLibManager} from '../utils/monomer-lib/lib-manager';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {_package} from '../package-test';
 
@@ -45,7 +44,7 @@ category('renderers: monomerPlacer', () => {
         'id1,m1-M-m3-mon4-mon5-N-T-MON8-N9\n' +
         'id2,m1-mon2-m3-mon4-mon5-Num--MON8-N9\n' +
         'id3,\n' + // empty
-        'id4,mon1-M-mon3-mon4-mon5---MON8-N9\n',
+        'id4,mon1-M-mon3-mon4-mon5---MON8-N9\n', // [ 5, 38, 71, 104, 137, 170, 203, 236, 269, 295 ]
       testList: [
         {src: {row: 0, x: -1}, tgt: {pos: null}},
         {src: {row: 1, x: 0}, tgt: {pos: null}},
@@ -59,7 +58,7 @@ category('renderers: monomerPlacer', () => {
         {src: {row: 2, x: 20}, tgt: {pos: null}}, // empty value
         {src: {row: 3, x: 170}, tgt: {pos: 4}},
         {src: {row: 3, x: 200}, tgt: {pos: 5}},
-        {src: {row: 3, x: 282}, tgt: {pos: null}},
+        {src: {row: 3, x: 297}, tgt: {pos: null}},
       ]
     },
     fastaMsa: {
@@ -88,6 +87,8 @@ id3,QHIRE--LT
 
   for (const [testName, testData] of Object.entries(tests)) {
     test(`getPosition-${testName}`, async () => {
+      const libHelper = await getMonomerLibHelper();
+      const monomerLib = libHelper.getBioLib();
       const df: DG.DataFrame = DG.DataFrame.fromCsv(testData.csv);
       await grok.data.detectSemanticTypes(df);
       const seqCol: DG.Column = df.getCol('seq');
@@ -95,7 +96,7 @@ id3,QHIRE--LT
       const monLength: number = 3;
       const charWidth: number = 7;
       const sepWidth: number = 12;
-      const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, () => {
+      const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, _package.logger, () => {
         const sh = SeqHandler.forColumn(seqCol);
         return {
           seqHandler: sh,
@@ -103,18 +104,18 @@ id3,QHIRE--LT
           separatorWidth: sepWidth,
           monomerToShort: monomerToShort,
           monomerLengthLimit: monLength,
-          monomerLib: MonomerLibManager.instance.getBioLib(),
         };
       });
 
+      const width: number = 10000;
       const testList = testData.testList;
       // simulate rendering
       for (let rowI: number = 0; rowI < seqCol.length; ++rowI)
-        colTemp.getCellMonomerLengths(rowI);
+        colTemp.getCellMonomerLengths(rowI, 10000);
 
       const errorList: string[] = [];
       for (const [test, _testI] of wu.enumerate(testList)) {
-        const res = {pos: colTemp.getPosition(test.src.row, test.src.x)};
+        const res = {pos: colTemp.getPosition(test.src.row, test.src.x, width)};
         if (test.tgt.pos != res.pos) {
           errorList.push(`Test src ${JSON.stringify(test.src)} expected tgt ${JSON.stringify(test.tgt)},` +
             ` but get ${JSON.stringify({res})}`);

package/src/tests/renderers-test.ts

@@ -56,7 +56,7 @@ category('renderers', () => {
 
   test('scatterPlotTooltip', async () => {
     await _testScatterPlotTooltip();
-  });
+  }, {skipReason: 'GROK-15679'});
 
   async function _rendererMacromoleculeFasta() {
     const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/FASTA.csv');

package/src/tests/scoring.ts

@@ -4,9 +4,9 @@ import * as DG from 'datagrok-api/dg';
 
 import {category, test, expectFloat, before, after} from '@datagrok-libraries/utils/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
-import {sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
+import {getMonomerLibHelper, sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
 import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';

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

@@ -185,7 +185,8 @@ category('bio-substructure-filters', async () => {
       dlg.close();
     }
     await filter.awaitRendered();
-  });
+    await delay(3000); //TODO: await for grid.onLookChanged
+  }, {skipReason: 'GROK-15678'});
 
   // Generates unhandled exception accessing isFiltering before bioFilter created
   test('helm-view', async () => {
@@ -308,7 +309,8 @@ 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-15678'});
 
   // two seq columns
 

package/src/tests/to-atomic-level-tests.ts

@@ -7,7 +7,7 @@ import wu from 'wu';
 
 import {before, after, category, test, expectArray, expect} from '@datagrok-libraries/utils/src/test';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {

package/src/tests/utils.ts

@@ -2,10 +2,12 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {delay, expect, testEvent} from '@datagrok-libraries/utils/src/test';
+import {asRenderer, IRenderer, isRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 
 import {startDockerContainer} from '../utils/docker';
 
 import {_package} from '../package-test';
+import {CellRendererBackBase, getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 export async function loadFileAsText(name: string): Promise<string> {
   return await _package.files.readAsText(name);
@@ -38,4 +40,17 @@ export async function awaitGrid(grid: DG.Grid, timeout: number = 5000): Promise<
   await delay(0);
   await testEvent(grid.onAfterDrawContent, () => {},
     () => { grid.invalidate(); }, timeout);
+
+  const colCount = grid.columns.length;
+  for (let colI = 0; colI < colCount; ++colI) {
+    const gridCol = grid.columns.byIndex(colI);
+    if (gridCol) {
+      const gridCell = grid.cell(gridCol.name, 0);
+      const [_gridCol, _tableCol, temp] =
+        getGridCellRendererBack<void, CellRendererBackBase<void>>(gridCell);
+
+      const renderer = asRenderer(temp.rendererBack);
+      if (renderer) await renderer.awaitRendered();
+    }
+  }
 }

package/src/utils/cell-renderer.ts

@@ -3,7 +3,6 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import wu from 'wu';
-import {Unsubscribable} from 'rxjs';
 
 import {printLeftOrCentered, DrawStyle, TAGS as mmcrTAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
@@ -22,7 +21,8 @@ import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-ha
 import {ISeqSplitted, SeqSplittedBase} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {alphabetPolymerTypes, IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {alphabetPolymerTypes, IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 import {
   Temps as mmcrTemps, Tags as mmcrTags,
@@ -30,14 +30,16 @@ import {
 } from '../utils/cell-renderer-consts';
 import * as C from './constants';
 
-import {_package, getBioLib} from '../package';
+import {_package, getMonomerLib} from '../package';
 
 type TempType = { [tagName: string]: any };
 
 const undefinedColor = 'rgb(100,100,100)';
 const monomerToShortFunction: MonomerToShortFunc = monomerToShort;
 
-function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number, dpr: number): number {
+function getUpdatedWidth(
+  grid: DG.Grid | null | undefined, g: CanvasRenderingContext2D, x: number, w: number, dpr: number
+): number {
   return !!grid ? Math.max(Math.min(grid.canvas.width / dpr - x, w)) : Math.max(g.canvas.width / dpr - x, 0);
 }
 
@@ -63,27 +65,6 @@ type RendererGridCellTemp = {
   [mmcrTemps.monomerPlacer]: MonomerPlacer
 }
 
-function getRendererFridCellTempTemp(gridCell: DG.GridCell): RendererGridCellTemp {
-  /** Primarily store/get MonomerPlacer at GridColumn, fallback at (Table) Column for scatter plot tooltip  */
-  let temp: RendererGridCellTemp | null = null;
-
-  let gridCol: DG.GridColumn | null = null;
-  try { gridCol = gridCell.gridColumn; } catch { gridCol = null; }
-  temp = gridCol && gridCol.dart ? gridCol.temp as RendererGridCellTemp : null;
-
-  if (!temp) {
-    let tableCol: DG.Column | null = null;
-    try { tableCol = gridCell.cell.column; } catch { tableCol = null; }
-    if (!tableCol) {
-      const k = 42;
-    }
-    temp = tableCol ? tableCol.temp as RendererGridCellTemp : null;
-  }
-  if (temp === null)
-    throw new Error(`Monomer placer store (GridColumn or Column) not found.`);
-  return temp;
-}
-
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   private padding: number = 5;
 
@@ -105,9 +86,9 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
     //   return;
 
-    const tableCol: DG.Column = gridCell.cell.column;
-    //const tableColTemp: TempType = tableCol.temp;
-    const seqColTemp: MonomerPlacer = getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer];
+    const [_gridCol, tableCol, temp] =
+      getGridCellRendererBack<string, MonomerPlacer>(gridCell);
+    const seqColTemp: MonomerPlacer = temp['rendererBack'];
     if (!seqColTemp) return; // Can do nothing without precalculated data
 
     const gridCellBounds: DG.Rect = gridCell.bounds;
@@ -119,9 +100,9 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     //   maxLengthWordsSum[posI] = maxLengthWordsSum[posI - 1] + maxLengthWords[posI];
     // const maxIndex = maxLengthWords.length;
     const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
-    const left: number | null = seqColTemp.getPosition(gridCell.tableRowIndex!, argsX);
+    const left: number | null = seqColTemp.getPosition(gridCell.tableRowIndex!, argsX, gridCellBounds.width);
 
-    const seqCList: SeqSplittedBase = SeqHandler.forColumn(seqColTemp.col)
+    const seqCList: SeqSplittedBase = SeqHandler.forColumn(tableCol)
       .getSplitted(gridCell.tableRowIndex!).canonicals;
     if (left !== null && left < seqCList.length) {
       const monomerSymbol: string = seqCList[left];
@@ -133,8 +114,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
           const alphabet = sh.alphabet ?? ALPHABET.UN;
           const polymerType = alphabetPolymerTypes[alphabet as ALPHABET];
 
-          const lib: IMonomerLib = seqColTemp.props.monomerLib!;
-          return lib.getTooltip(polymerType, monomerSymbol);
+          const lib: IMonomerLib | null = getMonomerLib();
+          return lib ? lib.getTooltip(polymerType, monomerSymbol) : ui.divText('Monomer library is not available');
         })();
       }
       tooltipElements.push(monomerDiv);
@@ -162,23 +143,17 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     _cellStyle: DG.GridCellStyle
   ): void {
     const logPrefix: string = 'MacromoleculeSequenceCellRenderer.render()';
+
+    const dpr = window.devicePixelRatio;
+    const [gridCol, tableCol, _temp] =
+      getGridCellRendererBack<string, MonomerPlacer>(gridCell);
+    if (!tableCol) return;
+    const tableColTemp: TempType = tableCol.temp;
+
     let gapLength = 0;
     const msaGapLength = 8;
     let maxLengthOfMonomer = 50; // in case of long monomer representation, do not limit max length
 
-    // TODO: Store temp data to GridColumn
-    // Now the renderer requires data frame table Column underlying GridColumn
-    let grid: DG.Grid | undefined = undefined;
-    try { grid = gridCell.grid; } catch (err: any) {
-      grid = undefined;
-      const [errMsg, errStack] = errInfo(err);
-      _package.logger.error(errMsg, undefined, errStack);
-    }
-    const tableCol: DG.Column = gridCell.cell.column;
-    if (!grid || !tableCol) return;
-
-    const tableColTemp: TempType = tableCol.temp;
-
     // Cell renderer settings
     const tempMonomerWidth: string | null = tableColTemp[tempTAGS.monomerWidth];
     const monomerWidth: string = (tempMonomerWidth != null) ? tempMonomerWidth : 'short';
@@ -190,44 +165,41 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         (!isNaN(tagMaxMonomerLength) ? tagMaxMonomerLength : _package.properties?.MaxMonomerLength) ?? 4;
     }
 
-    let seqColTemp: MonomerPlacer = getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer];
+    const [_gc, _tc, temp] =
+      getGridCellRendererBack<string, MonomerPlacer>(gridCell);
+    let seqColTemp: MonomerPlacer = temp.rendererBack;
     if (!seqColTemp) {
-      seqColTemp = new MonomerPlacer(grid, tableCol,
+      seqColTemp = temp.rendererBack = new MonomerPlacer(gridCol, tableCol, _package.logger,
         () => {
           const sh = SeqHandler.forColumn(tableCol);
           return {
             seqHandler: sh,
             monomerCharWidth: 7, separatorWidth: !sh.isMsa() ? gapLength : msaGapLength,
             monomerToShort: monomerToShortFunction, monomerLengthLimit: maxLengthOfMonomer,
-            monomerLib: getBioLib()
           };
         });
     }
 
-    if (tableCol.tags[mmcrTags.RendererSettingsChanged] === rendererSettingsChangedState.true) {
-      gapLength = tableColTemp[mmcrTemps.gapLength] as number ?? gapLength;
-      // this event means that the mm renderer settings have changed, particularly monomer representation and max width.
-      seqColTemp.setMonomerLengthLimit(maxLengthOfMonomer);
-      seqColTemp.setSeparatorWidth(seqColTemp.isMsa() ? msaGapLength : gapLength);
-      tableCol.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.false);
-    }
-
-    const [maxLengthWords, maxLengthWordsSum]: [number[], number[]] =
-      seqColTemp.getCellMonomerLengths(gridCell.tableRowIndex!);
-    const _maxIndex = maxLengthWords.length;
-
-    // Store updated seqColTemp to the col temp
-    if (seqColTemp.updated) getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer] = seqColTemp;
-
     g.save();
     try {
-      const dpr = window.devicePixelRatio;
-      const grid = gridCell.gridRow !== -1 ? gridCell.grid : null;
+      if (tableCol.tags[mmcrTags.RendererSettingsChanged] === rendererSettingsChangedState.true) {
+        gapLength = tableColTemp[mmcrTemps.gapLength] as number ?? gapLength;
+        // this event means that the mm renderer settings have changed,
+        // particularly monomer representation and max width.
+        seqColTemp.setMonomerLengthLimit(maxLengthOfMonomer);
+        seqColTemp.setSeparatorWidth(seqColTemp.isMsa() ? msaGapLength : gapLength);
+        tableCol.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.false);
+      }
+
+      const [maxLengthWords, maxLengthWordsSum]: [number[], number[]] =
+        seqColTemp.getCellMonomerLengths(gridCell.tableRowIndex!, w);
+      const _maxIndex = maxLengthWords.length;
+
       const value: any = gridCell.cell.value;
       const rowIdx = gridCell.cell.rowIndex;
       const paletteType = tableCol.getTag(bioTAGS.alphabet);
       const minDistanceRenderer = 50;
-      w = getUpdatedWidth(grid, g, x, w, dpr);
+      w = getUpdatedWidth(gridCol?.grid, g, x, w, dpr);
       g.beginPath();
       g.rect(x + this.padding, y + this.padding, w - this.padding - 1, h - this.padding * 2);
       g.clip();
@@ -241,7 +213,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       const palette = getPaletteByType(paletteType);
 
       const separator = tableCol.getTag(bioTAGS.separator) ?? '';
-      const splitLimit = w / 5;
+      const minMonWidth = seqColTemp.props.separatorWidth + 1 * seqColTemp.props.monomerCharWidth;
+      const splitLimit = w / minMonWidth;
       const sh = SeqHandler.forColumn(tableCol);
 
       const tempReferenceSequence: string | null = tableColTemp[tempTAGS.referenceSequence];
@@ -265,7 +238,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       if (aligned && aligned.includes('MSA') && units == NOTATION.SEPARATOR)
         drawStyle = DrawStyle.MSA;
 
-      for (let posIdx: number = 0; posIdx < subParts.length; ++posIdx) {
+      const visibleSeqLength = Math.min(subParts.length, splitLimit);
+      for (let posIdx: number = 0; posIdx < visibleSeqLength; ++posIdx) {
         const amino: string = subParts.getOriginal(posIdx);
         color = palette.get(amino);
         g.fillStyle = undefinedColor;
@@ -277,8 +251,9 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         if (minDistanceRenderer > w) break;
       }
     } catch (err: any) {
-      const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Error \'undefined\'';
-      _package.logger.error(`Bio: MacromoleculeSequenceCellRenderer.render() error: ${errMsg}`);
+      const [errMsg, errStack] = errInfo(err);
+      seqColTemp.logger.error(errMsg, undefined, errStack);
+      seqColTemp.errors.push(err);
       //throw err; // Do not throw to prevent disabling renderer
     } finally {
       g.restore();

package/src/utils/{poly-tool/cyclized.ts → cyclized.ts}

@@ -1,8 +1,5 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {GAP_SYMBOL, INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {GAP_SYMBOL, INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc}
+  from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {getSplitterWithSeparator, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -33,9 +30,8 @@ export class CyclizedSeqSplitted extends StringListSeqSplitted {
     if (!this._canonicals) {
       const len = this.length;
       this._canonicals = new Array<string>(len);
-      for (let posIdx = 0; posIdx < len; ++posIdx) {
+      for (let posIdx = 0; posIdx < len; ++posIdx)
         this._canonicals[posIdx] = this.getCanonical(posIdx);
-      }
     }
     return this._canonicals;
   }