@datagrok/bio 2.22.3 → 2.22.4

package/package.json

@@ -2,10 +2,10 @@
   "name": "@datagrok/bio",
   "friendlyName": "Bio",
   "author": {
-    "name": "Leonid Stolbov",
-    "email": "lstolbov@datagrok.ai"
+    "name": "Davit Rizhinashvili",
+    "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.22.3",
+  "version": "2.22.4",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -44,12 +44,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.54.1",
+    "@datagrok-libraries/bio": "^5.54.4",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
-    "@datagrok-libraries/ml": "^6.10.2",
+    "@datagrok-libraries/ml": "^6.10.4",
     "@datagrok-libraries/tutorials": "^1.6.1",
-    "@datagrok-libraries/utils": "^4.5.7",
+    "@datagrok-libraries/utils": "^4.6.3",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -73,7 +73,7 @@
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",
     "@typescript-eslint/parser": "^8.8.1",
-    "datagrok-tools": "^4.14.29",
+    "datagrok-tools": "^4.14.37",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-rxjs": "^5.0.3",

package/src/package-api.ts

@@ -133,7 +133,7 @@ export namespace funcs {
   /**
   Detects pairs of molecules with similar structure and significant difference in any given property
   */
-  export async function activityCliffs(table: DG.DataFrame , molecules: DG.Column , activities: DG.Column , similarity: number , methodName: string , similarityMetric: string , preprocessingFunction: any , options?: any , demo?: boolean ): Promise<any> {
+  export async function activityCliffs(table: DG.DataFrame , molecules: DG.Column , activities: DG.Column , similarity: number , methodName: string , similarityMetric: string , preprocessingFunction: any , options?: any , demo?: boolean ): Promise<void> {
     return await grok.functions.call('Bio:ActivityCliffs', { table, molecules, activities, similarity, methodName, similarityMetric, preprocessingFunction, options, demo });
   }
 

package/src/package.ts

@@ -455,17 +455,17 @@ export async function getRegionTopMenu(
 //input: func preprocessingFunction
 //input: object options {optional: true}
 //input: bool demo {optional: true}
-//output: viewer result
 //editor: Bio:SeqActivityCliffsEditor
 export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<string>, activities: DG.Column,
   similarity: number, methodName: DimReductionMethods,
   similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics, preprocessingFunction: DG.Func,
   options?: (IUMAPOptions | ITSNEOptions) & Options, demo?: boolean): Promise<DG.Viewer | undefined> {
   //workaround for functions which add viewers to tableView (can be run only on active table view)
-  if (table.name !== grok.shell.tv.dataFrame.name) {
+  if (table !== grok.shell.tv.dataFrame) {
     grok.shell.error(`Table ${table.name} is not a current table view`);
     return;
   }
+  const tv = grok.shell.tv;
   if (!checkInputColumnUI(molecules, 'Activity Cliffs'))
     return;
   const axesNames = getEmbeddingColsNames(table);
@@ -509,7 +509,7 @@ export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<s
   }
 
   const pi = DG.TaskBarProgressIndicator.create(`Running sequence activity cliffs ...`);
-  return new Promise<DG.Viewer | undefined>((resolve, reject) => {
+  const scRes = (await new Promise<DG.Viewer | undefined>((resolve, reject) => {
     if (table.rowCount > fastRowCount && !options?.[BYPASS_LARGE_DATA_WARNING]) {
       ui.dialog().add(ui.divText(`Activity cliffs analysis might take several minutes.
     Do you want to continue?`))
@@ -524,7 +524,13 @@ export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<s
     const [errMsg, errStack] = errInfo(err);
     _package.logger.error(errMsg, undefined, errStack);
     throw err;
-  }).finally(() => { pi.close(); });
+  }).finally(() => { pi.close(); })) as DG.ScatterPlotViewer | undefined;
+  if (scRes?.props?.xColumnName && scRes?.props?.yColumnName && table.col(scRes.props.xColumnName) && table.col(scRes.props.yColumnName)) {
+    table.col(scRes.props.xColumnName)!.set(0, table.col(scRes.props.xColumnName)!.get(0)); // to trigger rendering
+    table.col(scRes.props.yColumnName)!.set(0, table.col(scRes.props.yColumnName)!.get(0)); // to trigger rendering
+  }
+
+  return scRes;
 }
 
 //name: Encode Sequences

package/src/tests/activity-cliffs-utils.ts

@@ -12,7 +12,7 @@ export async function _testActivityCliffsOpen(df: DG.DataFrame, drMethod: DimRed
   similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics, preprocessingFunction: DG.Func,
 ): Promise<void> {
   await grok.data.detectSemanticTypes(df);
-  const scatterPlot = (await grok.functions.call('Bio:activityCliffs', {
+  (await grok.functions.call('Bio:activityCliffs', {
     table: df,
     molecules: df.getCol(seqColName),
     activities: df.getCol(activityColName),
@@ -23,7 +23,8 @@ export async function _testActivityCliffsOpen(df: DG.DataFrame, drMethod: DimRed
     options: {[`${BYPASS_LARGE_DATA_WARNING}`]: true},
     demo: false,
   })) as DG.Viewer | undefined;
-  expect(scatterPlot != null, true);
+  const scatterPlot = Array.from(grok.shell.tv.viewers)[1];
+  expect(scatterPlot?.type === DG.VIEWER.SCATTER_PLOT, true);
 
   await awaitCheck(() => {
     const link = Array.from(scatterPlot!.root.getElementsByClassName('scatter_plot_link'));

package/src/widgets/sequence-scrolling-widget.ts

@@ -15,6 +15,7 @@ import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-h
 import * as RxJs from 'rxjs';
 import {filter} from 'rxjs/operators';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import wu from 'wu';
 
 // ============================================================================
 // OPTIMIZED VIEWPORT-AWARE CACHING WITH FORCE UPDATE SUPPORT
@@ -462,7 +463,7 @@ export function handleSequenceHeaderRendering() {
 
                   if (cur !== scrollerCur) {
                     seqCol.setTag(bioTAGS.selectedPosition, (scrollerCur).toString());
-                    if (scrollerCur >= 0 && !positionStatsViewerAddedOnce && grid.tableView) {
+                    if (scrollerCur >= 0 && !positionStatsViewerAddedOnce && grid.tableView && wu(grid.dataFrame?.columns.numerical).find((_c) => true)) {
                       positionStatsViewerAddedOnce = true;
                       const v = grid.tableView.addViewer('Sequence Position Statistics', {sequenceColumnName: seqCol.name});
                       grid.tableView.dockManager.dock(v, DG.DOCK_TYPE.DOWN, null, 'Sequence Position Statistics', 0.4);
@@ -475,7 +476,7 @@ export function handleSequenceHeaderRendering() {
                 if (grid.isDetached || _newHeight < STRICT_THRESHOLDS.WITH_TITLE) return;
                 setTimeout(() => grid.props.colHeaderHeight = _newHeight);
               },
-            });
+            }, gCol);
 
             scroller.setupTooltipHandling();
 
@@ -511,12 +512,12 @@ export function handleSequenceHeaderRendering() {
               scroller.positionWidth = font + 8; // MSA always has padding
 
               const start = getStart();
-              const startPadding = 0; // MSA doesn't need extra padding
+
 
               scroller.draw(
-                cellBounds.x + startPadding,
+                cellBounds.x,
                 cellBounds.y,
-                cellBounds.width - startPadding,
+                cellBounds.width,
                 cellBounds.height,
                 getCurrent(),
                 start,