@datagrok/peptides 1.21.5 → 1.21.6

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.21.5",
+  "version": "1.21.6",
   "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;
 
 
@@ -1173,6 +1177,9 @@ 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 +1202,8 @@ 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 +1336,7 @@ 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();