@datagrok/peptides 1.14.1 → 1.15.1

package/src/utils/misc.ts

@@ -36,7 +36,7 @@ export function scaleActivity(activityCol: DG.Column<number>, scaling: C.SCALING
       const val = activityColData[i];
       return val === DG.FLOAT_NULL || val === DG.INT_NULL ? val : formula(val);
     });
-
+  scaledCol.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
   return scaledCol;
 }
 
@@ -131,4 +131,5 @@ export function setGridProps(grid: DG.Grid): void {
   grid.props.showRowHeader = false;
   grid.props.showCurrentRowIndicator = false;
   grid.root.style.width = '100%';
+  grid.root.style.maxWidth = '100%';
 }

package/src/utils/parallel-mutation-cliffs.ts

@@ -0,0 +1,106 @@
+
+import * as type from './types';
+
+export type ParallelMutationReturnType = {
+    // monomers1: string[],
+    // monomers2: string[],
+    pos: string[],
+    seq1Idxs: Uint32Array,
+    seq2Idxs: Uint32Array,
+}
+export class ParallelMutationCliffs {
+  private _workers: Worker[];
+  private _workerCount: number;
+
+  constructor() {
+    const threadCount = navigator.hardwareConcurrency;
+    this._workerCount = Math.max(threadCount - 2, 1);
+    this._workers = new Array(this._workerCount).fill(null)
+      .map(() => new Worker(new URL('../workers/mutation-cliffs-worker', import.meta.url)));
+  }
+
+  public async calc(activityArray: type.RawData, monomerInfoArray: type.RawColumn[],
+    settings: type.PeptidesSettings = {},
+    targetOptions: {targetCol?: type.RawColumn | null, currentTarget?: string | null} = {},
+  ): Promise<type.MutationCliffs> {
+    const substitutionsInfo: type.MutationCliffs = new Map();
+    try {
+      const currentTargetIdx = targetOptions.targetCol?.cat!.indexOf(targetOptions.currentTarget!) ?? -1;
+
+      const len = activityArray.length;
+      const promises = new Array<Promise<ParallelMutationReturnType>>(this._workerCount);
+      const matSize = len * (len - 1) / 2; // size of reduced upper triangular matrix
+      this._workerCount = Math.min(this._workerCount, matSize);
+      const chunkSize = matSize / this._workerCount;
+      // monomerInfoArray[m].cat and targetCol can contain some function from datagrok-api,
+      //which the worker can't serialize and fails. so we need to remove it
+      monomerInfoArray.forEach((monomerInfo) => {
+        monomerInfo.cat = monomerInfo.cat?.slice();
+      });
+      targetOptions.targetCol?.cat && (targetOptions.targetCol.cat = targetOptions.targetCol.cat.slice());
+      for (let idx = 0; idx < this._workerCount; idx++) {
+        promises[idx] = new Promise((resolveWorker, rejectWorker) => {
+          const startIdx = Math.floor(idx * chunkSize);
+          const endIdx = idx === this._workerCount - 1 ? matSize : Math.floor((idx + 1) * chunkSize);
+          this._workers[idx].postMessage(
+            {startIdx, endIdx, activityArray, monomerInfoArray, settings, currentTargetIdx, targetOptions});
+          this._workers[idx].onmessage = ({data: {pos, seq1Idxs, seq2Idxs, error}}): void => {
+            if (error) {
+              this._workers[idx]?.terminate();
+              rejectWorker(error);
+            } else {
+              this._workers[idx].terminate();
+              resolveWorker({pos, seq1Idxs, seq2Idxs});
+            }
+          };
+        });
+      }
+
+      const results = await Promise.all(promises);
+      const monomerPositionsMap = new Map<string, number>();
+      monomerInfoArray.forEach((monomerInfo, i) => {
+        monomerPositionsMap.set(monomerInfo.name, i);
+      });
+      results.filter(Boolean).forEach((result) => {
+        for (let i = 0; i< result.pos.length; i++) {
+        //getting monomers from monomerInfoArray by position
+          const monomerPos = monomerPositionsMap.get(result.pos[i])!;
+          const monomer1Cat = monomerInfoArray[monomerPos].rawData[result.seq1Idxs[i]];
+          const monomer1 = monomerInfoArray[monomerPos].cat![monomer1Cat];
+          const monomer2Cat = monomerInfoArray[monomerPos].rawData[result.seq2Idxs[i]];
+          const monomer2 = monomerInfoArray[monomerPos].cat![monomer2Cat];
+
+          // filling map
+          if (!substitutionsInfo.has(monomer1))
+            substitutionsInfo.set(monomer1, new Map());
+          if (!substitutionsInfo.has(monomer2))
+            substitutionsInfo.set(monomer2, new Map());
+          const position1Map = substitutionsInfo.get(monomer1)!;
+          const position2Map = substitutionsInfo.get(monomer2)!;
+          if (!position1Map.has(result.pos[i]))
+            position1Map.set(result.pos[i], new Map());
+          if (!position2Map.has(result.pos[i]))
+            position2Map.set(result.pos[i], new Map());
+          const indexes1Map = position1Map.get(result.pos[i])!;
+          const indexes2Map = position2Map.get(result.pos[i])!;
+          if (!indexes1Map.has(result.seq1Idxs[i]))
+            indexes1Map.set(result.seq1Idxs[i], []);
+          if (!indexes2Map.has(result.seq2Idxs[i]))
+            indexes2Map.set(result.seq2Idxs[i], []);
+          const indexes1 = indexes1Map.get(result.seq1Idxs[i])!;
+          const indexes2 = indexes2Map.get(result.seq2Idxs[i])!;
+          (indexes1 as number[]).push(result.seq2Idxs[i]);
+          (indexes2 as number[]).push(result.seq1Idxs[i]);
+        }
+      });
+    } catch (error) {
+      this.terminate();
+      console.error(error);
+    }
+    return substitutionsInfo;
+  }
+
+  public terminate(): void {
+    this._workers?.forEach((worker) => worker?.terminate());
+  }
+}

package/src/utils/types.ts

@@ -18,7 +18,6 @@ export type PeptidesSettings = {
   clustersColumnName?: string,
   targetColumnName?: string,
   scaling?: SCALING_METHODS,
-  isBidirectional?: boolean,
   showMonomerPosition?: boolean,
   showMostPotentResidues?: boolean,
   showLogoSummaryTable?: boolean,
@@ -39,6 +38,7 @@ export type DrawOptions = {
   marginHorizontal?: number,
   headerStyle?: string,
   textHeight?: number,
+  selectionWidth?: number,
 };
 
 export type StatsInfo = {

package/src/viewers/logo-summary.ts

@@ -13,6 +13,7 @@ import {getActivityDistribution, getDistributionLegend, getStatsTableMap} from '
 import {getStatsSummary, prepareTableForHistogram} from '../utils/misc';
 import BitArray from '@datagrok-libraries/utils/src/bit-array';
 import {SelectionItem} from '../utils/types';
+import {_package} from '../package';
 
 const getAggregatedColName = (aggF: string, colName: string): string => `${aggF}(${colName})`;
 
@@ -213,7 +214,6 @@ export class LogoSummaryTable extends DG.JsViewer {
     this.viewerGrid.sort([C.LST_COLUMN_NAMES.MEMBERS], [false]);
     this.updateFilter();
     const gridClustersCol = this.viewerGrid.col(C.LST_COLUMN_NAMES.CLUSTER)!;
-    // gridClustersCol.column!.name = C.LST_COLUMN_NAMES.CLUSTER;
     gridClustersCol.visible = true;
     this.viewerGrid.columns.setOrder([C.LST_COLUMN_NAMES.CLUSTER, C.LST_COLUMN_NAMES.MEMBERS,
       C.LST_COLUMN_NAMES.WEB_LOGO, C.LST_COLUMN_NAMES.DISTRIBUTION, C.LST_COLUMN_NAMES.MEAN_DIFFERENCE,
@@ -223,7 +223,7 @@ export class LogoSummaryTable extends DG.JsViewer {
 
     const webLogoCache = new DG.LruCache<number, DG.Viewer & IWebLogoViewer>();
     const distCache = new DG.LruCache<number, DG.Viewer<DG.IHistogramLookSettings>>();
-    const maxSequenceLen = this.model.splitSeqDf.columns.length;
+    const maxSequenceLen = this.model.positionColumns.toArray().length;
     const webLogoGridCol = this.viewerGrid.columns.byName(C.LST_COLUMN_NAMES.WEB_LOGO)!;
     webLogoGridCol.cellType = 'html';
     webLogoGridCol.width = 350;
@@ -269,7 +269,7 @@ export class LogoSummaryTable extends DG.JsViewer {
             const webLogoTable = this.createWebLogoDf(pepCol, clusterBitSet);
             viewer = await webLogoTable.plot
               .fromType('WebLogo', {positionHeight: this.webLogoMode, horizontalAlignment: HorizontalAlignments.LEFT,
-                maxHeight: 1000, minHeight: height, positionWidth: positionWidth});
+                maxHeight: 1000, minHeight: height, positionWidth: positionWidth, showPositionLabels: false});
             webLogoCache.set(currentRowIdx, viewer);
           }
           gridCell.element = viewer.root;
@@ -302,7 +302,7 @@ export class LogoSummaryTable extends DG.JsViewer {
       }
     });
     this.viewerGrid.root.addEventListener('mouseleave', (_ev) => this.model.unhighlight());
-    this.viewerGrid.onCurrentCellChanged.subscribe((gridCell) => {
+    DG.debounce(this.viewerGrid.onCurrentCellChanged, 500).subscribe((gridCell) => {
       if (!gridCell.isTableCell)
         return;
 
@@ -328,6 +328,10 @@ export class LogoSummaryTable extends DG.JsViewer {
       const selection = this.getCluster(gridCell);
       this.model.modifyClusterSelection(selection, {shiftPressed: ev.shiftKey, ctrlPressed: ev.ctrlKey});
       this.viewerGrid.invalidate();
+
+      _package.files.readAsText('help/logo-summary-table.md').then((text) => {
+        grok.shell.windows.help.showHelp(ui.markdown(text));
+      }).catch((e) => grok.log.error(e));
     });
     this.viewerGrid.onCellTooltip((gridCell, x, y) => {
       if (!gridCell.isTableCell) {
@@ -347,7 +351,6 @@ export class LogoSummaryTable extends DG.JsViewer {
     gridProps.allowRowSelection = false;
     gridProps.allowBlockSelection = false;
     gridProps.allowColSelection = false;
-    gridProps.showRowHeader = false;
     gridProps.showCurrentRowIndicator = false;
 
     return this.viewerGrid;
@@ -381,7 +384,7 @@ export class LogoSummaryTable extends DG.JsViewer {
 
     this.bitsets.push(currentSelection.clone());
 
-    const newClusterName = viewerDfCols.getUnusedName('New Cluster');
+    const newClusterName = this.model.df.columns.getUnusedName('New Cluster');
     const aggregatedValues: {[colName: string]: number} = {};
     const aggColsEntries = Object.entries(this.model.settings.columns ?? {});
     for (const [colName, aggFn] of aggColsEntries) {

package/src/viewers/sar-viewer.ts

@@ -9,6 +9,7 @@ import {PeptidesModel, PositionStats, VIEWER_TYPE} from '../model';
 import wu from 'wu';
 import {SelectionItem} from '../utils/types';
 import {Stats} from '../utils/statistics';
+import {_package} from '../package';
 
 export enum SELECTION_MODE {
   MUTATION_CLIFFS = 'Mutation Cliffs',
@@ -26,7 +27,7 @@ export class MonomerPosition extends DG.JsViewer {
   _titleHost = ui.divText(SELECTION_MODE.MUTATION_CLIFFS, {id: 'pep-viewer-title'});
   _viewerGrid!: DG.Grid;
   _model!: PeptidesModel;
-  colorCol: string;
+  color: string;
   aggregation: string;
   target: string;
   keyPressed: boolean = false;
@@ -36,7 +37,7 @@ export class MonomerPosition extends DG.JsViewer {
     super();
     this.target = this.string(MONOMER_POSITION_PROPERTIES.TARGET, null,
       {category: SELECTION_MODE.MUTATION_CLIFFS, choices: []});
-    this.colorCol = this.string(MONOMER_POSITION_PROPERTIES.COLOR_COLUMN_NAME, C.COLUMNS_NAMES.ACTIVITY_SCALED,
+    this.color = this.string(MONOMER_POSITION_PROPERTIES.COLOR_COLUMN_NAME, C.COLUMNS_NAMES.ACTIVITY_SCALED,
       {category: SELECTION_MODE.INVARIANT_MAP,
         choices: wu(grok.shell.t.columns.numerical).toArray().map((col) => col.name)});
     this.aggregation = this.string(MONOMER_POSITION_PROPERTIES.AGGREGATION, DG.AGG.AVG,
@@ -81,14 +82,14 @@ export class MonomerPosition extends DG.JsViewer {
   onPropertyChanged(property: DG.Property): void {
     super.onPropertyChanged(property);
     if (property.name === MONOMER_POSITION_PROPERTIES.TARGET)
-      this.model.updateMutationCliffs();
+      this.model.updateMutationCliffs().then(() => this.render(true));
 
-    this.render();
+    this.render(true);
   }
 
   createMonomerPositionDf(): DG.DataFrame {
     const uniqueMonomers = new Set<string>();
-    const splitSeqCols = this.model.splitSeqDf.columns;
+    const splitSeqCols = this.model.positionColumns.toArray();
     for (const col of splitSeqCols) {
       const colCat = col.categories;
       for (const cat of colCat) {
@@ -111,12 +112,11 @@ export class MonomerPosition extends DG.JsViewer {
     const monomerPositionDf = this.createMonomerPositionDf();
     this.viewerGrid = monomerPositionDf.plot.grid();
     this.viewerGrid.sort([C.COLUMNS_NAMES.MONOMER]);
-    this.viewerGrid.columns.setOrder([C.COLUMNS_NAMES.MONOMER, ...this.model.splitSeqDf.columns.names()]);
+    this.viewerGrid.columns.setOrder([C.COLUMNS_NAMES.MONOMER, ...this.model.positionColumns.toArray().map((col) => col.name)]);
     const monomerCol = monomerPositionDf.getCol(C.COLUMNS_NAMES.MONOMER);
     CR.setMonomerRenderer(monomerCol, this.model.alphabet);
     this.viewerGrid.onCellRender.subscribe((args: DG.GridCellRenderArgs) => renderCell(args, this.model,
-      this.mode === SELECTION_MODE.INVARIANT_MAP, this.dataFrame.getCol(this.colorCol),
-      this.aggregation as DG.AggregationType));
+      this.mode === SELECTION_MODE.INVARIANT_MAP, this.dataFrame.getCol(this.color), this.aggregation as DG.AGG));
 
     this.viewerGrid.onCellTooltip((gridCell: DG.GridCell, x: number, y: number) => {
       if (!gridCell.isTableCell) {
@@ -128,7 +128,7 @@ export class MonomerPosition extends DG.JsViewer {
       return this.model.showTooltip(monomerPosition, x, y, true);
     });
     this.viewerGrid.root.addEventListener('mouseleave', (_ev) => this.model.unhighlight());
-    this.viewerGrid.onCurrentCellChanged.subscribe((gridCell: DG.GridCell) => {
+    DG.debounce(this.viewerGrid.onCurrentCellChanged, 500).subscribe((gridCell: DG.GridCell) => {
       try {
         if (!this.keyPressed)
           return;
@@ -166,11 +166,19 @@ export class MonomerPosition extends DG.JsViewer {
         this.model.modifyMutationCliffsSelection(monomerPosition, {shiftPressed: ev.shiftKey, ctrlPressed: ev.ctrlKey});
 
       this.viewerGrid.invalidate();
+
+      this.showHelp();
     });
 
     setViewerGridProps(this.viewerGrid, false);
   }
 
+  showHelp(): void {
+    _package.files.readAsText('help/monomer-position.md').then((text) => {
+      grok.shell.windows.help.showHelp(ui.markdown(text));
+    }).catch((e) => grok.log.error(e));
+  }
+
   getMonomerPosition(gridCell: DG.GridCell): SelectionItem {
     return {monomerOrCluster: gridCell.cell.dataFrame.get(C.COLUMNS_NAMES.MONOMER, gridCell!.tableRowIndex!) as string,
       positionOrClusterType: gridCell!.tableColumn!.name};
@@ -186,6 +194,7 @@ export class MonomerPosition extends DG.JsViewer {
           invariantMapMode.value = false;
           mutationCliffsMode.value = true;
           this.mode = SELECTION_MODE.MUTATION_CLIFFS;
+          this.showHelp();
         });
         mutationCliffsMode.setTooltip('Statistically significant changes in activity');
         const invariantMapMode = ui.boolInput(SELECTION_MODE.INVARIANT_MAP, this.mode === SELECTION_MODE.INVARIANT_MAP);
@@ -193,6 +202,7 @@ export class MonomerPosition extends DG.JsViewer {
           mutationCliffsMode.value = false;
           invariantMapMode.value = true;
           this.mode = SELECTION_MODE.INVARIANT_MAP;
+          this.showHelp();
         });
         invariantMapMode.setTooltip('Number of sequences having monomer-position');
         const setDefaultProperties = (input: DG.InputBase): void => {
@@ -351,13 +361,13 @@ export class MostPotentResidues extends DG.JsViewer {
         return false;
       return this.model.showTooltip(monomerPosition, x, y, true);
     });
-    this.viewerGrid.onCurrentCellChanged.subscribe((gridCell: DG.GridCell) => {
+    DG.debounce(this.viewerGrid.onCurrentCellChanged, 500).subscribe((gridCell: DG.GridCell) => {
       try {
         if ((this.keyPressed && mostPotentResiduesDf.currentCol.name !== C.COLUMNS_NAMES.MEAN_DIFFERENCE) || !this.keyPressed)
           return;
         const monomerPosition = this.getMonomerPosition(gridCell);
         if (this.currentGridRowIdx !== null) {
-          const previousMonomerPosition = this.getMonomerPosition(this.viewerGrid.cell(C.COLUMNS_NAMES.MEAN_DIFFERENCE, this.currentGridRowIdx));
+          const previousMonomerPosition = this.getMonomerPosition(this.viewerGrid.cell('Diff', this.currentGridRowIdx));
           this.model.modifyMutationCliffsSelection(previousMonomerPosition, {shiftPressed: true, ctrlPressed: true}, false);
         }
         if (this.model.mutationCliffs?.get(monomerPosition.monomerOrCluster)?.get(monomerPosition.positionOrClusterType)?.size)
@@ -380,6 +390,10 @@ export class MostPotentResidues extends DG.JsViewer {
         return;
       this.model.modifyMutationCliffsSelection(monomerPosition, {shiftPressed: ev.shiftKey, ctrlPressed: ev.ctrlKey});
       this.viewerGrid.invalidate();
+
+      _package.files.readAsText('help/most-potent-residues.md').then((text) => {
+        grok.shell.windows.help.showHelp(ui.markdown(text));
+      }).catch((e) => grok.log.error(e));
     });
     const mdCol: DG.GridColumn = this.viewerGrid.col(C.COLUMNS_NAMES.MEAN_DIFFERENCE)!;
     mdCol.name = 'Diff';
@@ -405,8 +419,8 @@ export class MostPotentResidues extends DG.JsViewer {
 }
 
 function renderCell(args: DG.GridCellRenderArgs, model: PeptidesModel, isInvariantMap?: boolean,
-  colorCol?: DG.Column<number>, colorAgg?: DG.AggregationType, renderNums?: boolean): void {
-  const renderColNames = [...model.splitSeqDf.columns.names(), C.COLUMNS_NAMES.MEAN_DIFFERENCE];
+  colorCol?: DG.Column<number>, colorAgg?: DG.AGG, renderNums?: boolean): void {
+  const renderColNames = [...model.positionColumns.toArray().map((col) => col.name), C.COLUMNS_NAMES.MEAN_DIFFERENCE];
   const canvasContext = args.g;
   const bound = args.bounds;
 
@@ -464,7 +478,7 @@ function renderCell(args: DG.GridCellRenderArgs, model: PeptidesModel, isInvaria
       canvasContext, currentMonomer, currentPosition, model.invariantMapSelection, value, bound, color);
   } else {
     CR.renderMutationCliffCell(canvasContext, currentMonomer, currentPosition, model.monomerPositionStats, bound,
-      model.mutationCliffsSelection, model.mutationCliffs, model.settings.isBidirectional, renderNums);
+      model.mutationCliffsSelection, model.mutationCliffs, renderNums);
   }
   args.preventDefault();
   canvasContext.restore();

package/src/widgets/mutation-cliffs.ts

@@ -147,11 +147,11 @@ export function mutationCliffsWidget(table: DG.DataFrame, model: PeptidesModel):
 
   const gridCols = model.analysisView.grid.columns;
   const originalGridColCount = gridCols.length;
-  const positionColumns = model.splitSeqDf.columns;
+  const positionColumns = model.positionColumns.toArray().map((col) => col.name);
   const columnNames: string[] = [];
   for (let colIdx = 1; colIdx < originalGridColCount; colIdx++) {
     const gridCol = gridCols.byIndex(colIdx);
-    if (gridCol?.name === model.settings.sequenceColumnName || (gridCol?.visible === true && !positionColumns.contains(gridCol.name)))
+    if (gridCol?.name === model.settings.sequenceColumnName || (gridCol?.visible === true && !positionColumns.includes(gridCol.name)))
       columnNames.push(gridCol!.name);
   }
 

package/src/widgets/peptides.ts

@@ -122,7 +122,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>): {h
     bitsetChanged.unsubscribe();
     if (sequencesCol) {
       const model = await startAnalysis(activityColumnChoice.value!, sequencesCol, clustersColumnChoice.value, df,
-        scaledCol, activityScalingMethod.value ?? C.SCALING_METHODS.NONE, targetColumnChoice.value);
+        scaledCol, activityScalingMethod.value ?? C.SCALING_METHODS.NONE, targetColumnChoice.value, {addSequenceSpace: true});
       return model !== null;
     }
     return false;
@@ -155,9 +155,11 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>): {h
   return {host: mainHost, callback: startAnalysisCallback};
 }
 
+type AnalysisOptions = {addSequenceSpace?: boolean};
+
 export async function startAnalysis(activityColumn: DG.Column<number>, peptidesCol: DG.Column<string>,
   clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaledCol: DG.Column<number>, scaling: C.SCALING_METHODS,
-  targetColumn: DG.Column<string> | null = null): Promise<PeptidesModel | null> {
+  targetColumn: DG.Column<string> | null = null, options: AnalysisOptions = {}): Promise<PeptidesModel | null> {
   const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
   let model = null;
   if (activityColumn.type === DG.COLUMN_TYPE.FLOAT || activityColumn.type === DG.COLUMN_TYPE.INT) {
@@ -165,15 +167,19 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
     const newDf = DG.DataFrame.create(currentDf.rowCount);
     const newDfCols = newDf.columns;
     newDfCols.add(scaledCol);
-    for (const col of currentDf.columns)
-      newDfCols.add(col);
+    for (const col of currentDf.columns) {
+      if (col.getTag(C.TAGS.ANALYSIS_COL) !== `${true}`) {
+        if (col.name === scaledCol.name)
+          col.name = currentDf.columns.getUnusedName(col.name);
+        newDfCols.add(col);
+      }
+    }
 
     newDf.name = 'Peptides analysis';
     const settings: type.PeptidesSettings = {
       sequenceColumnName: peptidesCol.name,
       activityColumnName: activityColumn.name,
       scaling: scaling,
-      isBidirectional: false,
       columns: {},
       maxMutations: 1,
       minActivityDelta: 0,
@@ -212,6 +218,10 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
       await model.addLogoSummaryTable();
     await model.addMonomerPosition();
     await model.addMostPotentResidues();
+
+    // FIXME: enable by default for tests
+    if (options.addSequenceSpace ?? false)
+      model.addSequenceSpace();
   } else
     grok.shell.error('The activity column must be of numeric type!');
   progress.close();

package/src/widgets/selection.ts

@@ -33,6 +33,7 @@ export function getSelectionWidget(table: DG.DataFrame, model: PeptidesModel): H
   }
   const grid = newTable.plot.grid();
   grid.props.showRowHeader = false;
+  grid.root.style.maxWidth = '100%';
 
   DG.debounce(ui.onSizeChanged(grid.root), 50).subscribe((_) => {
     const panel = grid.root.parentElement;
@@ -49,5 +50,13 @@ export function getSelectionWidget(table: DG.DataFrame, model: PeptidesModel): H
 
   const gridHost = ui.box(grid.root);
   gridHost.style.marginLeft = '0px';
+  setTimeout(() => {
+    for (let gridColIdx = 1; gridColIdx < sourceGrid.columns.length; gridColIdx++) {
+      const gridCol = sourceGrid.columns.byIndex(gridColIdx)!;
+      if (!gridCol.visible)
+        continue;
+      grid.col(gridCol.name)!.width = gridCol.width;
+    }
+  }, 500);
   return gridHost;
 }

package/src/widgets/settings.ts

@@ -22,7 +22,6 @@ export enum SETTINGS_PANES {
 export enum GENERAL_INPUTS {
   ACTIVITY = 'Activity',
   ACTIVITY_SCALING = 'Activity scaling',
-  BIDIRECTIONAL_ANALYSIS = 'Bidirectional analysis',
 }
 
 export enum VIEWERS_INPUTS {
@@ -51,7 +50,7 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
   const accordion = ui.accordion();
   const settings = model.settings;
   const currentScaling = settings.scaling ?? C.SCALING_METHODS.NONE;
-  const currentBidirectional = settings.isBidirectional ?? false;
+  // const currentBidirectional = settings.isBidirectional ?? false;
   const currentMaxMutations = settings.maxMutations ?? 1;
   const currentMinActivityDelta = settings.minActivityDelta ?? 0;
   const currentColumns = settings.columns ?? {};
@@ -69,13 +68,9 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
     ui.choiceInput(GENERAL_INPUTS.ACTIVITY_SCALING, currentScaling, Object.values(C.SCALING_METHODS),
       () => result.scaling = activityScaling.value as C.SCALING_METHODS) as DG.InputBase<C.SCALING_METHODS>;
   activityScaling.setTooltip('Activity column transformation method');
-  const bidirectionalAnalysis = ui.boolInput(GENERAL_INPUTS.BIDIRECTIONAL_ANALYSIS, currentBidirectional,
-    () => result.isBidirectional = bidirectionalAnalysis.value) as DG.InputBase<boolean>;
-  bidirectionalAnalysis.setTooltip('Distinguish between positive and negative mean activity difference in ' +
-    'Monomer-Position and Most Potent Residues viewers');
 
-  accordion.addPane(SETTINGS_PANES.GENERAL, () => ui.inputs([activityCol, activityScaling, bidirectionalAnalysis]), true);
-  inputs[SETTINGS_PANES.GENERAL] = [activityCol, activityScaling, bidirectionalAnalysis];
+  accordion.addPane(SETTINGS_PANES.GENERAL, () => ui.inputs([activityCol, activityScaling]), true);
+  inputs[SETTINGS_PANES.GENERAL] = [activityCol, activityScaling];
 
   // Viewers pane options
   /* FIXME: combinations of adding and deleting viewers are not working properly

package/src/workers/mutation-cliffs-worker.ts

@@ -0,0 +1,77 @@
+
+onmessage = async (event): Promise<void> => {
+  const {startIdx, endIdx, activityArray, monomerInfoArray, settings, currentTargetIdx, targetOptions} = event.data;
+  // const monomers1: string[] = [];
+  // const monomers2: string[] = [];
+  const pos: string[] = [];
+  const seq1Idxs: number[] = [];
+  const seq2Idxs: number[] = [];
+  const chunkSize = endIdx - startIdx;
+  //const mi = startRow;
+  //const mj = startCol;
+  let cnt = 0;
+  const startRow = activityArray.length - 2 - Math.floor(
+    Math.sqrt(-8 * startIdx + 4 * activityArray.length * (activityArray.length - 1) - 7) / 2 - 0.5);
+  const startCol = startIdx - activityArray.length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);
+  let seq1Idx = startRow;
+  let seq2Idx = startCol;
+  const tempData = new Array(monomerInfoArray.length);
+  while (cnt < chunkSize) {
+    if (!(currentTargetIdx !== -1 && (targetOptions.targetCol?.rawData[seq1Idx] !== currentTargetIdx ||
+        targetOptions.targetCol?.rawData[seq2Idx] !== currentTargetIdx))) {
+      let substCounter = 0;
+      const activityValSeq1 = activityArray[seq1Idx];
+      const activityValSeq2 = activityArray[seq2Idx];
+      const delta = activityValSeq1 - activityValSeq2;
+      if (Math.abs(delta) >= settings.minActivityDelta) {
+        let substCounterFlag = false;
+        let tempDataIdx = 0;
+        for (const monomerInfo of monomerInfoArray) {
+          const seq1categoryIdx = monomerInfo.rawData[seq1Idx];
+          const seq2categoryIdx = monomerInfo.rawData[seq2Idx];
+          if (seq1categoryIdx === seq2categoryIdx)
+            continue;
+
+          substCounter++;
+          substCounterFlag = substCounter > settings.maxMutations;
+          if (substCounterFlag)
+            break;
+
+          tempData[tempDataIdx++] = {
+            pos: monomerInfo.name,
+            // seq1monomer: monomerInfo.cat![seq1categoryIdx],
+            // seq2monomer: monomerInfo.cat![seq2categoryIdx],
+            seq1Idx: seq1Idx,
+            seq2Idx: seq2Idx,
+          };
+        }
+        if (!(substCounterFlag || substCounter === 0)) {
+          for (let i = 0; i < tempDataIdx; i++) {
+            const tempDataElement = tempData[i];
+            const position = tempDataElement.pos;
+            // const seq1monomer = tempDataElement.seq1monomer;
+            // const seq2monomer = tempDataElement.seq2monomer;
+            // monomers1.push(seq1monomer);
+            // monomers2.push(seq2monomer);
+            pos.push(position);
+            seq1Idxs.push(seq1Idx);
+            seq2Idxs.push(seq2Idx);
+          }
+        }
+      }
+    }
+    cnt++;
+    seq2Idx++;
+    if (seq2Idx === activityArray.length) {
+      seq1Idx++;
+      seq2Idx = seq1Idx + 1;
+    }
+  }
+  postMessage({
+    // monomers1: monomers1,
+    // monomers2: monomers2,
+    pos: pos,
+    seq1Idxs: new Uint32Array(seq1Idxs),
+    seq2Idxs: new Uint32Array(seq2Idxs),
+  });
+};