@datagrok/peptides 1.9.0 → 1.9.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.9.0",
+  "version": "1.9.1",
   "author": {
     "name": "Volodymyr Dyma",
     "email": "vdyma@datagrok.ai"

package/src/model.ts

@@ -115,6 +115,14 @@ export class PeptidesModel {
     return dataFrame.temp[PeptidesModel.modelName] as PeptidesModel;
   }
 
+  get id(): string {
+    const id = this.df.getTag(C.TAGS.UUID);
+    if (id === null || id === '')
+      throw new Error('PeptidesError: UUID is not defined');
+
+    return id;
+  }
+
   get treeHelper(): ITreeHelper {
     this._treeHelper ??= getTreeHelperInstance();
     return this._treeHelper;
@@ -202,9 +210,9 @@ export class PeptidesModel {
 
   get analysisView(): DG.TableView {
     this._analysisView ??=
-      wu(grok.shell.tableViews).find(({dataFrame}) => dataFrame.getTag(C.TAGS.UUID) == this.df.getTag(C.TAGS.UUID)) ??
+      wu(grok.shell.tableViews).find(({dataFrame}) => dataFrame.getTag(C.TAGS.UUID) === this.id) ??
         grok.shell.addTableView(this.df);
-    if (this.df.getTag(C.MULTIPLE_VIEWS) != '1')
+    if (this.df.getTag(C.TAGS.MULTIPLE_VIEWS) !== '1')
       grok.shell.v = this._analysisView;
 
     return this._analysisView;
@@ -271,7 +279,7 @@ export class PeptidesModel {
 
   get splitByPos(): boolean {
     const splitByPosFlag = (this.df.tags['distributionSplit'] || '00')[0];
-    return splitByPosFlag == '1' ? true : false;
+    return splitByPosFlag === '1' ? true : false;
   }
 
   set splitByPos(flag: boolean) {
@@ -281,7 +289,7 @@ export class PeptidesModel {
 
   get splitByAAR(): boolean {
     const splitByPosFlag = (this.df.tags['distributionSplit'] || '00')[1];
-    return splitByPosFlag == '1' ? true : false;
+    return splitByPosFlag === '1' ? true : false;
   }
 
   set splitByAAR(flag: boolean) {
@@ -410,7 +418,7 @@ export class PeptidesModel {
 
     const monomerCol = matrixDf.getCol(C.COLUMNS_NAMES.MONOMER);
     for (let i = 0; i < monomerCol.length; ++i) {
-      if (monomerCol.get(i) == '') {
+      if (monomerCol.get(i) === '') {
         matrixDf.rows.removeAt(i);
         break;
       }
@@ -555,12 +563,12 @@ export class PeptidesModel {
       colNames.push(sourceGridCols.byIndex(i)!);
 
     colNames.sort((a, b) => {
-      if (a.column!.semType == C.SEM_TYPES.MONOMER) {
-        if (b.column!.semType == C.SEM_TYPES.MONOMER)
+      if (a.column!.semType === C.SEM_TYPES.MONOMER) {
+        if (b.column!.semType === C.SEM_TYPES.MONOMER)
           return 0;
         return -1;
       }
-      if (b.column!.semType == C.SEM_TYPES.MONOMER)
+      if (b.column!.semType === C.SEM_TYPES.MONOMER)
         return 1;
       return 0;
     });
@@ -589,7 +597,7 @@ export class PeptidesModel {
 
       for (let categoryIndex = 0; categoryIndex < posColCateogries.length; ++categoryIndex) {
         const monomer = posColCateogries[categoryIndex];
-        if (monomer == '')
+        if (monomer === '')
           continue;
 
         const bitArray = BitArray.fromSeq(sourceDfLen, (i: number) => posColData[i] === categoryIndex);
@@ -604,7 +612,7 @@ export class PeptidesModel {
   }
 
   getSummaryStats(genObj: SummaryStats, stats: Stats | null = null, summaryStats: SummaryStats | null = null): void {
-    if (stats == null && summaryStats == null)
+    if (stats === null && summaryStats === null)
       throw new Error(`MonomerPositionStatsError: either stats or summaryStats must be present`);
 
     const possibleMaxCount = stats?.count ?? summaryStats!.maxCount;
@@ -671,9 +679,9 @@ export class PeptidesModel {
     const customClustStats: ClusterStats = {};
 
     for (let clustType = 0; clustType < 2; ++clustType) {
-      const masks = clustType == 0 ? origClustMasks : customClustMasks;
-      const clustNames = clustType == 0 ? origClustColCat : customClustColNamesList;
-      const resultStats = clustType == 0 ? origClustStats : customClustStats;
+      const masks = clustType === 0 ? origClustMasks : customClustMasks;
+      const clustNames = clustType === 0 ? origClustColCat : customClustColNamesList;
+      const resultStats = clustType === 0 ? origClustStats : customClustStats;
       for (let maskIdx = 0; maskIdx < masks.length; ++maskIdx) {
         const mask = masks[maskIdx];
         const stats = getStats(activityColData, mask);
@@ -706,15 +714,15 @@ export class PeptidesModel {
 
       const filteredMonomerStats = Object.entries(positionStats).filter((v) => {
         const key = v[0];
-        if (key == 'general')
+        if (key === 'general')
           return false;
 
-        return (v[1] as Stats).pValue == generalPositionStats.minPValue;
+        return (v[1] as Stats).pValue === generalPositionStats.minPValue;
       }) as [string, Stats][];
 
       let maxEntry: [string, Stats];
       for (const [monomer, monomerStats] of filteredMonomerStats) {
-        if (typeof maxEntry! == 'undefined' || maxEntry[1].meanDifference < monomerStats.meanDifference)
+        if (typeof maxEntry! === 'undefined' || maxEntry[1].meanDifference < monomerStats.meanDifference)
           maxEntry = [monomer, monomerStats];
       }
 
@@ -753,7 +761,7 @@ export class PeptidesModel {
     const sourceView = this.analysisView.grid;
     const eventAction = (ev: MouseEvent): void => {
       const cell = sourceView.hitTest(ev.offsetX, ev.offsetY);
-      if (cell?.isColHeader && cell.tableColumn?.semType == C.SEM_TYPES.MONOMER) {
+      if (cell?.isColHeader && cell.tableColumn?.semType === C.SEM_TYPES.MONOMER) {
         const newBarPart = this.findAARandPosition(cell, ev);
         this.requestBarchartAction(ev, newBarPart);
       }
@@ -790,7 +798,7 @@ export class PeptidesModel {
       this.modifyMonomerPositionSelection(monomer, position, false);
     } else {
       const bar = `${position} = ${monomer}`;
-      if (this.cachedWebLogoTooltip.bar == bar)
+      if (this.cachedWebLogoTooltip.bar === bar)
         ui.tooltip.show(this.cachedWebLogoTooltip.tooltip!, ev.clientX, ev.clientY);
       else
         this.cachedWebLogoTooltip = {bar: bar, tooltip: this.showTooltipAt(monomer, position, ev.clientX, ev.clientY)};
@@ -815,16 +823,16 @@ export class PeptidesModel {
         ctx.clip();
 
         //TODO: optimize
-        if (gcArgs.cell.isColHeader && col?.semType == C.SEM_TYPES.MONOMER) {
+        if (gcArgs.cell.isColHeader && col?.semType === C.SEM_TYPES.MONOMER) {
           const stats = this.monomerPositionStats[col.name];
           //TODO: precalc on stats creation
           const sortedStatsOrder = Object.keys(stats).sort((a, b) => {
-            if (a == '' || a == '-')
+            if (a === '' || a === '-')
               return -1;
-            else if (b == '' || b == '-')
+            else if (b === '' || b === '-')
               return +1;
             return 0;
-          }).filter((v) => v != 'general');
+          }).filter((v) => v !== 'general');
 
           this.webLogoBounds[col.name] = CR.drawLogoInBounds(ctx, bounds, stats, sortedStatsOrder, this.df.rowCount,
             this.cp, this.headerSelectedMonomers[col.name]);
@@ -1011,7 +1019,7 @@ export class PeptidesModel {
     this.headerSelectedMonomers = calculateSelected(this.df);
 
     const acc = this.createAccordion();
-    if (acc != null) {
+    if (acc !== null) {
       grok.shell.o = acc.root;
       for (const pane of acc.panes)
         pane.expanded = true;
@@ -1092,7 +1100,7 @@ export class PeptidesModel {
       return;
     this.isInitialized = true;
 
-    if (!this.isRibbonSet && this.df.getTag(C.MULTIPLE_VIEWS) != '1') {
+    if (!this.isRibbonSet && this.df.getTag(C.TAGS.MULTIPLE_VIEWS) !== '1') {
       //TODO: don't pass model, pass parameters instead
       const settingsButton = ui.iconFA('wrench', () => getSettingsDialog(this), 'Peptides analysis settings');
       this.analysisView.setRibbonPanels([[settingsButton]], false);
@@ -1158,18 +1166,21 @@ export class PeptidesModel {
     this.analysisView.grid.col(newClusterCol.name)!.visible = false;
   }
 
-  createNewView(): void {
+  createNewView(): string {
     const rowMask = this.getCompoundBitset();
-    if (!rowMask.anyTrue)
-      return grok.shell.warning('Cannot create a new view, there are no visible selected rows in your dataset');
+    const newDfId = uuid.v4();
 
     const newDf = this.df.clone(rowMask);
     for (const [tag, value] of newDf.tags)
-      newDf.setTag(tag, tag == C.TAGS.SETTINGS ? value : '');
+      newDf.setTag(tag, tag === C.TAGS.SETTINGS ? value : '');
+
     newDf.name = 'Peptides Multiple Views';
-    newDf.setTag(C.MULTIPLE_VIEWS, '1');
-    newDf.setTag(C.TAGS.UUID, uuid.v4());
+    newDf.setTag(C.TAGS.MULTIPLE_VIEWS, '1');
+    newDf.setTag(C.TAGS.UUID, newDfId);
+
     const view = grok.shell.addTableView(newDf);
-    view.addViewer('logo-summary-viewer');
+    view.addViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE);
+
+    return newDfId;
   }
 }

package/src/tests/core.ts

@@ -39,7 +39,7 @@ category('Core', () => {
       simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledCol, C.SCALING_METHODS.MINUS_LG);
     expect(model instanceof PeptidesModel, true);
 
-    if (model != null)
+    if (model !== null)
       model.monomerPositionSelection = {'11': ['D']};
   });
 
@@ -59,7 +59,7 @@ category('Core', () => {
       complexActivityCol, complexAlignedSeqCol, null, complexTable, complexScaledCol, C.SCALING_METHODS.MINUS_LG);
     expect(model instanceof PeptidesModel, true);
 
-    if (model != null)
+    if (model !== null)
       model.monomerPositionSelection = {'13': ['-']};
   });
 

package/src/tests/model.ts

@@ -8,6 +8,7 @@ import {scaleActivity} from '../utils/misc';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {COLUMNS_NAMES, SCALING_METHODS} from '../utils/constants';
 import {LogoSummaryTable} from '../viewers/logo-summary';
+import {TEST_COLUMN_NAMES} from './utils';
 
 category('Model: Settings', () => {
   let df: DG.DataFrame;
@@ -22,12 +23,12 @@ category('Model: Settings', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
     scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(activityCol, sequenceCol, clusterCol, df, scaledActivityCol,
       SCALING_METHODS.NONE);
     if (tempModel === null)

package/src/tests/table-view.ts

@@ -7,6 +7,7 @@ import {startAnalysis} from '../widgets/peptides';
 import {scaleActivity} from '../utils/misc';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {COLUMNS_NAMES, SCALING_METHODS} from '../utils/constants';
+import {TEST_COLUMN_NAMES} from './utils';
 
 category('Table view', () => {
   let df: DG.DataFrame;
@@ -24,12 +25,12 @@ category('Table view', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
     scaledActivityCol = scaleActivity(activityCol, scaling);
-    clusterCol = df.getCol('cluster');
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(activityCol, sequenceCol, clusterCol, df, scaledActivityCol, scaling);
     if (tempModel === null)
       throw new Error('Model is null');
@@ -50,7 +51,7 @@ category('Table view', () => {
       const tableColName = col.column!.name;
       const expectedVisibility = posCols.includes(tableColName) || (tableColName === COLUMNS_NAMES.ACTIVITY_SCALED) ||
       visibleColumns.includes(tableColName);
-      expect(col.visible, expectedVisibility, `Column ${tableColName} is visible == ${col.visible} but should be ` +
+      expect(col.visible, expectedVisibility, `Column ${tableColName} is visible === ${col.visible} but should be ` +
         `${expectedVisibility}`);
     }
   });

package/src/tests/utils.ts

@@ -8,6 +8,12 @@ import {
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
 import {StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 
+export enum TEST_COLUMN_NAMES {
+  SEQUENCE = 'sequence',
+  ACTIVITY = 'activity',
+  CLUSTER = 'cluster',
+}
+
 /**
  * Tests if a table has non zero rows and columns.
  *

package/src/tests/viewers.ts

@@ -11,7 +11,7 @@ import {MONOMER_POSITION_MODE, MonomerPosition, MostPotentResiduesViewer, showTo
 import {SCALING_METHODS} from '../utils/constants';
 import {LST_PROPERTIES, LogoSummaryTable} from '../viewers/logo-summary';
 import {PositionHeight} from '@datagrok-libraries/bio/src/viewers/web-logo';
-
+import {TEST_COLUMN_NAMES} from './utils';
 
 category('Viewers: Basic', () => {
   const df = DG.DataFrame.fromCsv(aligned1);
@@ -34,12 +34,12 @@ category('Viewers: Monomer-Position', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
     scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(
       activityCol, sequenceCol, clusterCol, df, scaledActivityCol, SCALING_METHODS.NONE);
     if (tempModel === null)
@@ -83,12 +83,12 @@ category('Viewers: Most Potent Residues', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
     scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(
       activityCol, sequenceCol, clusterCol, df, scaledActivityCol, SCALING_METHODS.NONE);
     if (tempModel === null)
@@ -116,12 +116,12 @@ category('Viewers: Logo Summary Table', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
     scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(
       activityCol, sequenceCol, clusterCol, df, scaledActivityCol, SCALING_METHODS.NONE);
     if (tempModel === null)

package/src/tests/widgets.ts

@@ -1,15 +1,19 @@
+import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, before, expect} from '@datagrok-libraries/utils/src/test';
+import {category, test, before, expect, delay} from '@datagrok-libraries/utils/src/test';
 import {_package} from '../package-test';
-import {PeptidesModel} from '../model';
+import {PeptidesModel, VIEWER_TYPE} from '../model';
 import {scaleActivity} from '../utils/misc';
 import {startAnalysis} from '../widgets/peptides';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SCALING_METHODS} from '../utils/constants';
+import * as C from '../utils/constants';
 import {PANES_INPUTS, SETTINGS_PANES, getSettingsDialog} from '../widgets/settings';
 import {getDistributionWidget} from '../widgets/distribution';
 import {mutationCliffsWidget} from '../widgets/mutation-cliffs';
+import {TEST_COLUMN_NAMES} from './utils';
+import wu from 'wu';
+import {LogoSummaryTable} from '../viewers/logo-summary';
 
 category('Widgets: Settings', () => {
   let df: DG.DataFrame;
@@ -21,14 +25,14 @@ category('Widgets: Settings', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
-    scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    scaledActivityCol = scaleActivity(activityCol, C.SCALING_METHODS.NONE);
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(activityCol, sequenceCol, clusterCol, df, scaledActivityCol,
-      SCALING_METHODS.NONE);
+      C.SCALING_METHODS.NONE);
     if (tempModel === null)
       throw new Error('Model is null');
     model = tempModel;
@@ -62,14 +66,14 @@ category('Widgets: Distribution panel', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
-    scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    scaledActivityCol = scaleActivity(activityCol, C.SCALING_METHODS.NONE);
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(activityCol, sequenceCol, clusterCol, df, scaledActivityCol,
-      SCALING_METHODS.NONE);
+      C.SCALING_METHODS.NONE);
     if (tempModel === null)
       throw new Error('Model is null');
     model = tempModel;
@@ -94,14 +98,14 @@ category('Widgets: Mutation cliffs', () => {
 
   before(async () => {
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
-    activityCol = df.getCol('activity');
-    sequenceCol = df.getCol('sequence');
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
     sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
-    scaledActivityCol = scaleActivity(activityCol, SCALING_METHODS.NONE);
-    clusterCol = df.getCol('cluster');
+    scaledActivityCol = scaleActivity(activityCol, C.SCALING_METHODS.NONE);
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
     const tempModel = await startAnalysis(activityCol, sequenceCol, clusterCol, df, scaledActivityCol,
-      SCALING_METHODS.NONE);
+      C.SCALING_METHODS.NONE);
     if (tempModel === null)
       throw new Error('Model is null');
     model = tempModel;
@@ -121,15 +125,84 @@ category('Widgets: Mutation cliffs', () => {
 });
 
 category('Widgets: Actions', () => {
+  let df: DG.DataFrame;
+  let model: PeptidesModel;
+  let activityCol: DG.Column<number>;
+  let sequenceCol: DG.Column<string>;
+  let clusterCol: DG.Column<any>;
+  let scaledActivityCol: DG.Column<number>;
+
+  before(async () => {
+    df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
+    activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
+    sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
+    sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+    scaledActivityCol = scaleActivity(activityCol, C.SCALING_METHODS.NONE);
+    clusterCol = df.getCol(TEST_COLUMN_NAMES.CLUSTER);
+    const tempModel = await startAnalysis(activityCol, sequenceCol, clusterCol, df, scaledActivityCol,
+      C.SCALING_METHODS.NONE);
+    if (tempModel === null)
+      throw new Error('Model is null');
+    model = tempModel;
+  });
+
   test('New view', async () => {
+    // Set compound bitset: filter out 2 rows and select 1 among them
+    const filter = model.df.filter;
+    filter.setAll(false, false);
+    filter.set(0, true, false);
+    filter.set(1, true, false);
 
-  }, {skipReason: 'Not implemented yet'});
+    const selection = model.df.selection;
+    selection.set(0, true, false);
 
-  test('New cluster', async () => {
+    const newViewId = model.createNewView();
+    const currentTable = grok.shell.t;
 
-  });
+    expect(currentTable.getTag(C.TAGS.MULTIPLE_VIEWS), '1', 'Current table is expected to have multiple views tag');
+    expect(currentTable.getTag(C.TAGS.UUID), newViewId, 'Current table is expected to have the same UUID as new view');
+    expect(currentTable.rowCount, 1, 'Current table is expected to have 1 row');
 
-  test('Remove cluster', async () => {
+    await delay(500);
 
-  }, {skipReason: 'Not implemented yet'});
+    const currentTableModel = currentTable.temp[PeptidesModel.modelName] as PeptidesModel;
+    const lstViewer = currentTableModel.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE);
+    expect(lstViewer !== null, true, 'New view is expected to have Logo Summary Table viewer attached');
+  });
+
+  test('Custom clusters', async () => {
+    // Set compound bitset: filter out 2 rows and select 1 among them
+    const filter = model.df.filter;
+    filter.setAll(false, false);
+    filter.set(0, true, false);
+    filter.set(1, true, false);
+
+    const selection = model.df.selection;
+    selection.set(0, true, false);
+
+    const lstViewer = model.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE) as LogoSummaryTable;
+
+    // Check that custom clusters are not created yet
+    expect(wu(model.customClusters).toArray().length, 0, 'Expected to have 0 custom clusters before creating one');
+
+    // Create custom cluster
+    model._newClusterSubject.next();
+    const customClusterList = wu(model.customClusters).toArray();
+    expect(customClusterList.length, 1, 'Expected to have 1 custom cluster');
+    const clustName = customClusterList[0].name;
+    expect(model.df.col(clustName) !== null, true,
+      'Expected to have custom cluster column in the table');
+    expect(lstViewer.viewerGrid.table.getCol(C.LST_COLUMN_NAMES.CLUSTER).categories.indexOf(clustName) !== -1, true,
+      'Expected to have custom cluster in the Logo Summary Table');
+
+    // Remove custom cluster
+    model.modifyClusterSelection(clustName);
+    model._removeClusterSubject.next();
+    expect(wu(model.customClusters).toArray().length, 0, 'Expected to have 0 custom clusters after removing one');
+    expect(model.df.col(clustName) === null, true,
+      'Expected to have no custom cluster column in the table');
+    expect(lstViewer.viewerGrid.table.getCol(C.LST_COLUMN_NAMES.CLUSTER).categories.indexOf(clustName) === -1, true,
+      'Expected to have no custom cluster in the Logo Summary Table');
+  });
 });

package/src/utils/algorithms.ts

@@ -8,7 +8,7 @@ export function findMutations(activityArray: type.RawData, monomerInfoArray: typ
   settings: type.PeptidesSettings = {},
   targetOptions: {targetCol?: type.RawColumn | null, currentTarget?: string | null} = {}): type.MutationCliffs {
   const nCols = monomerInfoArray.length;
-  if (nCols == 0)
+  if (nCols === 0)
     throw new Error(`PepAlgorithmError: Couldn't find any column of semType '${C.SEM_TYPES.MONOMER}'`);
 
   settings.minActivityDelta ??= 0;
@@ -37,7 +37,7 @@ export function findMutations(activityArray: type.RawData, monomerInfoArray: typ
       for (const monomerInfo of monomerInfoArray) {
         const seq1category = monomerInfo.rawData[seq1Idx];
         const seq2category = monomerInfo.rawData[seq2Idx];
-        if (seq1category == seq2category)
+        if (seq1category === seq2category)
           continue;
 
         substCounter++;
@@ -54,7 +54,7 @@ export function findMutations(activityArray: type.RawData, monomerInfoArray: typ
         });
       }
 
-      if (substCounterFlag || substCounter == 0)
+      if (substCounterFlag || substCounter === 0)
         continue;
 
       for (const tempDataElement of tempData) {

package/src/utils/cell-renderer.ts

@@ -67,7 +67,7 @@ export function renderMutationCliffCell(canvasContext: CanvasRenderingContext2D,
     canvasContext.shadowColor = DG.Color.toHtml(DG.Color.white);
     let substValue = 0;
     substitutionsInfo.get(currentAAR)?.get(currentPosition)?.forEach((idxs) => substValue += idxs.length);
-    if (substValue && substValue != 0)
+    if (substValue && substValue !== 0)
       canvasContext.fillText(substValue.toString(), midX, midY);
   }
 

package/src/utils/constants.ts

@@ -38,6 +38,7 @@ export enum TAGS {
   CUSTOM_CLUSTER = 'customCluster',
   UUID = 'pep-uuid',
   MONOMER_POSITION_MODE = 'monomerPositionMode',
+  MULTIPLE_VIEWS = 'isMultipleViews',
 }
 
 export enum SEM_TYPES {
@@ -47,8 +48,6 @@ export enum SEM_TYPES {
 
 export const EMBEDDING_STATUS = 'embeddingStatus';
 
-export const MULTIPLE_VIEWS = 'isMultipleViews';
-
 export enum SCALING_METHODS {
   NONE = 'none',
   LG = 'lg',

package/src/utils/misc.ts

@@ -59,8 +59,8 @@ export function calculateSelected(df: DG.DataFrame): type.MonomerSelectionStats
 }
 
 // export function isGridCellInvalid(gc: DG.GridCell | null): boolean {
-//   return !gc || !gc.cell.value || !gc.tableColumn || gc.tableRowIndex == null || gc.tableRowIndex == -1 ||
-//     gc.cell.value == DG.INT_NULL || gc.cell.value == DG.FLOAT_NULL;
+//   return !gc || !gc.cell.value || !gc.tableColumn || gc.tableRowIndex === null || gc.tableRowIndex === -1 ||
+//     gc.cell.value === DG.INT_NULL || gc.cell.value === DG.FLOAT_NULL;
 // }
 
 export function extractColInfo(col: DG.Column<string>): type.RawColumn {

package/src/utils/peptide-similarity-space.ts

@@ -68,7 +68,7 @@ export async function createPeptideSimilaritySpaceViewer(table: DG.DataFrame, me
     const axisCol = table.col(axis);
     const newCol = edf.getCol(axis);
 
-    if (axisCol != null) {
+    if (axisCol !== null) {
       for (let i = 0; i < newCol.length; ++i) {
         const v = newCol.get(i);
         table.set(axis, i, v);
@@ -204,7 +204,7 @@ export class PeptideSimilaritySpaceWidget {
       for (const v of this.view.viewers) {
         const opts = v.getOptions() as {[name: string]: any};
 
-        if (opts.type == 'Scatter plot' && opts.look.xColumnName == '~X' && opts.look.yColumnName == '~Y')
+        if (opts.type === 'Scatter plot' && opts.look.xColumnName === '~X' && opts.look.yColumnName === '~Y')
           found = true;
       }