@datagrok/peptides 1.23.2 → 1.23.4

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.23.2",
+  "version": "1.23.4",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"

package/src/model.ts

@@ -378,20 +378,27 @@ export class PeptidesModel {
       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) {
+        model._analysisView.dataFrame !== dataFrame) {
           wasEmptySelectionBefore = !dataFrame?.selection?.anyTrue;
           return;
         }
-        model.webLogoSelection = initSelection(model.positionColumns!);
+        if (model.positionColumns)
+          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 posCols = model.positionColumns ?? mpViewer.positionColumns;
+          if (posCols) {
+            mpViewer.invariantMapSelection = initSelection(posCols);
+            mpViewer.mutationCliffsSelection = initSelection(posCols);
+          }
         }
         const mprViewer = model.findViewer(VIEWER_TYPE.MOST_POTENT_RESIDUES) as MostPotentResidues | null;
         if (mprViewer != null) {
-          mprViewer.mutationCliffsSelection = initSelection(model.positionColumns!);
-          mprViewer.invariantMapSelection = initSelection(model.positionColumns!);
+          const posCols = model.positionColumns ?? mprViewer.positionColumns;
+          if (posCols) {
+            mprViewer.mutationCliffsSelection = initSelection(posCols);
+            mprViewer.invariantMapSelection = initSelection(posCols);
+          }
         }
         const lstViewer = model.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE) as LogoSummaryTable | null;
         if (lstViewer != null) {

package/src/widgets/mutation-cliffs.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as C from '../utils/constants';
@@ -83,7 +84,7 @@ function cliffsPairsWidgetParts(table: DG.DataFrame, options: MutationCliffsOpti
 
 
   const substitutionsArray: string[] = [];
-  const deltaArray: number[] = [];
+  const deltaArray: (number | null)[] = [];
   const substitutedToArray: string[] = [];
   const mutationsGroupsArray: string[] = [];
   const fromIdxArray: number[] = [];
@@ -123,7 +124,8 @@ function cliffsPairsWidgetParts(table: DG.DataFrame, options: MutationCliffsOpti
         const forbiddentIndexes = seenIndexes.get(referenceIdx) ?? [];
         const baseSequence = alignedSeqColCategories[alignedSeqColData[referenceIdx]];
         const baseActivity = activityScaledColData[referenceIdx];
-
+        // activities can be null, and when getting raw data, they will come up as DG.FLOAT_NULL, so very close to 0, leading to incorrect deltas.
+        const actBaseActivity = options.activityCol.isNone(referenceIdx) ? null : baseActivity;
         for (const subIdx of indexArray) {
           if (forbiddentIndexes.includes(subIdx) || !filteredIndexes.includes(subIdx))
             continue;
@@ -134,11 +136,13 @@ function cliffsPairsWidgetParts(table: DG.DataFrame, options: MutationCliffsOpti
 
 
           const subSeq = alignedSeqColCategories[alignedSeqColData[subIdx]];
-
+          // same here, check for null
+          const actActivity = options.activityCol.isNone(subIdx) ? null : activityScaledColData[subIdx];
+          const delta = actBaseActivity == null || actActivity == null ? null : actBaseActivity - actActivity;
           seenIndexes.get(subIdx)!.push(referenceIdx);
           substitutionsArray.push(`${baseSequence}#${subSeq}`);
           mutationsGroupsArray.push(`${group}`);
-          deltaArray.push(baseActivity - activityScaledColData[subIdx]);
+          deltaArray.push(delta);
           substitutedToArray.push(posColCategories[posColData[subIdx]]);
           fromIdxArray.push(referenceIdx);
           toIdxArray.push(subIdx);
@@ -238,6 +242,18 @@ function cliffsPairsWidgetParts(table: DG.DataFrame, options: MutationCliffsOpti
     pairsGrid.invalidate();
     uniqueSequencesGrid.invalidate();
   });
+
+
+  // just a cosmetic thing, draw null values in delta column as N/A
+  pairsGrid.onCellPrepare((gc) => {
+    if (gc?.isTableCell && gc?.gridColumn?.name?.toLowerCase() == 'delta' && (gc?.cell?.value == null || gc?.cell?.value == DG.FLOAT_NULL)) {
+      try {
+        gc.customText = 'N/A';
+      } catch (_) {
+      }
+    }
+  });
+
   pairsGrid.onCellRender.subscribe((gcArgs) => {
     if (gcArgs.cell.tableColumn?.name !== substCol.name || !pairsSelectedIndexes.includes(gcArgs.cell.tableRowIndex!))
       return;

package/src/widgets/selection.ts

@@ -30,7 +30,6 @@ export function getSelectionWidget(table: DG.DataFrame, options: SelectionWidget
   const newTable = DG.DataFrame.create(table.rowCount);
   newTable.name = 'Selected compounds';
   newTable.filter.copyFrom(options.tableSelection);
-  const numericalCols = wu(table.columns.numerical);
   let gridSortOrder: {cols: DG.Column[], types: boolean[]} | null = null;
   for (let gridColIdx = 1; gridColIdx < options.gridColumns.length; gridColIdx++) {
     const gridCol = options.gridColumns.byIndex(gridColIdx)!;
@@ -57,14 +56,14 @@ export function getSelectionWidget(table: DG.DataFrame, options: SelectionWidget
       sourceColCategories = sourceCol.categories;
     } catch (_e) {
     }
-    const getValue = !sourceColRawData || !sourceColCategories ?
+    const getValue = (!sourceColRawData || !sourceColCategories ?
       (i: number): any => sourceCol.get(i) :
-      numericalCols
-        .some((col) => col.name === sourceCol.name) ? (i: number): number => sourceColRawData[i] :
-        (i: number): string => sourceColCategories[sourceColRawData[i]];
+      (sourceCol.isNumerical ? (i: number): number => sourceColRawData[i] :
+        (i: number): string => sourceColCategories[sourceColRawData[i]]));
+    const getNullableValue = (i: number): any => sourceCol.isNone(i) ? null : getValue(i);
     const col = sourceCol.name === options.activityColumn.name ?
-      newTable.columns.addNewFloat(gridCol.name).init((i) => getValue(i) as number) :
-      newTable.columns.addNewVirtual(gridCol.name, (i) => getValue(i) as unknown, sourceCol.type as DG.TYPE);
+      newTable.columns.addNewFloat(gridCol.name).init((i) => getNullableValue(i) as number) :
+      newTable.columns.addNewVirtual(gridCol.name, (i) => getNullableValue(i) as unknown, sourceCol.type as DG.TYPE);
     for (const [tag, value] of sourceCol.tags)
       col.setTag(tag, value);
   }