@datagrok/peptides 1.27.7 → 1.27.8

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.27.7",
+  "version": "1.27.8",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -13,7 +13,7 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.63.2",
+    "@datagrok-libraries/bio": "^5.63.6",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.7",
     "@datagrok-libraries/statistics": "^1.2.12",

package/src/model.ts

@@ -50,6 +50,7 @@ import {ITSNEOptions, IUMAPOptions}
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 import {AggregationColumns, MonomerPositionStats} from './utils/statistics';
 import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
+import {MONOMER_CANONICALIZER_FUNC_TAG} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {getDbscanWorker} from '@datagrok-libraries/math';
 import {DistanceAggregationMethods} from '@datagrok-libraries/ml/src/distance-matrix/types';
 import {ClusterMaxActivityViewer, IClusterMaxActivity} from './viewers/cluster-max-activity-viewer';
@@ -748,9 +749,14 @@ export class PeptidesModel {
     const positionColumns = splitSeqDf.columns.names();
     if (positionColumns.every((colName) => cols.contains(colName))) {
       positionColumns.forEach((colName) => {
-        this.df.col(colName)!.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
-        this.df.col(colName)!.setTag(C.TAGS.POSITION_COL, `${true}`);
-        CR.setMonomerRenderer(this.df.col(colName)!, this.alphabet);
+        const col = this.df.col(colName)!;
+        col.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
+        col.setTag(C.TAGS.POSITION_COL, `${true}`);
+        // Propagate canonicalizer tag from split columns if present
+        const canonTag = splitSeqDf.getCol(colName).getTag(MONOMER_CANONICALIZER_FUNC_TAG);
+        if (canonTag)
+          col.setTag(MONOMER_CANONICALIZER_FUNC_TAG, canonTag);
+        CR.setMonomerRenderer(col, this.alphabet);
       });
     } else {
       for (const colName of positionColumns) {
@@ -763,6 +769,10 @@ export class PeptidesModel {
         col = cols.addNew(newCol.name, newCol.type).init((i) => newColCat[newColData[i]]);
         col.setTag(C.TAGS.ANALYSIS_COL, `${true}`);
         col.setTag(C.TAGS.POSITION_COL, `${true}`);
+        // Propagate canonicalizer tag from split columns if present
+        const canonTag = newCol.getTag(MONOMER_CANONICALIZER_FUNC_TAG);
+        if (canonTag)
+          col.setTag(MONOMER_CANONICALIZER_FUNC_TAG, canonTag);
         CR.setMonomerRenderer(col, this.alphabet);
       }
     }

package/src/viewers/mutation-cliffs-viewer.ts

@@ -10,6 +10,8 @@ import $ from 'cash-dom';
 import {PeptidesModel} from '../model';
 import {extractColInfo} from '../utils/misc';
 import {Subscription} from 'rxjs';
+import {SeqTemps} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {MONOMER_CANONICALIZER_FUNC_TAG} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 export type MutationCliffsWithMonomers = {
   cliffs: MutationCliffs,
   monomers: string[]
@@ -267,15 +269,20 @@ export class MutationCliffsViewer extends DG.JsViewer {
       this._positionColumns = posCols;
       return this._positionColumns;
     }
-    // fallback: generate columns
+    // fallback: generate columns using original (non-canonical) monomers
     const seqCol = this.dataFrame.col(this.sequenceColumnName)!;
     const seqHelper = PeptideUtils.getSeqHelper();
     const seqHandler = seqHelper.getSeqHandler(seqCol);
     const length = seqHandler.maxLength;
     const cols: DG.Column[] = [];
+    // Propagate canonicalizer tag if the source column has a notation provider with one
+    const notationProvider: any = seqCol.temp[SeqTemps.notationProvider] ?? null;
+    const canonFuncName: string | null = notationProvider?.monomerCanonicalizerFuncName ?? null;
     for (let i = 0; i < length; i++) {
-      const monomersAtPosition = seqHandler.getMonomersAtPosition(i, true);
+      const monomersAtPosition = seqHandler.getMonomersAtPosition(i, false);
       const monomerCol = DG.Column.fromList('string', `Position ${i + 1}`, monomersAtPosition);
+      if (canonFuncName)
+        monomerCol.setTag(MONOMER_CANONICALIZER_FUNC_TAG, canonFuncName);
       cols.push(monomerCol);
     }
     this._positionColumns = cols;

package/src/viewers/position-statistics-viewer.ts

@@ -93,8 +93,8 @@ export class SequencePositionStatsViewer extends DG.JsViewer {
     const seqHandler = seqHelper.getSeqHandler(sequenceColumn);
     const maxPos = seqHandler.maxLength;
 
-    const canonicals = positions.map((p) => seqHandler.getMonomersAtPosition(p - 1, true));
-    this._positionColumn.init((i) => canonicals.map((c) => c[i]).join(MONOMER_MOTIF_SPLITTER));
+    const originals = positions.map((p) => seqHandler.getMonomersAtPosition(p - 1, false));
+    this._positionColumn.init((i) => originals.map((c) => c[i]).join(MONOMER_MOTIF_SPLITTER));
 
     this._boxPlotViewer = this.dataFrame.plot.box({categoryColumnNames: [this._positionColumn.name], plotStyle: 'violin',
       valueColumnName: this.valueColumnName, colorColumnName: this._positionColumn.name, showColorSelector: false, showSizeSelector: false, showCategorySelector: false,

package/src/viewers/sar-viewer.ts

@@ -36,7 +36,7 @@ import {
 } from '../utils/misc';
 import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
 import {LogoSummaryTable} from './logo-summary';
-import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {TAGS as bioTAGS, MONOMER_CANONICALIZER_FUNC_TAG} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
@@ -246,6 +246,16 @@ export abstract class SARViewer extends DG.JsViewer implements ISARViewer {
     return this._positionColumns!;
   }
 
+  /** Copies the monomer canonicalizer tag from the sequence column to a monomer column. */
+  protected propagateCanonicalizerTag(monomerCol: DG.Column): void {
+    const seqCol = this.dataFrame?.col(this.sequenceColumnName);
+    if (!seqCol) return;
+    const notationProvider: any = seqCol.temp[SeqTemps.notationProvider] ?? null;
+    const canonFuncName: string | null = notationProvider?.monomerCanonicalizerFuncName ?? null;
+    if (canonFuncName)
+      monomerCol.setTag(MONOMER_CANONICALIZER_FUNC_TAG, canonFuncName);
+  }
+
   _monomerPositionStats: MonomerPositionStats | null = null;
 
   /**
@@ -469,7 +479,8 @@ export abstract class SARViewer extends DG.JsViewer implements ISARViewer {
    */
   onPropertyChanged(property: DG.Property): void {
     super.onPropertyChanged(property);
-
+    if (!this.dataFrame)
+      return;
 
     this.doRender = true;
     switch (property.name) {
@@ -899,6 +910,8 @@ export class MonomerPosition extends SARViewer {
    */
   onPropertyChanged(property: DG.Property): void {
     super.onPropertyChanged(property);
+    if (!this.dataFrame)
+      return;
     switch (property.name) {
     case SAR_PROPERTIES.SEQUENCE:
       this._invariantMapSelection = null;
@@ -1066,6 +1079,7 @@ export class MonomerPosition extends SARViewer {
       sumGridCol.visible = false;
     const monomerCol = monomerPositionDf.getCol(C.COLUMNS_NAMES.MONOMER);
     CR.setMonomerRenderer(monomerCol, this.alphabet, true);
+    this.propagateCanonicalizerTag(monomerCol);
     this.cacheInvariantMapColors();
 
     grid.onCellRender.subscribe((args: DG.GridCellRenderArgs) => renderCell(args, this,
@@ -1266,7 +1280,7 @@ export class MonomerPosition extends SARViewer {
   /** Renders the MonomerPosition viewer body. */
   render(): void {
     $(this.root).empty();
-    if (!this.activityColumnName || !this.sequenceColumnName) {
+    if (!this.dataFrame || !this.activityColumnName || !this.sequenceColumnName) {
       this.root.appendChild(ui.divText('Please, select a sequence and activity columns in the viewer properties'));
       return;
     }
@@ -1493,6 +1507,7 @@ export class MostPotentResidues extends SARViewer {
 
     // Setting Monomer column renderer
     CR.setMonomerRenderer(monomerCol, this.alphabet, true);
+    this.propagateCanonicalizerTag(monomerCol);
     grid.onCellRender.subscribe(
       (args: DG.GridCellRenderArgs) => renderCell(args, this, false, undefined, undefined));
 
@@ -1625,7 +1640,7 @@ export class MostPotentResidues extends SARViewer {
   /** Renders the MostPotentResidues viewer body. */
   render(): void {
     $(this.root).empty();
-    if (!this.activityColumnName || !this.sequenceColumnName) {
+    if (!this.dataFrame || !this.activityColumnName || !this.sequenceColumnName) {
       this.root.appendChild(ui.divText('Please, select a sequence and activity columns in the viewer properties'));
       return;
     }

package/src/widgets/manual-alignment.ts

@@ -24,7 +24,7 @@ export function manualAlignmentWidget(alignedSequenceCol: DG.Column<string>, cur
     const affectedRowIndex = currentDf.currentRowIdx;
     alignedSequenceCol.set(affectedRowIndex, newSequence);
     for (let i = 0; i < splitSequence.length; i++) {
-      const part = splitSequence.getCanonical(i);
+      const part = splitSequence.getOriginal(i);
       if (currentDf.col(i.toString()) !== null)
         currentDf.set(i.toString(), affectedRowIndex, part);
     }