@datagrok/peptides 1.21.5 → 1.21.7

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.21.5",
+  "version": "1.21.7",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"

package/src/demo/fasta.ts

@@ -7,15 +7,33 @@ import * as C from '../utils/constants';
 import {scaleActivity} from '../utils/misc';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {PeptidesModel} from '../model';
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {MCLSettings} from '../utils/types';
 
 export async function macromoleculeSarFastaDemoUI(): Promise<void> {
   grok.shell.windows.showContextPanel = true;
   const alignedSequenceCol = 'AlignedSequence';
   const simpleActivityColName = 'IC50';
   const simpleTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
-  grok.shell.addTableView(simpleTable);
-  await delay(0);
+  simpleTable.name = 'Simple peptides';
+  if (!simpleTable.id)
+    simpleTable.id = `Simple-peptides-analysis-table-id-${Math.random()}-${Date.now()}`;
+  const view = grok.shell.addTableView(simpleTable);
+  await delay(50);
+  const grid = view.grid;
+  await new Promise((res) => {
+    let timer: any = null;
+    const sub = grid?.onAfterDrawContent?.subscribe(() => {
+      if (timer)
+        clearTimeout(timer);
+      sub.unsubscribe();
+      res(undefined);
+    });
+    timer = setTimeout(() => {
+      sub.unsubscribe();
+      res(undefined);
+    }, 3000);
+  });
   const simpleActivityCol = simpleTable.getCol(simpleActivityColName);
   const simpleAlignedSeqCol = simpleTable.getCol(alignedSequenceCol);
   simpleAlignedSeqCol.semType = DG.SEMTYPE.MACROMOLECULE;
@@ -28,7 +46,9 @@ export async function macromoleculeSarFastaDemoUI(): Promise<void> {
     sequenceCol: simpleAlignedSeqCol,
     clustersCol,
   });
+  const mclSettings = new MCLSettings();
+  mclSettings.threshold = 94;
   const model: PeptidesModel = await startAnalysis(simpleActivityCol, alignedCol, null, simpleTable, simpleScaledCol,
-    C.SCALING_METHODS.MINUS_LG) as PeptidesModel;
-  model.modifyWebLogoSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
+    C.SCALING_METHODS.MINUS_LG, {addMCL: true, useEmbeddingsClusters: true, mclSettings: mclSettings}) as PeptidesModel;
+  // model.modifyWebLogoSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
 }

package/src/model.ts

@@ -146,11 +146,15 @@ export class PeptidesModel {
   get analysisView(): DG.TableView {
     if (this._analysisView === undefined) {
       this._analysisView = this.id ? wu(grok.shell.tableViews).find(({dataFrame}) => dataFrame?.getTag(DG.TAGS.ID) === this.id) : undefined;
-      if (typeof this._analysisView === 'undefined')
+
+      if (!this._analysisView && (grok.shell.v as any)?.preview instanceof DG.TableView && (grok.shell.v as any)?.preview?.dataFrame === this.df)
+        this._analysisView = (grok.shell.v as any)!.preview as any as DG.TableView;
+
+      if (!this._analysisView)
         this._analysisView = grok.shell.addTableView(this.df);
     }
 
-    if (this.df.getTag(C.TAGS.MULTIPLE_VIEWS) !== '1' && !this._layoutEventInitialized)
+    if (this.df.getTag(C.TAGS.MULTIPLE_VIEWS) !== '1' && !this._layoutEventInitialized && !grok.shell.isInDemo)
       grok.shell.v = this._analysisView;
 
 
@@ -369,8 +373,37 @@ export class PeptidesModel {
       // this is important bit. settings are written by startAnalysis function or other viewers, but separate viewers will not init the peptides model
       if (settings)
         model.init(settings);
+
+      let wasEmptySelectionBefore = true;
+      model.subs.push(DG.debounce(dataFrame.onSelectionChanged, 10).subscribe((_) => {
+      //clear all selections if user cleared the selection.
+        if (wasEmptySelectionBefore || dataFrame.selection.anyTrue || !model._analysisView || !document.contains(model._analysisView.root) ||
+        model._analysisView.dataFrame !== dataFrame || !model.positionColumns) {
+          wasEmptySelectionBefore = !dataFrame?.selection?.anyTrue;
+          return;
+        }
+        model.webLogoSelection = initSelection(model.positionColumns!);
+        const mpViewer = model.findViewer(VIEWER_TYPE.SEQUENCE_VARIABILITY_MAP) as MonomerPosition | null;
+        if (mpViewer != null) {
+          mpViewer.invariantMapSelection = initSelection(model.positionColumns!);
+          mpViewer.mutationCliffsSelection = initSelection(model.positionColumns!);
+        }
+        const mprViewer = model.findViewer(VIEWER_TYPE.MOST_POTENT_RESIDUES) as MostPotentResidues | null;
+        if (mprViewer != null)
+          mprViewer.mutationCliffsSelection = initSelection(model.positionColumns!);
+        const lstViewer = model.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE) as LogoSummaryTable | null;
+        if (lstViewer != null) {
+          lstViewer.initClusterSelection({notify: true});
+          lstViewer.render();
+        }
+        wasEmptySelectionBefore = true;
+        //model.fireBitsetChanged();
+      }));
     }
-    return dataFrame.temp[PeptidesModel.modelName] as PeptidesModel;
+
+    const model = dataFrame.temp[PeptidesModel.modelName] as PeptidesModel;
+
+    return model;
   }
 
   /**
@@ -403,7 +436,7 @@ export class PeptidesModel {
    * @return {DG.Accordion | null} - Accordion with analysis info based on current selection
    */
   createAccordion(): DG.Accordion | null {
-    const trueModel: PeptidesModel | undefined = grok.shell.t?.temp[PeptidesModel.modelName];
+    const trueModel: PeptidesModel | undefined = this.df?.temp[PeptidesModel.modelName];
     if (!trueModel)
       return null;
 
@@ -428,41 +461,43 @@ export class PeptidesModel {
     const selectedClusters: string = (trueLSTViewer === null ? [] :
       trueLSTViewer.clusterSelection[CLUSTER_TYPE.ORIGINAL].concat(trueLSTViewer.clusterSelection[CLUSTER_TYPE.CUSTOM]))
       .join(', ');
-    if (selectedClusters.length !== 0) {
-      selectionDescription.push(ui.h1('Logo summary table selection'));
-      selectionDescription.push(ui.divText(`Selected clusters: ${selectedClusters}`));
+    const htmlTextEl = (t: string): HTMLElement => {
+      const el = ui.divText(t);
+      el.innerHTML = t;
+      return el;
     }
+    if (selectedClusters.length !== 0)
+      selectionDescription.push(htmlTextEl(`<b>Logo Summary Table</b> clusters: ${selectedClusters}`));
 
     // Monomer-Position viewer selection overview
     const trueMPViewer = trueModel.findViewer(VIEWER_TYPE.SEQUENCE_VARIABILITY_MAP) as MonomerPosition | null;
     const selectedMonomerPositions = getSelectionString(trueMPViewer?.invariantMapSelection ?? {});
     const selectedMutationCliffs = getSelectionString(trueMPViewer?.mutationCliffsSelection ?? {});
-    if (selectedMonomerPositions.length !== 0 || selectedMutationCliffs.length !== 0)
-      selectionDescription.push(ui.h1('Sequence Variabily Map viewer selection'));
+    // if (selectedMonomerPositions.length !== 0 || selectedMutationCliffs.length !== 0)
+    //   selectionDescription.push(ui.h1('Sequence Variabily Map viewer selection'));
 
 
     if (selectedMonomerPositions.length !== 0)
-      selectionDescription.push(ui.divText(`Selected monomer-positions: ${selectedMonomerPositions}`));
+      selectionDescription.push(htmlTextEl(`<b>Invariant map</b>: ${selectedMonomerPositions}`));
 
 
     if (selectedMutationCliffs.length !== 0)
-      selectionDescription.push(ui.divText(`Selected mutation cliffs pairs: ${selectedMutationCliffs}`));
+      selectionDescription.push(htmlTextEl(`<b>Mutation cliffs</b>: ${selectedMutationCliffs}`));
 
 
     // Most Potent Residues viewer selection overview
     const trueMPRViewer = trueModel.findViewer(VIEWER_TYPE.MOST_POTENT_RESIDUES) as MostPotentResidues | null;
     const selectedMPRMonomerPositions = getSelectionString(trueMPRViewer?.mutationCliffsSelection ?? {});
-    if (selectedMPRMonomerPositions.length !== 0) {
-      selectionDescription.push(ui.h1('Most Potent Residues viewer selection'));
-      selectionDescription.push(ui.divText(`Selected monomer-positions: ${selectedMPRMonomerPositions}`));
-    }
+    if (selectedMPRMonomerPositions.length !== 0)
+      selectionDescription.push(htmlTextEl(`<b>Most potent residues</b>: ${selectedMPRMonomerPositions}`));
 
     // WebLogo selection overview
     const selectedMonomers = getSelectionString(trueModel.webLogoSelection);
-    if (selectedMonomers.length !== 0) {
-      selectionDescription.push(ui.h1('WebLogo selection'));
-      selectionDescription.push(ui.divText(`Selected monomers: ${selectedMonomers}`));
-    }
+    if (selectedMonomers.length !== 0)
+      selectionDescription.push(htmlTextEl(`<b>WebLogo</b>: ${selectedMonomers}`));
+
+    if (selectionDescription.length !== 0)
+      selectionDescription.unshift(ui.h1('Selection Sources'));
 
     const descritionsHost = ui.div(ui.divV(selectionDescription));
     acc.addTitle(ui.divV([
@@ -836,15 +871,23 @@ export class PeptidesModel {
 
     const selection = this.df.selection;
     const filter = this.df.filter;
-
+    let prevTimer: any = null;
     const showAccordion = (): void => {
       try {
+        if (prevTimer != null) {
+          clearTimeout(prevTimer);
+          prevTimer = null;
+        }
         const acc = this.createAccordion();
         if (acc === null)
           return;
 
-
+        // these shinanigans are needed to prevent frozen custom accordion from sticking
         grok.shell.o = acc.root;
+        prevTimer = setTimeout(() => {
+          if (grok.shell.o != acc.root)
+            grok.shell.o = acc.root;
+        }, 1500);
       } catch (e) {
         console.error(e);
       }
@@ -1134,6 +1177,8 @@ export class PeptidesModel {
     };
     const logoSummaryTable = await this.df.plot
       .fromType(VIEWER_TYPE.LOGO_SUMMARY_TABLE, viewerProperties) as LogoSummaryTable;
+    if (grok.shell.isInDemo)
+      this.analysisView.addViewer(logoSummaryTable);
     this.analysisView.dockManager.dock(logoSummaryTable, DG.DOCK_TYPE.RIGHT, null, VIEWER_TYPE.LOGO_SUMMARY_TABLE);
 
     logoSummaryTable.viewerGrid.invalidate();
@@ -1173,6 +1218,9 @@ export class PeptidesModel {
     };
     const monomerPosition = await this.df.plot
       .fromType(VIEWER_TYPE.SEQUENCE_VARIABILITY_MAP, viewerProperties) as MonomerPosition;
+    // for browse mode, we need to add viewer to the analysis view before docking. remove with release of 1.25
+    if (grok.shell.isInDemo)
+      this.analysisView.addViewer(monomerPosition);
     const mostPotentResidues = this.findViewer(VIEWER_TYPE.MOST_POTENT_RESIDUES) as MostPotentResidues | null;
     const dm = this.analysisView.dockManager;
     const [dockType, refNode, ratio] = mostPotentResidues === null ? [DG.DOCK_TYPE.DOWN, null, undefined] :
@@ -1195,6 +1243,8 @@ export class PeptidesModel {
     };
     const mostPotentResidues =
       await this.df.plot.fromType(VIEWER_TYPE.MOST_POTENT_RESIDUES, viewerProperties) as MostPotentResidues;
+    if (grok.shell.isInDemo)
+      this.analysisView.addViewer(mostPotentResidues);
     const monomerPosition = this.findViewer(VIEWER_TYPE.SEQUENCE_VARIABILITY_MAP) as MonomerPosition | null;
     const dm = this.analysisView.dockManager;
     const [dockType, refNode, ratio] = monomerPosition === null ? [DG.DOCK_TYPE.DOWN, null, undefined] :
@@ -1327,7 +1377,7 @@ export class PeptidesModel {
       minClusterSize: mclParams.minClusterSize,
     } satisfies MCLSerializableOptions);
 
-    const tv = grok.shell.getTableView(this.df.name);
+    const tv = this.analysisView ?? grok.shell.getTableView(this.df.name);
     if (tv) {
       const func = DG.Func.find({package: 'EDA', name: 'markovClusteringViewer'})[0];
       if (!func)

package/src/package.ts

@@ -36,8 +36,7 @@ export async function initPeptides(): Promise<void> {
   try {
     monomerWorks ??= new MonomerWorks(await grok.functions.call('Bio:getBioLib'));
     treeHelper ??= await getTreeHelper();
-    await PeptideUtils.loadSeqHelper();
-    await PeptideUtils.loadMonomerLib();
+    await PeptideUtils.loadComponents();
   } catch (e) {
     grok.log.error(e as string);
   }
@@ -178,9 +177,9 @@ export function manualAlignment(_monomer: string): DG.Widget {
 }
 
 // --- Demo ---
-//name: Macromolecule SAR Analysis
-//description: Macromolecule SAR Analysis demo on peptide sequences in FASTA format
-//meta.demoPath: Bioinformatics | Macromolecule SAR Analysis
+//name: Peptide SAR
+//description: Peptide SAR Analysis demo on peptide sequences in FASTA format
+//meta.demoPath: Bioinformatics | Peptide SAR
 //meta.demoSkip: GROK-14320
 export async function macromoleculeSarFastaDemo(): Promise<void> {
   return await macromoleculeSarFastaDemoUI();

package/src/peptideUtils.ts

@@ -20,6 +20,11 @@ export class PeptideUtils {
     this._secHelper ??= await getSeqHelper();
   }
 
+  public static async loadComponents(): Promise<void> {
+    await this.loadSeqHelper();
+    await this.loadMonomerLib();
+  }
+
   public static async loadMonomerLib(): Promise<void> {
     this._monomerLibHelper ??= await getMonomerLibHelper();
     await this._monomerLibHelper.awaitLoaded();

package/src/tests/benchmarks.ts

@@ -17,7 +17,7 @@ const benchmarkDatasetSizes = [5, 50, 100, 200];
 
 category('Benchmarks: Mutation Cliffs', () => {
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
   });
   for (const size of benchmarkDatasetSizes)
     test(`${size}k sequences`, async () => await mutationCliffsBenchmark(size), {timeout: 300000});
@@ -25,7 +25,7 @@ category('Benchmarks: Mutation Cliffs', () => {
 
 category('Benchmarks: Cluster stats', () => {
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
   });
   for (const size of benchmarkDatasetSizes) {
     test(`${size}k sequences`, async () => {
@@ -49,7 +49,7 @@ category('Benchmarks: Cluster stats', () => {
 
 category('Benchmarks: Monomer-Position stats', () => {
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
   });
   for (const size of benchmarkDatasetSizes) {
     test(`${size}k sequences`, async () => {
@@ -78,7 +78,7 @@ category('Benchmarks: Monomer-Position stats', () => {
 
 category('Benchmarks: Analysis start', () => {
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
   });
   for (const size of benchmarkDatasetSizes) {
     test(`${size}k sequences`, async () => {

package/src/tests/core.ts

@@ -15,7 +15,7 @@ import {PeptideUtils} from '../peptideUtils';
 category('Core', () => {
   const alignedSequenceCol = 'AlignedSequence';
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
   });
   let model: PeptidesModel | null = null;
   test('Start analysis: simple', async () => {

package/src/tests/misc.ts

@@ -14,7 +14,7 @@ category('Algorithms', () => {
   let targetCol: type.RawColumn;
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     activityCol = DG.Column.fromList('int', 'test', [1, 2, 5]).getRawData();
     monomerColumns = [

package/src/tests/model.ts

@@ -63,8 +63,10 @@ category('Model: Settings', () => {
   };
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
+    df.name = 'HELM_small';
+    //df.id ??= `HELM_small-${Date.now()}`;
     activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
     sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
     sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;

package/src/tests/table-view.ts

@@ -27,7 +27,7 @@ category('Table view', () => {
   const secondCluster = {monomerOrCluster: '1', positionOrClusterType: CLUSTER_TYPE.ORIGINAL, count: 3};
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
     activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);

package/src/tests/viewers.ts

@@ -18,7 +18,7 @@ category('Viewers: Basic', () => {
   let df: DG.DataFrame;
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
     await delay(500);

package/src/tests/widgets.ts

@@ -26,7 +26,7 @@ category('Widgets: Settings', () => {
   let scaledActivityCol: DG.Column<number>;
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
     activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
@@ -73,7 +73,7 @@ category('Widgets: Distribution panel', () => {
   let scaledActivityCol: DG.Column<number>;
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
     activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
@@ -114,7 +114,7 @@ category('Widgets: Mutation cliffs', () => {
   let scaledActivityCol: DG.Column<number>;
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
     activityCol = df.getCol(TEST_COLUMN_NAMES.ACTIVITY);
@@ -159,7 +159,7 @@ category('Widgets: Actions', () => {
   let scaledActivityCol: DG.Column<number>;
 
   before(async () => {
-    await PeptideUtils.loadSeqHelper();
+    await PeptideUtils.loadComponents();
 
     df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
     await df.meta.detectSemanticTypes();

package/src/viewers/logo-summary.ts

@@ -714,8 +714,12 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     });
     grid.root.addEventListener('mouseleave', (_ev) => this.model.unhighlight());
     DG.debounce(grid.onCurrentCellChanged, 500).subscribe((gridCell) => {
-      if (!gridCell.isTableCell)
+      if (!gridCell.isTableCell || gridCell.gridRow === -1) {
+        this.initClusterSelection({notify: false});
+        this.model.fireBitsetChanged(VIEWER_TYPE.LOGO_SUMMARY_TABLE);
+        grid.invalidate();
         return;
+      }
 
 
       try {

package/src/viewers/sar-viewer.ts

@@ -882,6 +882,16 @@ export class MonomerPosition extends SARViewer {
       try {
         if (!gridCell || !gridCell.dart || !gridCell?.cell?.column?.name || this._monomerMetaColumns.has(gridCell.cell.column.name))
           return;
+        if (gridCell.gridRow === -1) {
+          if (this.mode === SELECTION_MODE.INVARIANT_MAP)
+            this._invariantMapSelection = initSelection(this.positionColumns);
+          else
+            this._mutationCliffsSelection = initSelection(this.positionColumns);
+
+          this.model.fireBitsetChanged(VIEWER_TYPE.SEQUENCE_VARIABILITY_MAP);
+          grid.invalidate();
+        }
+
         if (!this.keyPressed)
           return;
 
@@ -920,7 +930,10 @@ export class MonomerPosition extends SARViewer {
         setTimeout(() => grid?.invalidate(), 300);
       } finally {
         this.keyPressed = false;
-        this.currentGridCell = gridCell;
+        if (gridCell.tableColumn?.name && gridCell.grid)
+          this.currentGridCell = DG.GridCell.fromColumnRow(gridCell.grid, gridCell.tableColumn.name, gridCell.gridRow);
+        else
+          this.currentGridCell = null;
       }
     });
     grid.root.addEventListener('keydown', (ev) => {
@@ -1265,6 +1278,13 @@ export class MostPotentResidues extends SARViewer {
     });
     DG.debounce(grid.onCurrentCellChanged, 500).subscribe((gridCell: DG.GridCell) => {
       try {
+        if (gridCell.gridRow === -1) {
+          this._mutationCliffsSelection = initSelection(this.positionColumns);
+          this.model.fireBitsetChanged(VIEWER_TYPE.MOST_POTENT_RESIDUES);
+          grid.invalidate();
+          return;
+        }
+
         if ((this.keyPressed && mprDf.currentCol.name !== C.COLUMNS_NAMES.MEAN_DIFFERENCE) || !this.keyPressed)
           return;