@datagrok/peptides 1.3.2 → 1.3.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@datagrok/peptides",
-  "version": "1.3.2",
+  "version": "1.3.4",
   "author": {
     "name": "Volodymyr Dyma",
     "email": "vdyma@datagrok.ai"
@@ -12,10 +12,10 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.0.0",
+    "@datagrok-libraries/bio": "^5.1.0",
     "@datagrok-libraries/ml": "^2.0.1",
     "@datagrok-libraries/statistics": "^0.1.6",
-    "@datagrok-libraries/utils": "^1.10.1",
+    "@datagrok-libraries/utils": "^1.11.1",
     "cash-dom": "latest",
     "datagrok-api": "^1.6.0",
     "file-loader": "^6.2.0",

package/setup-unlink-clean.cmd

@@ -0,0 +1,19 @@
+set package_dir=%cd%
+
+set dirs=^
+\..\..\js-api\ ^
+\..\..\libraries\utils\ ^
+\..\..\libraries\ml\ ^
+\..\..\libraries\bio\ ^
+\
+
+call npm uninstall -g ^
+    datagrok-api ^
+    @datagrok-libraries/utils ^
+    @datagrok-libraries/ml ^
+    @datagrok-libraries/bio ^
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & rmdir /s /q node_modules
+for %%p in (%dirs%) do cd %package_dir%\%%p & rmdir /s /q dist
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & del "package-lock.json"

package/setup.cmd

@@ -1,18 +1,15 @@
-call npm unlink datagrok-api
-call npm unlink @datagrok-libraries/utils
-call npm unlink @datagrok-libraries/ml
-cd ../../js-api
-call npm install
-call npm link
-cd ../libraries/utils
-call npm install
-call npm link
-call npm link datagrok-api
-cd ../../libraries/ml
-call npm install
-call npm link
-call npm link @datagrok-libraries/utils
-cd ../../packages/Peptides
-call npm install
-call npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/ml
-webpack
+call setup-unlink-clean.cmd
+
+set package_dir=%cd%
+
+set dirs=^
+\..\..\js-api\ ^
+\..\..\libraries\utils\ ^
+\..\..\libraries\ml\ ^
+\..\..\libraries\bio\ ^
+\
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm install
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm link
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm run link-all
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm run build

package/src/model.ts

@@ -36,9 +36,9 @@ export class PeptidesModel {
   edf: DG.DataFrame | null = null;
   monomerPositionStatsDf!: DG.DataFrame;
   clusterStatsDf!: DG.DataFrame;
-  _mutationCliffsSelection: type.PositionToAARList = {};
-  _invariantMapSelection: type.PositionToAARList = {};
-  _logoSummarySelection: number[] = [];
+  _mutationCliffsSelection!: type.PositionToAARList;
+  _invariantMapSelection!: type.PositionToAARList;
+  _logoSummarySelection!: number[];
   substitutionsInfo: type.SubstitutionsInfo = new Map();
   isInitialized = false;
   currentView!: DG.TableView;
@@ -375,14 +375,15 @@ export class PeptidesModel {
   joinDataFrames(positionColumns: string[], splitSeqDf: DG.DataFrame, alphabet: string): void {
     // append splitSeqDf columns to source table and make sure columns are not added more than once
     const name = this.df.name;
+    const cols = this.df.columns;
     for (const colName of positionColumns) {
       const col = this.df.col(colName);
       const newCol = splitSeqDf.getCol(colName);
       if (col === null)
-        this.df.columns.add(newCol);
+        cols.add(newCol);
       else {
-        this.df.columns.remove(colName);
-        this.df.columns.add(newCol);
+        cols.remove(colName);
+        cols.add(newCol);
       }
       CR.setAARRenderer(newCol, alphabet, this.sourceGrid);
     }
@@ -409,21 +410,15 @@ export class PeptidesModel {
   }
 
   createScaledCol(activityScaling: string, splitSeqDf: DG.DataFrame): void {
-    const [scaledDf, _, newColName] =
-      scaleActivity(activityScaling, this.df.getCol(C.COLUMNS_NAMES.ACTIVITY));
+    const scaledCol = scaleActivity(activityScaling, this.df.getCol(C.COLUMNS_NAMES.ACTIVITY));
     //TODO: make another func
-    const scaledCol = scaledDf.getCol(C.COLUMNS_NAMES.ACTIVITY_SCALED);
-    scaledCol.semType = C.SEM_TYPES.ACTIVITY_SCALED;
     splitSeqDf.columns.add(scaledCol);
-    const oldScaledCol = this.df.getCol(C.COLUMNS_NAMES.ACTIVITY_SCALED);
-    this.df.columns.replace(oldScaledCol, scaledCol);
+    this.df.columns.replace(C.COLUMNS_NAMES.ACTIVITY_SCALED, scaledCol);
     const gridCol = this.sourceGrid.col(C.COLUMNS_NAMES.ACTIVITY_SCALED);
-    if (gridCol !== null) {
-      gridCol.name = newColName;
-      this.df.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED] = newColName;
-    }
+    if (gridCol)
+      gridCol.name = scaledCol.getTag('gridName');
 
-    this.sourceGrid.columns.setOrder([newColName]);
+    this.sourceGrid.columns.setOrder([scaledCol.getTag('gridName')]);
   }
 
   calculateMonomerPositionStatistics(matrixDf: DG.DataFrame): DG.DataFrame {
@@ -964,10 +959,10 @@ export class PeptidesModel {
       const getBitAt = (i: number): boolean => {
         for (const position of positionList) {
           const positionCol: DG.Column<string> = this.df.getCol(position);
-          if (this._mutationCliffsSelection[position].includes(positionCol.get(i)!))
+          if (this.mutationCliffsSelection[position].includes(positionCol.get(i)!))
             return true;
         }
-        if (this._logoSummarySelection.includes(clusterCol?.get(i)!))
+        if (this.logoSummarySelection.includes(clusterCol?.get(i)!))
           return true;
         return false;
       };
@@ -982,7 +977,7 @@ export class PeptidesModel {
       filter.init((i) => {
         let result = true;
         for (const position of positionList) {
-          const aarList = this._invariantMapSelection[position];
+          const aarList = this.invariantMapSelection[position];
           result &&= aarList.length == 0 || aarList.includes(this.df.get(position, i));
         }
         return result;
@@ -1077,9 +1072,9 @@ export class PeptidesModel {
 
     this.df.tags[C.PEPTIDES_ANALYSIS] = 'true';
     const scaledGridCol = this.sourceGrid.col(C.COLUMNS_NAMES.ACTIVITY_SCALED)!;
-    scaledGridCol.name = this.df.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED];
+    scaledGridCol.name = scaledGridCol.column!.getTag('gridName');
     scaledGridCol.format = '#.000';
-    this.sourceGrid.columns.setOrder([this.df.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED]]);
+    this.sourceGrid.columns.setOrder([scaledGridCol.name]);
     this.sourceGrid.props.allowColSelection = false;
 
     this.df.temp[C.EMBEDDING_STATUS] = false;

package/src/package-test.ts

@@ -1,5 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import {runTests, tests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
 
 import './tests/core';
 import './tests/peptide-space-test';
@@ -10,8 +10,9 @@ export {tests};
 //name: test
 //input: string category {optional: true}
 //input: string test {optional: true}
+//input: object testContext {optional: true}
 //output: dataframe result
-export async function test(category: string, test: string): Promise<DG.DataFrame> {
-  const data = await runTests({category, test: test});
+export async function test(category: string, test: string, testContext: TestContext): Promise<DG.DataFrame> {
+  const data = await runTests({category, test, testContext});
   return DG.DataFrame.fromObjects(data)!;
 }

package/src/tests/core.ts

@@ -13,14 +13,14 @@ category('Core', () => {
   let simpleTable: DG.DataFrame;
   let simpleActivityCol: DG.Column<number>;
   let simpleAlignedSeqCol: DG.Column<string>;
-  let simpleScaledDf: DG.DataFrame;
+  let simpleScaledCol: DG.Column<number>;
   let scalingFormula: (x: number) => number;
   let simpleScaledColName: string;
 
   let complexTable: DG.DataFrame;
   let complexActivityCol: DG.Column<number>;
   let complexAlignedSeqCol: DG.Column<string>;
-  let complexScaledDf: DG.DataFrame;
+  let complexScaledCol: DG.Column<number>;
   let complexScaledColName: string;
   const alignedSequenceCol = 'AlignedSequence';
 
@@ -35,10 +35,9 @@ category('Core', () => {
     simpleAlignedSeqCol.tags[C.TAGS.ALPHABET] = 'PT';
     simpleAlignedSeqCol.tags[DG.TAGS.UNITS] = 'fasta';
     simpleAlignedSeqCol.tags['aligned'] = 'SEQ.MSA';
-    [simpleScaledDf, scalingFormula, simpleScaledColName] = scaleActivity('-lg', simpleActivityCol);
+    simpleScaledCol = scaleActivity('-lg', simpleActivityCol);
 
-    model = await startAnalysis(
-      simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, scalingFormula, simpleScaledColName, '-lg', []);
+    model = await startAnalysis(simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledCol, '-lg');
     expect(model instanceof PeptidesModel, true);
 
     if (model != null) {
@@ -57,10 +56,10 @@ category('Core', () => {
     complexAlignedSeqCol.tags[DG.TAGS.UNITS] = 'separator';
     complexAlignedSeqCol.tags['aligned'] = 'SEQ.MSA';
     complexAlignedSeqCol.tags[C.TAGS.SEPARATOR] = '/';
-    [complexScaledDf, scalingFormula, complexScaledColName] = scaleActivity('-lg', complexActivityCol);
+    complexScaledCol = scaleActivity('-lg', complexActivityCol);
 
     model = await startAnalysis(
-      complexActivityCol, complexAlignedSeqCol, null, complexTable, scalingFormula, complexScaledColName, '-lg', []);
+      complexActivityCol, complexAlignedSeqCol, null, complexTable, complexScaledCol, '-lg');
     expect(model instanceof PeptidesModel, true);
 
     if (model != null) {
@@ -78,10 +77,9 @@ category('Core', () => {
     simpleAlignedSeqCol.tags[C.TAGS.ALPHABET] = 'PT';
     simpleAlignedSeqCol.tags[DG.TAGS.UNITS] = 'fasta';
     simpleAlignedSeqCol.tags['aligned'] = 'SEQ.MSA';
-    [simpleScaledDf, scalingFormula, simpleScaledColName] = scaleActivity('-lg', simpleActivityCol);
+    simpleScaledCol = scaleActivity('-lg', simpleActivityCol);
 
-    model = await startAnalysis(
-      simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, scalingFormula, simpleScaledColName, '-lg', []);
+    model = await startAnalysis(simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledCol, '-lg');
     let v = grok.shell.getTableView('Peptides analysis');
     const d = v.dataFrame;
     const layout = v.saveLayout();

package/src/utils/cell-renderer.ts

@@ -1,8 +1,7 @@
-import {SeqPaletteBase} from '@datagrok-libraries/bio/src/seq-palettes';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
 import * as C from './constants';
-import {getPalleteByType} from './misc';
 import * as types from './types';
 
 function renderCellSelection(canvasContext: CanvasRenderingContext2D, bound: DG.Rect): void {
@@ -104,7 +103,7 @@ export function renderLogoSummaryCell(canvasContext: CanvasRenderingContext2D, c
 export function renderBarchart(ctx: CanvasRenderingContext2D, col: DG.Column, monomerColStats: types.MonomerColStats,
   bounds: DG.Rect, max: number): types.BarCoordinates {
   let sum = col.length - (monomerColStats['-']?.count ?? 0);
-  const colorPalette = getPalleteByType(col.tags[C.TAGS.ALPHABET]);
+  const colorPalette = bio.getPaletteByType(col.tags[C.TAGS.ALPHABET]);
   const name = col.name;
   const colNameSize = ctx.measureText(name);
   const margin = 0.2;
@@ -144,7 +143,7 @@ export function renderBarchart(ctx: CanvasRenderingContext2D, col: DG.Column, mo
     ctx.fillStyle = color;
 
     if (textSize.width <= subBarHeight) {
-      if (color != SeqPaletteBase.undefinedColor)
+      if (color != bio.SeqPaletteBase.undefinedColor)
         ctx.fillRect(xStart, yStart, barWidth, subBarHeight);
       else {
         ctx.strokeRect(xStart + 0.5, yStart, barWidth - 1, subBarHeight);

package/src/utils/misc.ts

@@ -7,20 +7,6 @@ import {NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
 import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 
-export function getPalleteByType(paletteType: string): SeqPalette {
-  switch (paletteType) {
-  case 'PT':
-    return AminoacidsPalettes.GrokGroups;
-  case 'NT':
-  case 'DNA':
-  case 'RNA':
-    return NucleotidesPalettes.Chromatogram;
-    // other
-  default:
-    return UnknownSeqPalettes.Color;
-  }
-}
-
 export function getTypedArrayConstructor(
   maxNum: number): Uint8ArrayConstructor | Uint16ArrayConstructor | Uint32ArrayConstructor {
   return maxNum < 256 ? Uint8Array :
@@ -32,13 +18,10 @@ export function getSeparator(col: DG.Column<string>): string {
   return col.getTag(C.TAGS.SEPARATOR) ?? '';
 }
 
-export function scaleActivity(activityScaling: string, activityCol: DG.Column<number>, indexes?: number[],
-): [DG.DataFrame, (x: number) => number, string] {
-  const tempDf = DG.DataFrame.create(activityCol.length);
-
+export function scaleActivity(scaling: string, activityCol: DG.Column<number>): DG.Column<number> {
   let formula = (x: number): number => x;
   let newColName = 'activity';
-  switch (activityScaling) {
+  switch (scaling) {
   case 'none':
     break;
   case 'lg':
@@ -50,15 +33,16 @@ export function scaleActivity(activityScaling: string, activityCol: DG.Column<nu
     newColName = `-Log10(${newColName})`;
     break;
   default:
-    throw new Error(`ScalingError: method \`${activityScaling}\` is not available.`);
+    throw new Error(`ScalingError: method \`${scaling}\` is not available.`);
   }
-  tempDf.columns.addNewVirtual(
-    C.COLUMNS_NAMES.ACTIVITY_SCALED, (i) => {
-      const val = activityCol.get(indexes ? indexes[i] : i);
-      return val ? formula(val) : val;
-    }, DG.TYPE.FLOAT);
+  const scaledCol = DG.Column.float(C.COLUMNS_NAMES.ACTIVITY_SCALED, activityCol.length).init((i) => {
+    const val = activityCol.get(i);
+    return val ? formula(val) : val;
+  });
+  scaledCol.semType = C.SEM_TYPES.ACTIVITY_SCALED;
+  scaledCol.setTag('gridName', newColName);
 
-  return [tempDf, formula, newColName];
+  return scaledCol;
 }
 
 export function calculateBarsData(columns: DG.Column<string>[], selection: DG.BitSet): type.MonomerDfStats {

package/src/widgets/manual-alignment.ts

@@ -1,8 +1,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
-
-import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
+import * as bio from '@datagrok-libraries/bio';
 
 import $ from 'cash-dom';
 import '../styles.css';
@@ -20,7 +19,7 @@ export function manualAlignmentWidget(alignedSequenceCol: DG.Column<string>, cur
   const applyChangesBtn = ui.button('Apply', async () => {
     const newSequence = sequenceInput.value;
     const affectedRowIndex = currentDf.currentRowIdx;
-    const splitSequence = splitAlignedSequences(DG.Column.fromStrings('splitSequence', [newSequence]));
+    const splitSequence = bio.splitAlignedSequences(DG.Column.fromStrings('splitSequence', [newSequence]));
 
     alignedSequenceCol.set(affectedRowIndex, newSequence);
     for (const part of splitSequence.columns) {

package/src/widgets/peptides.ts

@@ -1,8 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import * as bio from '@datagrok-libraries/bio';
 
 import '../styles.css';
 import * as C from '../utils/constants';
@@ -27,32 +26,18 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   if (funcs.length == 0)
     return new DG.Widget(ui.label('Helm package is missing or out of date. Please install the latest version.'));
 
-  let tempCol = null;
-  let scaledDf: DG.DataFrame;
-  let newScaledColName: string;
-  let scalingFormula: (x: number) => number;
-
-  for (const column of df.columns.numerical)
-    tempCol = column.type === DG.TYPE.FLOAT ? column : null;
+  let scaledCol: DG.Column<number>;
 
-  const defaultActivityColumn: DG.Column<number> | null = df.col('activity') || df.col('IC50') || tempCol;
+  const defaultActivityColumn: DG.Column<number> | null =
+    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical);;
   const histogramHost = ui.div([], {id: 'pep-hist-host'});
 
-  const indexes: number[] = [];
-  const f = df.filter;
-  df.onFilterChanged.subscribe(() => {
-    for (let i = 0; i < f.length; ++i) {
-      if (f.get(i))
-        indexes.push(i);
-    }
-  });
   const activityScalingMethod = ui.choiceInput(
     'Scaling', 'none', ['none', 'lg', '-lg'],
     async (currentMethod: string): Promise<void> => {
-      [scaledDf, scalingFormula, newScaledColName] =
-        scaleActivity(currentMethod, activityColumnChoice.value!, indexes.length !== 0 ? indexes : undefined);
+      scaledCol = scaleActivity(currentMethod, activityColumnChoice.value!);
 
-      const hist = scaledDf.plot.histogram({
+      const hist = DG.DataFrame.fromColumns([scaledCol]).plot.histogram({
         filteringEnabled: false,
         valueColumnName: C.COLUMNS_NAMES.ACTIVITY_SCALED,
         legendVisibility: 'Never',
@@ -66,9 +51,9 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
     });
   activityScalingMethod.setTooltip('Function to apply for each value in activity column');
 
-  const activityScalingMethodState = (_: any): void => {
+  const activityScalingMethodState = (): void => {
     activityScalingMethod.enabled = (activityColumnChoice.value ?? false) &&
-      DG.Stats.fromColumn(activityColumnChoice.value!, df.filter).min > 0;
+      DG.Stats.fromColumn(activityColumnChoice.value!).min > 0;
     activityScalingMethod.fireChanged();
   };
   const activityColumnChoice = ui.columnInput('Activity', df, defaultActivityColumn, activityScalingMethodState);
@@ -78,13 +63,18 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
 
   const inputsList = [activityColumnChoice, activityScalingMethod, clustersColumnChoice];
 
+  const bitsetChanged = df.filter.onChanged.subscribe(() => {
+    activityScalingMethodState();
+  })
+
   const startBtn = ui.button('Launch SAR', async () => {
-    await startAnalysis(activityColumnChoice.value, col, clustersColumnChoice.value, df, scalingFormula,
-      newScaledColName, activityScalingMethod.value ?? 'none', indexes);
+    await startAnalysis(activityColumnChoice.value!, col, clustersColumnChoice.value, df, scaledCol,
+      activityScalingMethod.value ?? 'none');
+    bitsetChanged.unsubscribe();
   });
   startBtn.style.alignSelf = 'center';
 
-  const viewer = await df.plot.fromType('WebLogo') as WebLogo;
+  const viewer = await df.plot.fromType('WebLogo') as bio.WebLogo;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
@@ -100,43 +90,30 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   );
 }
 
-export async function startAnalysis(activityColumn: DG.Column<number> | null, peptidesCol: DG.Column<string>,
-  clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaleNum: (x: number) => number, newScaledColName: string,
-  scaling: string, indexes: number[]): Promise<PeptidesModel | null> {
+export async function startAnalysis(activityColumn: DG.Column<number>, peptidesCol: DG.Column<string>,
+  clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaledCol: DG.Column<number>, scaling: string,
+  ): Promise<PeptidesModel | null> {
   const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
   let model = null;
-  if (activityColumn?.type === DG.TYPE.FLOAT) {
-    const f = currentDf.filter;
+  if (activityColumn.type === DG.TYPE.FLOAT || activityColumn.type === DG.TYPE.INT) {
     //prepare new DF
-    const newDf = DG.DataFrame.create(f.trueCount);
-    const getIndex = indexes.length !== 0 ? (i: number) : number => indexes[i] : (i: number): number => i;
-    let activityCol: DG.Column<number> | null = null;
+    const newDf = DG.DataFrame.create(currentDf.rowCount);
+    const newDfCols = newDf.columns;
     for (const col of currentDf.columns.toList()) {
-      let virtualCol: DG.Column<any>;
-      if (col === activityColumn) {
-        virtualCol = newDf.columns.addNewVirtual(
-          C.COLUMNS_NAMES.ACTIVITY, (i) => activityColumn.get(getIndex(i)!), DG.TYPE.FLOAT);
-        activityCol = virtualCol;
-      } else if (col === peptidesCol) {
-        virtualCol = newDf.columns.addNewVirtual(
-          C.COLUMNS_NAMES.MACROMOLECULE, (i) => peptidesCol.get(getIndex(i)!), DG.TYPE.STRING);
-      } else
-        virtualCol = newDf.columns.addNewVirtual(col.name, (i) => col.get(getIndex(i)!), col.type as DG.TYPE);
-      virtualCol.setTag(C.TAGS.VISIBLE, '0');
+      const currentCol = newDfCols.add(col);
+      if (col === activityColumn)
+        currentCol.name = C.COLUMNS_NAMES.ACTIVITY;
+      else if (col === peptidesCol)
+        currentCol.name = C.COLUMNS_NAMES.MACROMOLECULE;
+      col.setTag(C.TAGS.VISIBLE, '0');
     }
-    activityCol!.semType = C.SEM_TYPES.ACTIVITY;
-    const activityScaledCol = newDf.columns.addNewVirtual(C.COLUMNS_NAMES.ACTIVITY_SCALED, (i) => {
-      const val = activityCol!.get(getIndex(i)!);
-      return val ? scaleNum(val) : val;
-    }, DG.TYPE.FLOAT);
-    activityScaledCol.semType = C.SEM_TYPES.ACTIVITY_SCALED;
+    activityColumn.semType = C.SEM_TYPES.ACTIVITY;
+    newDfCols.add(scaledCol);
     newDf.name = 'Peptides analysis';
-    newDf.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED] = newScaledColName;
     if (clustersColumn) {
       newDf.getCol(clustersColumn.name).name = C.COLUMNS_NAMES.CLUSTERS;
       newDf.tags[C.TAGS.CLUSTERS] = C.COLUMNS_NAMES.CLUSTERS;
     }
-    // newDf.tags[C.PEPTIDES_ANALYSIS] = 'true';
     newDf.tags['scaling'] = scaling;
 
     let monomerType = 'HELM_AA';
@@ -149,10 +126,9 @@ export async function startAnalysis(activityColumn: DG.Column<number> | null, pe
     }
 
     newDf.setTag('monomerType', monomerType);
-
     model = await PeptidesModel.getInstance(newDf);
   } else
-    grok.shell.error('The activity column must be of floating point number type!');
+    grok.shell.error('The activity column must be of numeric type!');
   progress.close();
   return model;
 }

package/{test-Peptides-916a90d7d48b-ea373bf5.html → test-Peptides-916a90d7d48b-d2f9014f.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit ea373bf5.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit d2f9014f.</title><style type="text/css">html,
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit ea373bf5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-13 13:02:52</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">89.905s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">73.37s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 501 : Peptides.Core.Start analysis: simple : Unable to get project asset "getMonomerLib"
-Test result : Failed : 438 : Peptides.Core.Start analysis: сomplex : Unable to get project asset "getMonomerLib"
-Test result : Failed : 431 : Peptides.Core.Save and load project : Unable to get project asset "getMonomerLib"
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit d2f9014f.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-18 15:00:21</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">96.772s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">78.593s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 459 : Peptides.Core.Start analysis: simple : Unable to get project asset "getMonomerLib"
+Test result : Failed : 247 : Peptides.Core.Start analysis: сomplex : Unable to get project asset "getMonomerLib"
+Test result : Failed : 532 : Peptides.Core.Save and load project : Unable to get project asset "getMonomerLib"
 
     at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:68:20
     at Generator.next (&lt;anonymous&gt;)
@@ -249,28 +249,28 @@ Test result : Failed : 431 : Peptides.Core.Save and load project : Unable to get
     at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:66:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Peptides.Peptide space.test_table.is_not_empty : OK
-Test result : Success : 6322 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
-Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
-Test result : Success : 1 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
-Test result : Success : 4207 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
-Test result : Success : 2954 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
-Test result : Success : 3304 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
-Test result : Success : 3696 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 199 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
-Test result : Success : 803 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 166 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
-Test result : Success : 622 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 7452 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
-Test result : Success : 8496 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 2071 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
-Test result : Success : 2746 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
-Test result : Success : 3306 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
-Test result : Success : 4189 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
-Test result : Success : 239 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
-Test result : Success : 732 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
-Test result : Success : 347 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
-Test result : Success : 659 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
-Test result : Success : 7587 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
-Test result : Success : 8158 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : Peptides.Peptide space.test_table.is_not_empty : OK
+Test result : Success : 5431 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
+Test result : Success : 3 : Peptides.Peptide space.test_deminsionality_reducer : OK
+Test result : Success : 0 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
+Test result : Success : 4271 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
+Test result : Success : 3805 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
+Test result : Success : 3355 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
+Test result : Success : 3861 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 202 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
+Test result : Success : 687 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 337 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
+Test result : Success : 639 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 7964 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
+Test result : Success : 8785 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 2114 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
+Test result : Success : 3464 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
+Test result : Success : 3603 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
+Test result : Success : 4096 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
+Test result : Success : 234 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
+Test result : Success : 733 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 349 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
+Test result : Success : 679 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 8408 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
+Test result : Success : 8267 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
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