@datagrok/peptides 0.8.15 → 1.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@datagrok/peptides",
-  "version": "0.8.15",
+  "version": "1.0.0",
   "description": "Provides advanced tools for analyzing collections of peptides.",
   "repository": {
     "type": "git",
@@ -34,7 +34,7 @@
     "jest": "^27.0.0",
     "@types/jest": "^27.0.0",
     "ts-jest": "^27.0.0",
-    "puppeteer": "latest"
+    "puppeteer": "^13.7.0"
   },
   "sources": [
     "common/ngl_viewer/ngl.js"
@@ -68,5 +68,6 @@
   ],
   "canView": [
     "All users"
-  ]
+  ],
+	"category": "Cheminformatics"
 }

package/src/model.ts

@@ -16,6 +16,8 @@ import {_package} from './package';
 import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
 import {PeptideSpaceViewer} from './viewers/peptide-space-viewer';
 import {setAARRenderer} from './utils/cell-renderer';
+import {substitutionsWidget} from './widgets/subst-table';
+import {getDistributionWidget} from './widgets/distribution';
 
 export class PeptidesModel {
   static _modelName = 'peptidesModel';
@@ -28,6 +30,7 @@ export class PeptidesModel {
   _isUpdating: boolean = false;
   _isSubstInitialized = false;
   isBitsetChangedInitialized = false;
+  isCellChanging = false;
 
   //viewer properties
   _filterMode!: boolean;
@@ -41,17 +44,20 @@ export class PeptidesModel {
   _sarVGrid!: DG.Grid;
   _sourceGrid!: DG.Grid;
   _dataFrame: DG.DataFrame;
-  splitCol!: DG.Column;
+  splitCol!: DG.Column<boolean>;
   stackedBarchart!: StackedBarChart;
+  edf: DG.DataFrame | null = null;
 
   substitutionsInfo: type.SubstitutionsInfo = new Map();
   isInitialized: boolean = false;
   currentView!: DG.TableView;
 
+  _currentSelection!: type.SelectionObject;
+  isPeptideSpaceChangingBitset: boolean = false;
+  isChangingEdfBitset: boolean = false;
+
   private constructor(dataFrame: DG.DataFrame) {
     this._dataFrame = dataFrame;
-    this._dataFrame.temp[C.PEPTIDES_ANALYSIS] = true;
-
     this.updateProperties();
   }
 
@@ -67,6 +73,8 @@ export class PeptidesModel {
 
   static get modelName(): string {return PeptidesModel._modelName;}
 
+  static get chemPalette(): typeof ChemPalette {return ChemPalette;}
+
   get onStatsDataFrameChanged(): Observable<DG.DataFrame> {return this._statsDataFrameSubject.asObservable();}
 
   get onSARGridChanged(): Observable<DG.Grid> {return this._sarGridSubject.asObservable();}
@@ -75,6 +83,31 @@ export class PeptidesModel {
 
   get onSubstTableChanged(): Observable<type.SubstitutionsInfo> {return this._substitutionTableSubject.asObservable();}
 
+  get currentSelection(): type.SelectionObject {
+    this._currentSelection ??= JSON.parse(this._dataFrame.tags[C.TAGS.SELECTION] || '{}');
+    return this._currentSelection;
+  }
+  set currentSelection(selection: type.SelectionObject) {
+    this._currentSelection = selection;
+    this._dataFrame.tags[C.TAGS.SELECTION] = JSON.stringify(selection);
+    this.invalidateSelection();
+  }
+
+  invalidateSelection(): void {
+    this.fireBitsetChanged();
+    this.invalidateGrids();
+  }
+
+  createAccordion() {
+    const acc = ui.accordion('Selection info');
+    acc.root.style.width = '100%';
+    acc.addTitle(ui.h1('Selection info'));
+    acc.addPane('Substitutions', () => substitutionsWidget(this._dataFrame, this).root, true);
+    acc.addPane('Distribtution', () => getDistributionWidget(this._dataFrame).root, true);
+
+    return acc;
+  }
+
   updateProperties(): void {
     this._activityScaling = this._dataFrame.tags['scaling'];
     this._filterMode = stringToBool(this._dataFrame.tags['filterMode']);
@@ -136,7 +169,7 @@ export class PeptidesModel {
       }
     }
     await this.updateBarchart();
-    this.invalidateGrids();
+    this.invalidateSelection();
 
     this._isUpdating = false;
   }
@@ -221,28 +254,10 @@ export class PeptidesModel {
 
     this.setInteractionCallback();
 
-    this.modifyOrCreateSplitCol(C.CATEGORIES.ALL, C.CATEGORIES.ALL);
-
     this.setBitsetCallback();
 
     this.postProcessGrids(this._sourceGrid, invalidIndexes, sarGrid, sarVGrid);
 
-    const currentAAR = this._dataFrame.tags[C.TAGS.AAR];
-    const currentPos = this._dataFrame.tags[C.TAGS.POSITION];
-    if (currentAAR !== currentPos) {
-      const sarDf = sarGrid.dataFrame;
-      const rowCount = sarDf.rowCount;
-      let index = -1;
-      const aarCol = sarDf.getCol(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE);
-      for (let i = 0; i < rowCount; i++) {
-        if (aarCol.get(i) === currentAAR) {
-          index = i;
-          break;
-        }
-      }
-      sarDf.currentCell = sarDf.cell(index, currentPos);
-    }
-
     //TODO: return class instead
     return [sarGrid, sarVGrid, statsDf];
   }
@@ -369,7 +384,7 @@ export class PeptidesModel {
     activityScaling: string, df: DG.DataFrame, sourceGrid: DG.Grid, splitSeqDf: DG.DataFrame,
   ): Promise<void> {
     const [scaledDf, newColName] = await PeptidesModel.scaleActivity(
-      activityScaling, df, df.temp[C.COLUMNS_NAMES.ACTIVITY]);
+      activityScaling, df, df.tags[C.COLUMNS_NAMES.ACTIVITY]);
     //TODO: make another func
     const scaledCol = scaledDf.getCol(C.COLUMNS_NAMES.ACTIVITY_SCALED);
     scaledCol.semType = C.SEM_TYPES.ACTIVITY_SCALED;
@@ -379,7 +394,7 @@ export class PeptidesModel {
     const gridCol = sourceGrid.col(C.COLUMNS_NAMES.ACTIVITY_SCALED);
     if (gridCol !== null) {
       gridCol.name = newColName;
-      df.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED] = newColName;
+      df.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED] = newColName;
     }
 
     sourceGrid.columns.setOrder([newColName]);
@@ -488,8 +503,8 @@ export class PeptidesModel {
     const sarVGrid = sequenceDf.plot.grid();
     sarVGrid.sort([C.COLUMNS_NAMES.POSITION]);
     const pValGridCol = sarVGrid.col(C.COLUMNS_NAMES.P_VALUE)!;
-    pValGridCol.format = 'four digits after comma';
-    pValGridCol.name = 'P-Value';
+    pValGridCol.format = '#.000';
+    pValGridCol.name = 'P-value';
 
     let tempCol = matrixDf.getCol(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE);
     if (tempCol)
@@ -532,9 +547,9 @@ export class PeptidesModel {
 
       if (cell.isTableCell && tableColName && tableRowIndex !== null && renderColNames.indexOf(tableColName) !== -1) {
         const gridTable = cell.grid.table;
-        const currentPosition = tableColName !== C.COLUMNS_NAMES.MEAN_DIFFERENCE ?
+        const currentPosition: string = tableColName !== C.COLUMNS_NAMES.MEAN_DIFFERENCE ?
           tableColName : gridTable.get(C.COLUMNS_NAMES.POSITION, tableRowIndex);
-        const currentAAR = gridTable.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, tableRowIndex);
+        const currentAAR: string = gridTable.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, tableRowIndex);
 
         const queryAAR = `${C.COLUMNS_NAMES.AMINO_ACID_RESIDUE} = ${currentAAR}`;
         if (cellValue) {
@@ -582,6 +597,14 @@ export class PeptidesModel {
             if (substValue && substValue != 0)
               canvasContext.fillText(substValue.toString(), midX, midY);
           }
+
+          //TODO: frame based on currentSelection
+          const aarSelection = this.currentSelection[currentPosition];
+          if (aarSelection && aarSelection.includes(currentAAR)) {
+            canvasContext.strokeStyle = '#000';
+            canvasContext.lineWidth = 1;
+            canvasContext.strokeRect(bound.x + 1, bound.y + 1, bound.width - 1, bound.height - 1);
+          }
         }
         args.preventDefault();
       }
@@ -640,46 +663,63 @@ export class PeptidesModel {
     const sarDf = this._sarGrid.dataFrame;
     const sarVDf = this._sarVGrid.dataFrame;
 
-    //rework, it doesn't even get into isVertical clause
-    const getAARandPosition = (isVertical = false): [string, string] => {
-      let aar : string;
-      let position: string;
-      if (isVertical) {
-        const currentRowIdx = sarVDf.currentRowIdx;
-        aar = sarVDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, currentRowIdx);
-        position = sarVDf.get(C.COLUMNS_NAMES.POSITION, currentRowIdx);
-      } else {
-        aar = sarDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, sarDf.currentRowIdx);
-        position = sarDf.currentCol.name;
-      }
-      return [aar, position];
+    const chooseAction = (aar: string, position: string, isShiftPressed: boolean) => {
+      isShiftPressed ? this.modifyCurrentSelection(aar, position) : this.initCurrentSelection(aar, position);
     };
 
-    this._sarGrid.onCurrentCellChanged.subscribe((gc) => {
-      const isNegativeRowIndex = sarDf.currentRowIdx === -1;
-      if (!sarDf.currentCol || (!sarDf.currentCell.value && !isNegativeRowIndex))
+    const gridCellValidation = (gc: DG.GridCell | null) => !gc || !gc.cell.value || !gc.tableColumn ||
+      gc.tableRowIndex == null || gc.tableRowIndex == -1;
+    this._sarGrid.root.addEventListener('click', (ev) => {
+      const gridCell = this._sarGrid.hitTest(ev.offsetX, ev.offsetY);
+      if (gridCellValidation(gridCell) || gridCell!.tableColumn!.name == C.COLUMNS_NAMES.AMINO_ACID_RESIDUE)
         return;
-      this.syncGrids(false, sarDf, sarVDf);
-      let aar: string = C.CATEGORIES.ALL;
-      let position: string = C.CATEGORIES.ALL;
-      if (!isNegativeRowIndex) {
-        [aar, position] = getAARandPosition();
-        this._dataFrame.tags[C.TAGS.AAR] = aar;
-        this._dataFrame.tags[C.TAGS.POSITION] = position;
-      } else
-        this._dataFrame.tags[C.TAGS.AAR] = this._dataFrame.tags[C.TAGS.POSITION] = '';
-
-      this.modifyOrCreateSplitCol(aar, position);
-      this.fireBitsetChanged();
-      this.invalidateGrids();
-      grok.shell.o = this._dataFrame;
+
+      const position = gridCell!.tableColumn!.name;
+      const aar = sarDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, gridCell!.tableRowIndex!);
+      chooseAction(aar, position, ev.shiftKey);
     });
 
-    this._sarVGrid.onCurrentCellChanged.subscribe((gc) => {
-      if (!sarVDf.currentCol || sarVDf.currentRowIdx === -1)
+    this._sarVGrid.root.addEventListener('click', (ev) => {
+      const gridCell = this._sarVGrid.hitTest(ev.offsetX, ev.offsetY);
+      if (gridCellValidation(gridCell) || gridCell!.tableColumn!.name != C.COLUMNS_NAMES.MEAN_DIFFERENCE)
         return;
-      this.syncGrids(true, sarDf, sarVDf);
+
+      const tableRowIdx = gridCell!.tableRowIndex!;
+      const position = sarVDf.get(C.COLUMNS_NAMES.POSITION, tableRowIdx);
+      const aar = sarVDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, tableRowIdx);
+      chooseAction(aar, position, ev.shiftKey);
     });
+
+    const cellChanged = (table: DG.DataFrame) => {
+      if (this.isCellChanging)
+        return;
+      this.isCellChanging = true;
+      table.currentRowIdx = -1;
+      this.isCellChanging = false;
+    };
+    this._sarGrid.onCurrentCellChanged.subscribe((_gc) => cellChanged(sarDf));
+    this._sarVGrid.onCurrentCellChanged.subscribe((_gc) => cellChanged(sarVDf));
+  }
+
+  modifyCurrentSelection(aar: string, position: string): void {
+    const tempSelection = this.currentSelection;
+    if (!tempSelection.hasOwnProperty(position))
+      tempSelection[position] = [aar];
+    else {
+      const tempSelectionAt = tempSelection[position];
+      const aarIndex = tempSelectionAt.indexOf(aar);
+      aarIndex == -1 ? tempSelectionAt.push(aar) :
+        tempSelectionAt.length == 1 ? delete tempSelection[position] :
+          tempSelectionAt.splice(aarIndex, 1);
+    }
+
+    this.currentSelection = tempSelection;
+  }
+
+  initCurrentSelection(aar: string, position: string): void {
+    const tempSelection: type.SelectionObject = {};
+    tempSelection[position] = [aar];
+    this.currentSelection = tempSelection;
   }
 
   invalidateGrids(): void {
@@ -698,10 +738,41 @@ export class PeptidesModel {
 
     const changeBitset = (currentBitset: DG.BitSet, previousBitset: DG.BitSet): void => {
       previousBitset.setAll(!this._filterMode, false);
-      currentBitset.init((i) => {
-        const currentCategory = this.splitCol.get(i);
-        return currentCategory !== C.CATEGORIES.OTHER && currentCategory !== C.CATEGORIES.ALL;
-      }, false);
+
+      const edfSelection = this.edf?.selection;
+      if (this.isPeptideSpaceChangingBitset) {
+        if (edfSelection == null)
+          return;
+
+        currentBitset.init((i) => edfSelection.get(i) ?? false, false);
+        return;
+      }
+
+      const updateEdfSelection = () => {
+        this.isChangingEdfBitset = true;
+        edfSelection?.copyFrom(currentBitset);
+        this.isChangingEdfBitset = false;
+      };
+
+      const positionList = Object.keys(this.currentSelection);
+      if (positionList.length == 0) {
+        currentBitset.init(() => false, false);
+        updateEdfSelection();
+        return;
+      }
+
+      //TODO: move out
+      const getBitAt = (i: number) => {
+        for (const position of positionList) {
+          const positionCol: DG.Column<string> = this._dataFrame.getCol(position);
+          if (this._currentSelection[position].includes(positionCol.get(i)))
+            return true;
+        }
+        return false;
+      };
+      currentBitset.init(getBitAt, false);
+
+      updateEdfSelection();
     };
 
     const recalculateStatistics =
@@ -718,7 +789,15 @@ export class PeptidesModel {
     this.isBitsetChangedInitialized = true;
   }
 
-  fireBitsetChanged(): void {(this._filterMode ? this._dataFrame.filter : this._dataFrame.selection).fireChanged();}
+  fireBitsetChanged(isPeptideSpaceSource: boolean = false): void {
+    this.isPeptideSpaceChangingBitset = isPeptideSpaceSource;
+    this.getBiteset().fireChanged();
+    this.isPeptideSpaceChangingBitset = false;
+    this.modifyOrCreateSplitCol();
+    grok.shell.o = this.createAccordion().root;
+  }
+
+  getBiteset(): DG.BitSet {return this._filterMode ? this._dataFrame.filter : this._dataFrame.selection;}
 
   //TODO: move out
   postProcessGrids(sourceGrid: DG.Grid, invalidIndexes: number[], sarGrid: DG.Grid, sarVGrid: DG.Grid): void {
@@ -732,70 +811,28 @@ export class PeptidesModel {
     mdCol.name = 'Diff';
 
     for (const grid of [sarGrid, sarVGrid]) {
-      grid.props.rowHeight = 20;
-      grid.columns.rowHeader!.width = 20;
-      for (let i = 0; i < grid.columns.length; ++i) {
-        const col = grid.columns.byIndex(i)!;
-        if (grid == sarVGrid && col.name !== 'Diff' && col.name !== C.COLUMNS_NAMES.AMINO_ACID_RESIDUE)
-          col.width = 45;
+      const gridProps = grid.props;
+      gridProps.rowHeight = 20;
+      const girdCols = grid.columns;
+      const colNum = girdCols.length;
+      for (let i = 0; i < colNum; ++i) {
+        const col = girdCols.byIndex(i)!;
+        const colName = col.name;
+        if (grid == sarVGrid && colName !== 'Diff' && colName !== C.COLUMNS_NAMES.AMINO_ACID_RESIDUE)
+          col.width = 50;
         else
-          col.width = grid.props.rowHeight;
+          col.width = gridProps.rowHeight + 10;
       }
     }
 
-    sarGrid.props.allowEdit = false;
-    sarVGrid.props.allowEdit = false;
-  }
-
-  //TODO: refactor, use this.sarDf and accept aar & position as parameters
-  syncGrids(sourceVertical: boolean, sarDf: DG.DataFrame, sarVDf: DG.DataFrame): void {
-    let otherColName: string;
-    let otherRowIndex: number;
-    const otherDf = sourceVertical ? sarDf : sarVDf;
-
-    if (otherDf.temp[C.FLAGS.CELL_CHANGING])
-      return;
-
-    //on vertical SAR viewer click
-    if (sourceVertical) {
-      const currentRowIdx = sarVDf.currentRowIdx;
-      const currentColName = sarVDf.currentCol.name;
-      if (currentColName !== C.COLUMNS_NAMES.MEAN_DIFFERENCE)
-        return;
-
-      otherColName = sarVDf.get(C.COLUMNS_NAMES.POSITION, currentRowIdx);
-      const otherRowName: string = sarVDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, currentRowIdx);
-      otherRowIndex = -1;
-      const rows = otherDf.rowCount;
-      for (let i = 0; i < rows; i++) {
-        if (otherDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, i) === otherRowName) {
-          otherRowIndex = i;
-          break;
-        }
-      }
-    //on SAR viewer click
-    } else {
-      otherColName = C.COLUMNS_NAMES.MEAN_DIFFERENCE;
-      const otherPos: string = sarDf.currentCol.name;
-      if (otherPos === C.COLUMNS_NAMES.AMINO_ACID_RESIDUE)
-        return;
+    const setViewerGridProps = (grid: DG.Grid) => {
+      grid.props.allowEdit = false;
+      grid.props.allowRowSelection = false;
+      grid.props.allowBlockSelection = false;
+    };
 
-      const otherAAR: string =
-        sarDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, sarDf.currentRowIdx);
-      otherRowIndex = -1;
-      for (let i = 0; i < sarVDf.rowCount; i++) {
-        if (
-          sarVDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, i) === otherAAR &&
-          sarVDf.get(C.COLUMNS_NAMES.POSITION, i) === otherPos
-        ) {
-          otherRowIndex = i;
-          break;
-        }
-      }
-    }
-    otherDf.temp[C.FLAGS.CELL_CHANGING] = true;
-    otherDf.currentCell = otherDf.cell(otherRowIndex, otherColName);
-    otherDf.temp[C.FLAGS.CELL_CHANGING] = false;
+    setViewerGridProps(sarGrid);
+    setViewerGridProps(sarVGrid);
   }
 
   getSplitColValueAt(index: number, aar: string, position: string, aarLabel: string): string {
@@ -803,26 +840,12 @@ export class PeptidesModel {
     return currentAAR === aar ? aarLabel : C.CATEGORIES.OTHER;
   }
 
-  modifyOrCreateSplitCol(aar: string, position: string): void {
-    const df = this._dataFrame;
-    this.splitCol = df.col(C.COLUMNS_NAMES.SPLIT_COL) ?? df.columns.addNew(C.COLUMNS_NAMES.SPLIT_COL, 'string');
-
-    if (aar === C.CATEGORIES.ALL && position === C.CATEGORIES.ALL) {
-      this.splitCol.init(() => C.CATEGORIES.ALL);
-      return;
-    }
-
-    const aarLabel = `${aar === '-' ? 'Gap' : aar} : ${position}`;
-    this.splitCol.init((i) => this.getSplitColValueAt(i, aar, position, aarLabel));
-
-    this.splitCol.setCategoryOrder([aarLabel]);
+  modifyOrCreateSplitCol(): void {
+    const bs = this.getBiteset();
+    this.splitCol = this._dataFrame.col(C.COLUMNS_NAMES.SPLIT_COL) ??
+      this._dataFrame.columns.addNewBool(C.COLUMNS_NAMES.SPLIT_COL);
+    this.splitCol.init((i) => bs.get(i));
     this.splitCol.compact();
-
-    const colorMap: {[index: string]: string | number} = {};
-
-    colorMap[C.CATEGORIES.OTHER] = DG.Color.blue;
-    colorMap[aarLabel] = DG.Color.orange;
-    this.splitCol.colors.setCategorical(colorMap);
   }
 
   static async scaleActivity(
@@ -835,7 +858,7 @@ export class PeptidesModel {
     const tempDf = df.clone(cloneBitset ? df.filter : null, [currentActivityColName]);
 
     let formula = '${' + currentActivityColName + '}';
-    let newColName = 'activity'; //originalActivityName ?? df.temp[C.COLUMNS_NAMES.ACTIVITY] ?? currentActivityColName;
+    let newColName = 'activity';
     switch (activityScaling) {
     case 'none':
       break;
@@ -921,13 +944,9 @@ export class PeptidesModel {
     ];
   }
 
-  getCurrentAARandPos(): {aar: string, pos: string} {
-    return {aar: this._dataFrame.getTag(C.TAGS.AAR) ?? 'All', pos: this._dataFrame.getTag(C.TAGS.POSITION) ?? 'All'};
-  }
-
   syncProperties(isSourceSAR = true): void {
-    const sarViewer = this._dataFrame.temp['sarViewer'];
-    const sarViewerVertical = this._dataFrame.temp['sarViewerVertical'];
+    const sarViewer: SARViewer = this._dataFrame.temp['sarViewer'];
+    const sarViewerVertical: SARViewerVertical = this._dataFrame.temp['sarViewerVertical'];
     const sourceViewer = isSourceSAR ? sarViewer : sarViewerVertical;
     const targetViewer = isSourceSAR ? sarViewerVertical : sarViewer;
     const properties = sourceViewer.props.getProperties();
@@ -935,24 +954,6 @@ export class PeptidesModel {
       targetViewer.props.set(property.name, property.get(sourceViewer));
   }
 
-  //TODO: move to viewer
-  setSARGridCellAt(aar: string, position: string): void {
-    const sarDf = this._sarGrid.dataFrame;
-    const aarCol = sarDf.getCol(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE);
-    const aarColLen = aarCol.length;
-    let index = -1;
-    for (let i = 0; i < aarColLen; i++) {
-      if (aarCol.get(i) === aar) {
-        index = i;
-        break;
-      }
-    }
-    position = position === C.CATEGORIES.ALL ? C.COLUMNS_NAMES.AMINO_ACID_RESIDUE : position;
-    sarDf.currentCell = sarDf.cell(index, position);
-  }
-
-  static get chemPalette(): typeof ChemPalette {return ChemPalette;}
-
   /** Class initializer */
   async init(): Promise<void> {
     if (this.isInitialized)
@@ -965,10 +966,16 @@ export class PeptidesModel {
     stats.setMask(this._dataFrame.selection);
     this._dataFrame.temp[C.STATS] = stats;
 
-    this.currentView = grok.shell.addTableView(this._dataFrame);
+    this.currentView = this._dataFrame.tags[C.PEPTIDES_ANALYSIS] == 'true' ? grok.shell.v as DG.TableView :
+      grok.shell.addTableView(this._dataFrame);
     const sourceGrid = this.currentView.grid;
-    sourceGrid.col(C.COLUMNS_NAMES.ACTIVITY_SCALED)!.name = this._dataFrame.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED];
-    sourceGrid.columns.setOrder([this._dataFrame.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED]]);
+    if (this._dataFrame.tags[C.PEPTIDES_ANALYSIS] == 'true')
+      return;
+
+    this._dataFrame.tags[C.PEPTIDES_ANALYSIS] = 'true';
+    sourceGrid.col(C.COLUMNS_NAMES.ACTIVITY_SCALED)!.name = this._dataFrame.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED];
+    sourceGrid.columns.setOrder([this._dataFrame.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED]]);
+
 
     this._dataFrame.temp[C.EMBEDDING_STATUS] = false;
     const adjustCellSize = (grid: DG.Grid): void => {
@@ -983,9 +990,8 @@ export class PeptidesModel {
     for (let i = 0; i < sourceGrid.columns.length; i++) {
       const aarCol = sourceGrid.columns.byIndex(i);
       if (aarCol && aarCol.name && aarCol.column?.semType !== C.SEM_TYPES.AMINO_ACIDS &&
-        aarCol.name !== this._dataFrame.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED]
-      )
-        sourceGrid.columns.byIndex(i)!.visible = false;
+        aarCol.name !== this._dataFrame.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED])
+        aarCol.visible = false;
     }
 
     const options = {scaling: this._dataFrame.tags['scaling']};
@@ -993,20 +999,19 @@ export class PeptidesModel {
 
     const dockManager = this.currentView.dockManager;
 
-    const sarViewer =
-      await this._dataFrame.plot.fromType('peptide-sar-viewer', options) as SARViewer;
-    this._dataFrame.temp['sarViewer'] = sarViewer;
+    const sarViewer = await this._dataFrame.plot.fromType('peptide-sar-viewer', options) as SARViewer;
 
     const sarViewerVertical =
       await this._dataFrame.plot.fromType('peptide-sar-viewer-vertical', options) as SARViewerVertical;
-    this._dataFrame.temp['sarViewerVertical'] = sarViewer;
 
     const sarViewersGroup: viewerTypes[] = [sarViewer, sarViewerVertical];
 
-    const peptideSpaceViewerOptions = {method: 't-SNE', measure: 'Levenshtein', cyclesCount: 100};
-    const peptideSpaceViewer =
-      await this._dataFrame.plot.fromType('peptide-space-viewer', peptideSpaceViewerOptions) as PeptideSpaceViewer;
-    dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.RIGHT, null, 'Peptide Space Viewer');
+    if (this._dataFrame.rowCount <= 10000) {
+      const peptideSpaceViewerOptions = {method: 'UMAP', measure: 'Levenshtein', cyclesCount: 100};
+      const peptideSpaceViewer =
+        await this._dataFrame.plot.fromType('peptide-space-viewer', peptideSpaceViewerOptions) as PeptideSpaceViewer;
+      dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.RIGHT, null, 'Peptide Space Viewer');
+    }
 
     dockViewers(sarViewersGroup, DG.DOCK_TYPE.RIGHT, dockManager, DG.DOCK_TYPE.DOWN);
 

package/src/package-test.ts

@@ -10,10 +10,10 @@ export {tests};
 
 //name: test
 //input: string category {optional: true}
-//input: string t {optional: true}
+//input: string test {optional: true}
 //output: dataframe result
 //top-menu: Tools | Dev | JS API Tests
-export async function test(category: string, t: string): Promise<DG.DataFrame> {
-  const data = await runTests({category, test: t});
+export async function test(category: string, test: string): Promise<DG.DataFrame> {
+  const data = await runTests({category, test: test});
   return DG.DataFrame.fromObjects(data)!;
 }

package/src/package.ts

@@ -18,9 +18,7 @@ import {manualAlignmentWidget} from './widgets/manual-alignment';
 import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
 import {peptideMoleculeWidget, getMolecule} from './widgets/peptide-molecule';
 import {runKalign, testMSAEnoughMemory} from './utils/multiple-sequence-alignment';
-import {substitutionsWidget} from './widgets/subst-table';
 import {msaWidget} from './widgets/multiple-sequence-alignment';
-import {getDistributionWidget} from './widgets/distribution';
 import {PeptideSpaceViewer} from './viewers/peptide-space-viewer';
 
 export const _package = new DG.Package();
@@ -236,26 +234,6 @@ export async function runTestMSAEnoughMemory(_table: DG.DataFrame, col: DG.Colum
   return col;
 }
 
-//name: Substitution
-//tags: panel, widgets
-//input: dataframe table {semType: Substitution}
-//output: widget result
-export async function peptideSubstitution(table: DG.DataFrame): Promise<DG.Widget> {
-  if (!table.temp[C.PEPTIDES_ANALYSIS])
-    return new DG.Widget(ui.divText('This widget is only applicable for peptides analysis'));
-  return substitutionsWidget(table);
-}
-
-//name: Distribution
-//tags: panel, widgets
-//input: dataframe table {semType: viewerTable}
-//output: widget result
-export function peptideDistribution(table: DG.DataFrame): DG.Widget {
-  if (!table.temp[C.PEPTIDES_ANALYSIS])
-    return new DG.Widget(ui.divText('This widget is only applicable for peptides analysis'));
-  return getDistributionWidget(table);
-}
-
 //name: Get Peptides Structure
 //tags: panel, widgets
 //input: column col {semType: alignedSequence}

package/src/tests/core.ts

@@ -36,9 +36,11 @@ category('Core', () => {
     model = await startAnalysis(
       simpleActivityCol, simpleAlignedSeqCol, simpleTable, simpleScaledDf, simpleScaledColName, _package);
     expect(model instanceof PeptidesModel, true);
-    model?.setSARGridCellAt('D', '11');
-    if (model != null)
+
+    if (model != null) {
+      model.currentSelection = {'11': ['D']};
       grok.shell.closeTable(model._dataFrame);
+    }
   });
 
   test('Start analysis: сomplex', async () => {
@@ -56,8 +58,10 @@ category('Core', () => {
     model = await startAnalysis(
       complexActivityCol, complexAlignedSeqCol, complexTable, complexScaledDf, complexScaledColName, _package);
     expect(model instanceof PeptidesModel, true);
-    model?.setSARGridCellAt('-', '13');
-    if (model != null)
+
+    if (model != null) {
+      model.currentSelection = {'13': ['-']};
       grok.shell.closeTable(model._dataFrame);
+    }
   });
 });