@datagrok/peptides 1.17.26 → 1.17.28

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.17.26",
+  "version": "1.17.28",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -15,11 +15,11 @@
   "dependencies": {
     "@datagrok-libraries/bio": "^5.40.0",
     "@datagrok-libraries/math": "1.1.12",
-    "@datagrok-libraries/ml": "^6.6.16",
+    "@datagrok-libraries/ml": "^6.6.17",
     "@datagrok-libraries/statistics": "^1.2.12",
     "@datagrok-libraries/tutorials": "^1.3.13",
     "@datagrok-libraries/utils": "^4.2.20",
-    "datagrok-api": "^1.20.1",
+    "datagrok-api": "^1.20.0",
     "@webgpu/types": "^0.1.40",
     "cash-dom": "latest",
     "file-loader": "latest",

package/src/demo/fasta.ts

@@ -20,7 +20,7 @@ export async function macromoleculeSarFastaDemoUI(): Promise<void> {
   const simpleAlignedSeqCol = simpleTable.getCol(alignedSequenceCol);
   simpleAlignedSeqCol.semType = DG.SEMTYPE.MACROMOLECULE;
   simpleAlignedSeqCol.setTag(C.TAGS.ALPHABET, ALPHABET.PT);
-  simpleAlignedSeqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+  simpleAlignedSeqCol.meta.units = NOTATION.FASTA;
   simpleAlignedSeqCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
   const simpleScaledCol = scaleActivity(simpleActivityCol, C.SCALING_METHODS.MINUS_LG);
   const clustersCol = DG.Column.string('Cluster', simpleTable.rowCount).init('0');

package/src/model.ts

@@ -147,7 +147,7 @@ export class PeptidesModel {
         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;
 
 

package/src/package.ts

@@ -167,7 +167,7 @@ export function manualAlignment(_monomer: string): DG.Widget {
 //meta.demoPath: Bioinformatics | Macromolecule SAR Analysis
 //meta.isDemoScript: False
 export async function macromoleculeSarFastaDemo(): Promise<void> {
-  return macromoleculeSarFastaDemoUI();
+  return await macromoleculeSarFastaDemoUI();
 }
 
 //name: LST Pie Chart

package/src/viewers/sar-viewer.ts

@@ -79,7 +79,7 @@ export enum PROPERTY_CATEGORIES {
 }
 
 const MUTATION_CLIFFS_CELL_WIDTH = 40;
-const AAR_CELL_WIDTH = 30;
+const AAR_CELL_WIDTH = 40;
 
 export interface ISARViewer {
   sequenceColumnName: string;

package/src/widgets/selection.ts

@@ -30,6 +30,7 @@ export function getSelectionWidget(table: DG.DataFrame, options: SelectionWidget
   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)!;
     if (!gridCol.visible)
@@ -40,15 +41,29 @@ export function getSelectionWidget(table: DG.DataFrame, options: SelectionWidget
     if (sourceCol.type === DG.COLUMN_TYPE.BOOL)
       continue;
 
+    // restore sorting
+    if (gridSortOrder === null && gridCol.grid && gridCol.grid.sortByColumns?.length > 0 &&
+       gridCol.grid.sortTypes?.length === gridCol.grid.sortByColumns.length)
+      gridSortOrder = {cols: gridCol.grid.sortByColumns, types: gridCol.grid.sortTypes};
 
-    const sourceColRawData = sourceCol.getRawData();
-    const sourceColCategories = sourceCol.categories;
-    const getValue = numericalCols
-      .some((col) => col.name === sourceCol.name) ? (i: number): number => sourceColRawData[i] :
-      (i: number): string => sourceColCategories[sourceColRawData[i]];
+
+    // bigint or qnum columns can throw an error when getting raw data (might be fixed in future versions)
+    let sourceColRawData: ArrayLike<number> | null = null;
+    let sourceColCategories: string[] | null = null;
+
+    try {
+      sourceColRawData = sourceCol.getRawData();
+      sourceColCategories = sourceCol.categories;
+    } catch (_e) {
+    }
+    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]];
     const col = sourceCol.name === options.activityColumn.name ?
-      newTable.columns.addNewFloat(gridCol.name).init((i) => getValue(i)) :
-      newTable.columns.addNewVirtual(gridCol.name, (i) => getValue(i), sourceCol.type as DG.TYPE);
+      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);
     for (const [tag, value] of sourceCol.tags)
       col.setTag(tag, value);
   }
@@ -72,6 +87,8 @@ export function getSelectionWidget(table: DG.DataFrame, options: SelectionWidget
   const gridHost = ui.box(grid.root);
   gridHost.style.marginLeft = '0px';
   setTimeout(() => {
+    if (gridSortOrder !== null)
+      grid.sort(gridSortOrder.cols, gridSortOrder.types);
     for (let gridColIdx = 1; gridColIdx < options.gridColumns.length; gridColIdx++) {
       const originalGridCol = options.gridColumns.byIndex(gridColIdx)!;
       if (!originalGridCol.visible)