@datagrok/peptides 0.8.8 → 0.8.9

package/src/package.ts

@@ -17,14 +17,14 @@ import {manualAlignmentWidget} from './widgets/manual-alignment';
 import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
 import {peptideMoleculeWidget, getMolecule} from './widgets/peptide-molecule';
 import {SubstViewer} from './viewers/subst-viewer';
-import {runKalign} from './utils/multiple-sequence-alignment';
-import { SemanticValue } from 'datagrok-api/dg';
+import {substTableWidget} from './widgets/subst-table';
+import {msaWidget} from './widgets/multiple-sequence-alignment';
 
 export const _package = new DG.Package();
-let tableGrid: DG.Grid;
-let currentDf: DG.DataFrame;
-let alignedSequenceCol: DG.Column;
-let view: DG.TableView;
+let currentGrid: DG.Grid;
+let currentTable: DG.DataFrame;
+let alignedSequenceColumn: DG.Column;
+let currentView: DG.TableView;
 
 async function main(chosenFile: string) {
   const pi = DG.TaskBarProgressIndicator.create('Loading Peptides');
@@ -33,7 +33,7 @@ async function main(chosenFile: string) {
   peptides.name = 'Peptides';
   peptides.setTag('dataType', 'peptides');
   const view = grok.shell.addTableView(peptides);
-  tableGrid = view.grid;
+  currentGrid = view.grid;
   view.name = 'PeptidesView';
   grok.shell.windows.showProperties = true;
 
@@ -86,14 +86,12 @@ export async function Peptides() {
 //input: column col {semType: alignedSequence}
 //output: widget result
 export async function peptidesPanel(col: DG.Column): Promise<DG.Widget> {
-  if (col.getTag('isAnalysisApplicable') === 'false')
+  if (!(col.temp['isAnalysisApplicable'] ?? true))
     return new DG.Widget(ui.divText('Analysis is not applicable'));
 
-  view = (grok.shell.v as DG.TableView);
-  tableGrid = view.grid;
-  currentDf = col.dataFrame;
-  alignedSequenceCol = col;
-  return await analyzePeptidesWidget(col, view, tableGrid, currentDf);
+  [currentView, currentGrid, currentTable, alignedSequenceColumn] =
+    getOrDefineWIP(currentView, currentGrid, currentTable, col);
+  return await analyzePeptidesWidget(col, currentView, currentGrid, currentTable);
 }
 
 //name: peptide-sar-viewer
@@ -143,7 +141,9 @@ export async function peptideMolecule(peptide: string): Promise<DG.Widget> {
 //input: string aar {semType: aminoAcids}
 //output: widget result
 export async function peptideMolecule2(aar: string): Promise<DG.Widget> {
-  const peptide = alignedSequenceCol.get(currentDf.currentRowIdx);
+  [currentView, currentGrid, currentTable, alignedSequenceColumn] =
+    getOrDefineWIP(currentView, currentGrid, currentTable, alignedSequenceColumn);
+  const peptide = alignedSequenceColumn.get(currentTable.currentRowIdx);
   return await peptideMolecule(peptide);
 }
 
@@ -182,8 +182,10 @@ export function logov() {
 //input: string monomer {semType: aminoAcids}
 //output: widget result
 export function manualAlignment(monomer: string) {
+  [currentView, currentGrid, currentTable, alignedSequenceColumn] =
+    getOrDefineWIP(currentView, currentGrid, currentTable, alignedSequenceColumn);
   //TODO: recalculate Molfile and Molecule panels on sequence update
-  return manualAlignmentWidget(alignedSequenceCol, currentDf);
+  return manualAlignmentWidget(alignedSequenceColumn, currentTable);
 }
 
 //name: Peptide Space
@@ -191,7 +193,9 @@ export function manualAlignment(monomer: string) {
 //input: column col {semType: alignedSequence}
 //output: widget result
 export async function peptideSpacePanel(col: DG.Column): Promise<DG.Widget> {
-  const widget = new PeptideSimilaritySpaceWidget(col, view ?? grok.shell.v);
+  [currentView, currentGrid, currentTable, alignedSequenceColumn] =
+    getOrDefineWIP(currentView, currentGrid, currentTable, col);
+  const widget = new PeptideSimilaritySpaceWidget(col, currentView);
   return await widget.draw();
 }
 
@@ -209,7 +213,9 @@ export async function peptideMolfile(peptide: string): Promise<DG.Widget> {
 //input: string aar { semType: aminoAcids }
 //output: widget result
 export async function peptideMolfile2(aar: string): Promise<DG.Widget> {
-  const peptide = alignedSequenceCol.get(currentDf.currentRowIdx);
+  [currentView, currentGrid, currentTable, alignedSequenceColumn] =
+    getOrDefineWIP(currentView, currentGrid, currentTable, alignedSequenceColumn);
+  const peptide = alignedSequenceColumn.get(currentTable.currentRowIdx);
   return await peptideMolfile(peptide);
 }
 
@@ -218,10 +224,7 @@ export async function peptideMolfile2(aar: string): Promise<DG.Widget> {
 //input: column col {semType: alignedSequence}
 //output: dataframe result
 export async function multipleSequenceAlignment(col: DG.Column): Promise<DG.DataFrame> {
-  const msaCol = await runKalign(col, true);
-  const table = col.dataFrame;
-  table.columns.add(msaCol);
-  return table;
+  return await msaWidget(col);
 }
 
 //name: Substitution
@@ -229,43 +232,7 @@ export async function multipleSequenceAlignment(col: DG.Column): Promise<DG.Data
 //input: dataframe table {semType: Substitution}
 //output: widget result
 export async function peptideSubstitution(table: DG.DataFrame): Promise<DG.Widget> {
-  if (!table) {
-    return new DG.Widget(ui.label('No difference'));
-  }
-  const peptideLength = 17;
-  let initialCol: DG.Column = table.columns.byName('Initial');
-  let substitutedCol: DG.Column = table.columns.byName('Substituted');
-  let substCounts = [];
-  let cnt = 0;
-
-  for (let i = 0; i < initialCol.length; ++i) {
-    const initialPeptide: string = initialCol.get(i);
-    const substPeptide: string = substitutedCol.get(i);
-    const concat = initialPeptide + '#' + substPeptide;
-
-    initialCol.set(i, concat);
-
-    const initialAminos = initialPeptide.split('-');
-    const substAminos = substPeptide.split('-');
-
-    for (let j = 0; j < peptideLength; ++j) {
-      if (initialAminos[j] != substAminos[j])
-        substCounts[cnt++] = j;
-    }
-  }
-
-  const countCol = DG.Column.fromInt32Array('substCounts', substCounts as unknown as Int32Array);
-  const df = DG.DataFrame.fromColumns([countCol]);
-  const barchart = df.plot.histogram({value: 'substCounts'});
-  if (barchart) {
-    barchart.root.style.width = '200px';
-    barchart.root.style.marginLeft = '30px';
-  }
-
-  initialCol.semType = 'alignedSequenceDifference';
-  initialCol.name = 'Substitution';
-  table.columns.remove('Substituted');
-  return new DG.Widget(ui.div([barchart?.root, table.plot.grid().root]));
+  return substTableWidget(table);
 }
 
 //name: alignedSequenceDifferenceCellRenderer
@@ -274,4 +241,17 @@ export async function peptideSubstitution(table: DG.DataFrame): Promise<DG.Widge
 //output: grid_cell_renderer result
 export function alignedSequenceDifferenceCellRenderer() {
   return new AlignedSequenceDifferenceCellRenderer();
-}
+}
+
+function getOrDefineWIP(
+  view?: DG.TableView, grid?: DG.Grid, dataframe?: DG.DataFrame, column?: DG.Column | null,
+): [DG.TableView, DG.Grid, DG.DataFrame, DG.Column] {
+  view ??= (grok.shell.v as DG.TableView);
+  grid ??= view.grid;
+  dataframe ??= grok.shell.t;
+  column ??= (dataframe.columns as DG.ColumnList).bySemType('alignedSequence');
+  if (column === null)
+    throw new Error('Table does not contain aligned sequence columns');
+
+  return [view, grid, dataframe, column];
+}

package/src/peptides.ts

@@ -1,22 +1,165 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {createPeptideSimilaritySpaceViewer} from './utils/peptide-similarity-space';
-import {addViewerToHeader} from './viewers/stacked-barchart-viewer';
-import {model} from './model';
+import {PeptidesModel} from './model';
 import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-// import $ from 'cash-dom';
-
-/**
- * Peptides controller class.
- *
- * @export
- * @class Peptides
- */
-export class Peptides {
-  private static _model = model;
-
-  static async recalculate() {
-    await Peptides._model.updateDefault();
+import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
+import {SubstViewer} from './viewers/subst-viewer';
+import {ChemPalette} from './utils/chem-palette';
+import {Observable} from 'rxjs';
+
+type viewerTypes = SARViewer | SARViewerVertical | SubstViewer;
+export class PeptidesController {
+  private static _controllerName: string = 'peptidesController';
+  private helpUrl = '/help/domains/bio/peptides.md';
+  private _dataFrame: DG.DataFrame;
+  private _model: PeptidesModel;
+
+  private constructor(dataFrame: DG.DataFrame) {
+    this._dataFrame = dataFrame;
+    this._model = PeptidesModel.getOrInit(this._dataFrame);
+    // this.getOrInitModel(this._dataFrame);
+  }
+
+  static getInstance(dataFrame: DG.DataFrame): PeptidesController {
+    dataFrame.temp[PeptidesController.controllerName] ??= new PeptidesController(dataFrame);
+    return dataFrame.temp[PeptidesController.controllerName];
+  }
+
+  static get controllerName() {
+    return PeptidesController._controllerName;
+  }
+
+  // getOrInitModel(): PeptidesModel {
+  //   this._model ??= PeptidesModel.getOrInit(this._dataFrame);
+  //   return this._model;
+  // }
+
+  get onStatsDataFrameChanged(): Observable<DG.DataFrame> {
+    return this._model.onStatsDataFrameChanged;
+  }
+
+  get onSARGridChanged(): Observable<DG.Grid> {
+    return this._model.onSARGridChanged;
+  }
+
+  get onSARVGridChanged(): Observable<DG.Grid> {
+    return this._model.onSARVGridChanged;
+  }
+
+  get onGroupMappingChanged(): Observable<StringDictionary> {
+    return this._model.onGroupMappingChanged;
+  }
+
+  get onSubstFlagChanged(): Observable<boolean> {
+    return this._model.onSubstFlagChanged;
+  }
+
+  async updateDefault() {
+    await this._model.updateDefault();
+  }
+
+  async updateData(
+    dataFrame: DG.DataFrame | null, activityCol: string | null, activityScaling: string | null,
+    sourceGrid: DG.Grid | null, twoColorMode: boolean | null, initialBitset: DG.BitSet | null,
+    grouping: boolean | null) {
+    await this._model.updateData(
+      dataFrame, activityCol, activityScaling, sourceGrid, twoColorMode, initialBitset, grouping);
+  }
+
+  static async scaleActivity(
+    activityScaling: string, activityColumn: string, activityColumnScaled: string, df: DG.DataFrame,
+  ): Promise<[DG.DataFrame, string]> {
+    // const df = sourceGrid.dataFrame!;
+    const tempDf = df.clone(null, [activityColumn]);
+
+    let formula = '${' + activityColumn + '}';
+    let newColName = activityColumn;
+    switch (activityScaling) {
+    case 'none':
+      break;
+    case 'lg':
+      formula = `Log10(${formula})`;
+      newColName = `Log10(${newColName})`;
+      break;
+    case '-lg':
+      formula = `-1*Log10(${formula})`;
+      newColName = `-Log10(${newColName})`;
+      break;
+    default:
+      throw new Error(`ScalingError: method \`${activityScaling}\` is not available.`);
+    }
+
+    await (tempDf.columns as DG.ColumnList).addNewCalculated(activityColumnScaled, formula);
+
+    return [tempDf, newColName];
+  }
+
+  static splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
+    const splitPeptidesArray: string[][] = [];
+    let currentSplitPeptide: string[];
+    let modeMonomerCount = 0;
+    let currentLength;
+    const colLength = peptideColumn.length;
+
+    // splitting data
+    const monomerLengths: {[index: string]: number} = {};
+    for (let i = 0; i < colLength; i++) {
+      currentSplitPeptide = peptideColumn.get(i).split('-').map((value: string) => value ? value : '-');
+      splitPeptidesArray.push(currentSplitPeptide);
+      currentLength = currentSplitPeptide.length;
+      monomerLengths[currentLength + ''] =
+        monomerLengths[currentLength + ''] ? monomerLengths[currentLength + ''] + 1 : 1;
+    }
+    //@ts-ignore: what I do here is converting string to number the most effective way I could find. parseInt is slow
+    modeMonomerCount = 1 * Object.keys(monomerLengths).reduce((a, b) => monomerLengths[a] > monomerLengths[b] ? a : b);
+
+    // making sure all of the sequences are of the same size
+    // and marking invalid sequences
+    let nTerminal: string;
+    const invalidIndexes: number[] = [];
+    let splitColumns: string[][] = Array.from({length: modeMonomerCount}, (_) => []);
+    modeMonomerCount--; // minus N-terminal
+    for (let i = 0; i < colLength; i++) {
+      currentSplitPeptide = splitPeptidesArray[i];
+      nTerminal = currentSplitPeptide.pop()!; // it is guaranteed that there will be at least one element
+      currentLength = currentSplitPeptide.length;
+      if (currentLength !== modeMonomerCount)
+        invalidIndexes.push(i);
+
+      for (let j = 0; j < modeMonomerCount; j++)
+        splitColumns[j].push(j < currentLength ? currentSplitPeptide[j] : '-');
+
+      splitColumns[modeMonomerCount].push(nTerminal);
+    }
+    modeMonomerCount--; // minus C-terminal
+
+    //create column names list
+    const columnNames = Array.from({length: modeMonomerCount}, (_, index) => `${index + 1 < 10 ? 0 : ''}${index + 1 }`);
+    columnNames.splice(0, 0, 'N-terminal');
+    columnNames.push('C-terminal');
+
+    // filter out the columns with the same values
+    if (filter) {
+      splitColumns = splitColumns.filter((positionArray, index) => {
+        const isRetained = new Set(positionArray).size > 1;
+        if (!isRetained)
+          columnNames.splice(index, 1);
+
+        return isRetained;
+      });
+    }
+
+    return [
+      DG.DataFrame.fromColumns(splitColumns.map((positionArray, index) => {
+        return DG.Column.fromList('string', columnNames[index], positionArray);
+      })),
+      invalidIndexes,
+    ];
+  }
+
+  static getChemPalette() {
+    return ChemPalette;
   }
 
   /**
@@ -30,12 +173,17 @@ export class Peptides {
    * @memberof Peptides
    */
   async init(
-    tableGrid: DG.Grid,
-    view: DG.TableView,
-    currentDf: DG.DataFrame,
-    options: StringDictionary,
-    col: DG.Column,
-  ) {
+    tableGrid: DG.Grid, view: DG.TableView, options: StringDictionary, col: DG.Column,
+    originalDfColumns: string[]) {
+    function adjustCellSize(grid: DG.Grid) {
+      const colNum = grid.columns.length;
+      for (let i = 0; i < colNum; ++i) {
+        const iCol = grid.columns.byIndex(i)!;
+        iCol.width = isNaN(parseInt(iCol.name)) ? 50 : 40;
+      }
+      grid.props.rowHeight = 20;
+    }
+
     for (let i = 0; i < tableGrid.columns.length; i++) {
       const aarCol = tableGrid.columns.byIndex(i);
       if (aarCol &&
@@ -47,48 +195,31 @@ export class Peptides {
       }
     }
 
-    const initialFiter = currentDf.filter.clone();
-    const originalDfColumns = (currentDf.columns as DG.ColumnList).names();
-    const originalDfName = currentDf.name;
+    const originalDfName = this._dataFrame.name;
+    const dockManager = view.dockManager;
 
-    // const substViewer = view.addViewer(
-    //   'substitution-analysis-viewer', {'activityColumnName': `${options['activityColumnName']}Scaled`},
-    // );
-    // const substNode = view.dockManager.dock(substViewer, DG.DOCK_TYPE.RIGHT, null, 'Substitution Analysis');
+    const sarViewer = await this._dataFrame.plot.fromType('peptide-sar-viewer', options) as SARViewer;
+    sarViewer.helpUrl = this.helpUrl;
 
-    // const layout1 = view.saveLayout();
-    // view.dockManager.close(substNode);
+    const sarViewerVertical = await this._dataFrame.plot.fromType('peptide-sar-viewer-vertical') as SARViewerVertical;
+    sarViewerVertical.helpUrl = this.helpUrl;
 
-    const helpUrl = '/help/domains/bio/peptides.md';
+    const sarViewersGroup: viewerTypes[] = [sarViewer, sarViewerVertical];
 
-    const sarViewer = view.addViewer('peptide-sar-viewer', options);
-    sarViewer.helpUrl = helpUrl;
-    const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
+    const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
+      this._dataFrame, col, 't-SNE', 'Levenshtein', 100, view, `${options['activityColumnName']}Scaled`);
+    dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.RIGHT, null, 'Peptide Space viewer');
 
-    const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
-    sarViewerVertical.helpUrl = helpUrl;
-    const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
+    let nodeList = dockViewers(sarViewersGroup, DG.DOCK_TYPE.RIGHT, dockManager, DG.DOCK_TYPE.DOWN);
+
+    const substViewer = await this._dataFrame.plot.fromType(
+      'substitution-analysis-viewer', {'activityColumnName': `${options['activityColumnName']}Scaled`}) as SubstViewer;
+    const substViewersGroup = [substViewer];
 
-    const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
-      currentDf,
-      col,
-      't-SNE',
-      'Levenshtein',
-      100,
-      view,
-      `${options['activityColumnName']}Scaled`,
-    );
-    const psNode = view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
-
-    // const layout2 = view.saveLayout();
-
-    const nodeList = [sarNode, sarVNode, psNode];
-
-    const StackedBarchartProm = currentDf.plot.fromType('StackedBarChartAA');
-    addViewerToHeader(tableGrid, StackedBarchartProm);
     tableGrid.props.allowEdit = false;
+    adjustCellSize(tableGrid);
 
-    const hideIcon = ui.iconFA('window-close', () => { //undo?, times?
+    const hideIcon = ui.iconFA('window-close', () => {
       const viewers = [];
       for (const viewer of view.viewers) {
         if (viewer.type !== DG.VIEWER.GRID)
@@ -96,76 +227,55 @@ export class Peptides {
       }
       viewers.forEach((v) => v.close());
 
-      const cols = (currentDf.columns as DG.ColumnList);
+      const cols = (this._dataFrame.columns as DG.ColumnList);
       for (const colName of cols.names()) {
         if (!originalDfColumns.includes(colName))
           cols.remove(colName);
       }
 
-      currentDf.selection.setAll(false);
-      currentDf.filter.setAll(true);
+      this._dataFrame.selection.setAll(false);
+      this._dataFrame.filter.setAll(true);
 
       tableGrid.setOptions({'colHeaderHeight': 20});
       tableGrid.columns.setVisible(originalDfColumns);
       tableGrid.props.allowEdit = true;
-      currentDf.name = originalDfName;
+      this._dataFrame.name = originalDfName;
 
       view.setRibbonPanels(ribbonPanels);
     }, 'Close viewers and restore dataframe');
 
     let isSA = false;
-    //TODO: fix layouts
-    // const switchViewers = ui.iconFA('toggle-on', () => {
-    //   if (isSA) {
-    //     view.loadLayout(layout1);
-    //     $(switchViewers).removeClass('fa-toggle-off');
-    //     $(switchViewers).addClass('fa-toggle-on');
-    //   } else {
-    //     view.loadLayout(layout2);
-    //     $(switchViewers).removeClass('fa-toggle-on');
-    //     $(switchViewers).addClass('fa-toggle-off');
-    //   }
-    //   isSA = !isSA;
-    // });
-    const switchViewers = ui.iconFA('toggle-on', async () => {
-      currentDf.filter.copyFrom(initialFiter);
-      currentDf.selection.setAll(false);
-      nodeList.forEach((node) => view.dockManager.close(node));
-      nodeList.length = 0;
-      if (isSA) {
-        const sarViewer = view.addViewer('peptide-sar-viewer', options);
-        sarViewer.helpUrl = helpUrl;
-        const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
-
-        const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
-        sarViewerVertical.helpUrl = helpUrl;
-        const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
-
-        const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
-          currentDf, col, 't-SNE', 'Levenshtein', 100, view, `${options['activityColumnName']}Scaled`);
-        const psNode = view.dockManager.dock(
-          peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
-
-        nodeList.push(sarNode);
-        nodeList.push(sarVNode);
-        nodeList.push(psNode);
-
-        $(switchViewers).removeClass('fa-toggle-off');
-        $(switchViewers).addClass('fa-toggle-on');
-      } else {
-        const substViewer = view.addViewer(
-          'substitution-analysis-viewer', {'activityColumnName': `${options['activityColumnName']}Scaled`},
-        );
-        substViewer.helpUrl = helpUrl;
-        nodeList.push(view.dockManager.dock(substViewer, DG.DOCK_TYPE.DOWN, null, 'Substitution Analysis'));
-        $(switchViewers).removeClass('fa-toggle-on');
-        $(switchViewers).addClass('fa-toggle-off');
-      }
+    const switchViewers = ui.iconFA('toggle-on', () => {
+      $(switchViewers).toggleClass('fa-toggle-off').toggleClass('fa-toggle-on');
+      nodeList?.forEach((node) => {
+        view.dockManager.close(node);
+        node.container.destroy();
+      });
+      const getCurrentViewerGroup = () => isSA ? substViewersGroup : sarViewersGroup;
+      getCurrentViewerGroup().forEach((v) => v.removeFromView());
       isSA = !isSA;
-    });
+      nodeList = dockViewers(getCurrentViewerGroup(), DG.DOCK_TYPE.LEFT, dockManager, DG.DOCK_TYPE.DOWN);
+    }, 'Toggle viewer group');
 
     const ribbonPanels = view.getRibbonPanels();
     view.setRibbonPanels([[hideIcon, switchViewers]]);
-    // view.setRibbonPanels([[hideIcon]]);
   }
 }
+
+function dockViewers(
+  viewerList: viewerTypes[], attachDirection: DG.DockType, dockManager: DG.DockManager,
+  initialAttachDirection?: DG.DockType): DG.DockNode[] | null {
+  const viewerListLength = viewerList.length;
+  if (viewerListLength === 0)
+    return null;
+
+  let currentViewer = viewerList[0];
+  const nodeList = [dockManager.dock(currentViewer, initialAttachDirection, null, currentViewer.name ?? '')];
+  const ratio = 1 / viewerListLength;
+
+  for (let i = 1; i < viewerListLength; i++) {
+    currentViewer = viewerList[i];
+    nodeList.push(dockManager.dock(currentViewer, attachDirection, nodeList[i - 1], currentViewer.name ?? '', ratio));
+  }
+  return nodeList;
+}

package/src/tests/peptide-space-test.ts

@@ -11,7 +11,7 @@ import {aligned1} from './test-data';
 
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
-import { StringMetrics } from '@datagrok-libraries/ml/src/typed-metrics';
+import {StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 
 export const _package = new DG.Package();
 

package/src/tests/peptides-tests.ts

@@ -1,9 +1,9 @@
 import {after, before, category, test} from '@datagrok-libraries/utils/src/test';
 import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-import {splitAlignedPeptides} from '../utils/split-aligned';
+// import {splitAlignedPeptides} from '../utils/split-aligned';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
-import {Peptides} from '../peptides';
+import {PeptidesController} from '../peptides';
 import {describe} from '../describe';
 import {analyzePeptidesWidget} from '../widgets/analyze-peptides';
 import {manualAlignmentWidget} from '../widgets/manual-alignment';
@@ -52,7 +52,7 @@ category('peptides', async () => {
   });
 
   test('utils.split-sequence', async () => {
-    splitAlignedPeptides(peptidesDf.getCol('AlignedSequence'));
+    PeptidesController.splitAlignedPeptides(peptidesDf.getCol('AlignedSequence'));
   });
 
   test('describe', async () => {
@@ -61,9 +61,9 @@ category('peptides', async () => {
       DG.BitSet.create(peptidesDf.rowCount, (i) => i % 2 === 0), true);
   });
 
-  test('Peptides-class', async () => {
-    const peptides = new Peptides();
-    peptides.init(peptidesGrid, pepView, peptidesDf, options, asCol);
+  test('Peptides-controller', async () => {
+    const peptides = PeptidesController.getInstance(peptidesDf);
+    peptides.init(peptidesGrid, pepView, options, asCol, peptidesDf.columns.names());
   });
 
   test('panel.peptides', async () => {

package/src/tests/utils.ts

@@ -6,7 +6,7 @@ import {
   createDimensinalityReducingWorker,
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
 import {runKalign} from '../utils/multiple-sequence-alignment';
-import { StringMetrics } from '@datagrok-libraries/ml/src/typed-metrics';
+import {StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 
 /**
  * Tests if a table has non zero rows and columns.
@@ -48,7 +48,8 @@ export async function _testDimensionalityReducer(columnData: Array<string>, meth
   let embcols;
 
   try {
-    embcols = await createDimensinalityReducingWorker({data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+    embcols = await createDimensinalityReducingWorker(
+      {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
   } catch (error) {
     noException = false;
   }