@datagrok/bio 2.21.12 → 2.22.1

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.21.12",
+  "version": "2.22.1",
   "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",
@@ -44,7 +44,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.53.3",
+    "@datagrok-libraries/bio": "^5.53.4",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
     "@datagrok-libraries/ml": "^6.10.2",

package/src/analysis/sequence-diversity-viewer.ts

@@ -32,8 +32,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
       return;
     if (this.dataFrame) {
       if (computeData && this.targetColumn) {
-        const sh = this.seqHelper.getSeqHandler(this.targetColumn);
-        await (sh.isFasta() ? this.computeByMM() : this.computeByChem());
+        await this.computeByMM();
 
         const diverseColumnName: string = this.diverseColumnLabel != null ? this.diverseColumnLabel :
           `diverse (${this.targetColumnName})`;
@@ -57,18 +56,6 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
     }
   }
 
-  private async computeByChem() {
-    const monomericMols = await getMonomericMols(this.targetColumn!, this.seqHelper);
-    //need to create df to calculate fingerprints
-    const _monomericMolsDf = DG.DataFrame.fromColumns([monomericMols]);
-    this.renderMolIds = await grok.functions.call('Chem:callChemDiversitySearch', {
-      col: monomericMols,
-      metricName: this.distanceMetric,
-      limit: this.limit,
-      fingerprint: this.fingerprint,
-    });
-  }
-
   private async computeByMM() {
     const encodedSequences =
       (await getEncodedSeqSpaceCol(this.targetColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;

package/src/package.ts

@@ -463,7 +463,7 @@ export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<s
   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) {
-    grok.shell.error(`Table ${table.name} is not an current table view`);
+    grok.shell.error(`Table ${table.name} is not a current table view`);
     return;
   }
   if (!checkInputColumnUI(molecules, 'Activity Cliffs'))
@@ -594,7 +594,7 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
 ): Promise<DG.ScatterPlotViewer | 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) {
-    grok.shell.error(`Table ${table.name} is not an current table view`);
+    grok.shell.error(`Table ${table.name} is not a current table view`);
     return;
   }
   const tableView =

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -283,6 +283,14 @@ class LibManagerView {
         this._duplicateManager.root],
       {style: {width: '100%', height: '100%'}},
       true);
+    if (this._view) {
+      try {
+        this._view.subs.forEach((s) => s.unsubscribe());
+        this._view.detach();
+        this._view.close();
+      } catch (_e) {
+      }
+    }
     this._view = DG.View.fromRoot(v);
     this._view.name = LibManagerView.viewName;
     if (addView)
@@ -304,7 +312,7 @@ class LibManagerView {
       this._view.subs.push(grok.events.onCurrentViewChanged.subscribe(() => {
         try {
           const inst = LibManagerView._instance;
-          if (inst && inst._view && 'id' in grok.shell.v && grok.shell.v.id === inst._view.id)
+          if (inst && inst._view && grok.shell.v && 'id' in grok.shell.v && grok.shell.v.id === inst._view.id)
             inst._duplicateManager?.refresh();
         } catch (e) {
           console.error(e);

package/src/viewers/web-logo-viewer.ts

@@ -30,10 +30,10 @@ import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 import {undefinedColor} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
 
 import {AggFunc, getAgg} from '../utils/agg';
-import {buildCompositionTable} from '../widgets/composition-analysis-widget';
 
 import {_package, getMonomerLibHelper} from '../package';
 import {numbersWithinMaxDiff} from './utils';
+import {buildCompositionTable} from '@datagrok-libraries/bio/src/utils/composition-table';
 
 declare global {
   interface HTMLCanvasElement {

package/src/widgets/composition-analysis-widget.ts

@@ -12,6 +12,7 @@ import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 
 import '../../css/composition-analysis.css';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {buildCompositionTable} from '@datagrok-libraries/bio/src/utils/composition-table';
 
 export function getCompositionAnalysisWidget(
   val: DG.SemanticValue, monomerLib: IMonomerLibBase, seqHelper: ISeqHelper
@@ -43,41 +44,3 @@ export function getCompositionAnalysisWidget(
   return new DG.Widget(host);
 }
 
-export function buildCompositionTable(
-  counts: { [m: string]: number }, biotype: HelmType, monomerLib: IMonomerLibBase
-): HTMLTableElement {
-  let sumValue: number = 0;
-  let maxValue: number | null = null;
-  for (const value of Object.values(counts)) {
-    sumValue = sumValue + value;
-    maxValue = maxValue === null ? value : Math.max(maxValue, value);
-  }
-  const maxRatio = maxValue! / sumValue;
-  const elMap: { [m: string]: HTMLElement } = Object.assign({}, ...Array.from(Object.entries(counts))
-    .sort((a, b) => b[1] - a[1])
-    .map(([cm, value]) => {
-      const ratio = value / sumValue;
-      const wem = monomerLib.getWebEditorMonomer(biotype, cm)!;
-      const color = wem.backgroundcolor!;
-      const barDiv = ui.div('', {classes: 'macromolecule-cell-comp-analysis-bar'});
-      barDiv.style.width = `${50 * ratio / maxRatio}px`;
-      barDiv.style.backgroundColor = color;
-      if (GAP_SYMBOL === cm) {
-        barDiv.style.borderWidth = '1px';
-        barDiv.style.borderStyle = 'solid';
-        barDiv.style.borderColor = DG.Color.toHtml(DG.Color.lightGray);
-      }
-      const displayMonomer: string = GAP_SYMBOL === cm ? '-' : cm;
-      const valueDiv = ui.div(`${(100 * ratio).toFixed(2)}%`);
-      const el = ui.div([barDiv, valueDiv], {classes: 'macromolecule-cell-comp-analysis-value'});
-      return ({[displayMonomer]: el});
-    }));
-
-  const table = ui.tableFromMap(elMap);
-  Array.from(table.rows).forEach((row) => {
-    const barCol = (row.getElementsByClassName('macromolecule-cell-comp-analysis-bar')[0] as HTMLDivElement)
-      .style.backgroundColor;
-    row.cells[0].style.color = barCol;
-  });
-  return table;
-}

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

@@ -14,6 +14,7 @@ import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/mon
 import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 import * as RxJs from 'rxjs';
 import {filter} from 'rxjs/operators';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 
 // ============================================================================
 // OPTIMIZED VIEWPORT-AWARE CACHING WITH FORCE UPDATE SUPPORT
@@ -110,7 +111,7 @@ class MSAViewportManager {
     });
   }
 
-  static getConservationForViewport(seqHandler: any, viewportStart: number, viewportEnd: number, maxLength: number): number[] {
+  static getConservationForViewport(seqHandler: ISeqHandler, viewportStart: number, viewportEnd: number, maxLength: number): number[] {
     // Create a full-sized array filled with zeros
     const result: number[] = new Array(maxLength).fill(0);
 
@@ -132,7 +133,7 @@ class MSAViewportManager {
     return result;
   }
 
-  static getWebLogoForViewport(seqHandler: any, viewportStart: number, viewportEnd: number, maxLength: number): Map<number, Map<string, number>> {
+  static getWebLogoForViewport(seqHandler: ISeqHandler, viewportStart: number, viewportEnd: number, maxLength: number): Map<number, Map<string, number>> {
     const result: Map<number, Map<string, number>> = new Map();
 
     // Calculate which chunks we need
@@ -161,7 +162,7 @@ class MSAViewportManager {
 // ============================================================================
 
 class LazyWebLogoTrack extends WebLogoTrack {
-  private seqHandler: any;
+  private seqHandler: ISeqHandler;
   private maxLength: number;
   private lastViewportStart: number = -1;
   private lastViewportEnd: number = -1;
@@ -169,7 +170,7 @@ class LazyWebLogoTrack extends WebLogoTrack {
   private forceNextUpdate: boolean = false;
 
   constructor(
-    seqHandler: any,
+    seqHandler: ISeqHandler,
     maxLength: number,
     height: number = 45,
     title: string = 'WebLogo'
@@ -239,7 +240,7 @@ class LazyWebLogoTrack extends WebLogoTrack {
 }
 
 class LazyConservationTrack extends ConservationTrack {
-  private seqHandler: any;
+  private seqHandler: ISeqHandler;
   private maxLength: number;
   private lastViewportStart: number = -1;
   private lastViewportEnd: number = -1;
@@ -247,7 +248,7 @@ class LazyConservationTrack extends ConservationTrack {
   private forceNextUpdate: boolean = false;
 
   constructor(
-    seqHandler: any,
+    seqHandler: ISeqHandler,
     maxLength: number,
     height: number = 45,
     colorScheme: 'default' | 'rainbow' | 'heatmap' = 'default',
@@ -406,7 +407,7 @@ export function handleSequenceHeaderRendering() {
 
         grid.sub(filterChangeSub);
 
-        const initializeHeaders = (monomerLib: any = null) => {
+        const initializeHeaders = (monomerLib: IMonomerLib) => {
           const tracks: { id: string, track: MSAHeaderTrack, priority: number }[] = [];
 
           // Create lazy tracks only if we have multiple sequences
@@ -433,7 +434,7 @@ export function handleSequenceHeaderRendering() {
 
           if (monomerLib) {
             webLogoTrack.setMonomerLib(monomerLib);
-            webLogoTrack.setBiotype(sh.defaultBiotype || 'PEPTIDE');
+            webLogoTrack.setBiotype(sh.defaultBiotype || 'HELM_AA');
           }
 
           webLogoTrack.setupDefaultTooltip();
@@ -478,13 +479,15 @@ export function handleSequenceHeaderRendering() {
 
           scroller.setSelectionData(df, seqCol, sh);
 
-          grid.props.colHeaderHeight = initialHeaderHeight;
+          if (maxSeqLen > 50) {
+            grid.props.colHeaderHeight = initialHeaderHeight;
 
-          // Set column width
-          setTimeout(() => {
-            if (grid.isDetached) return;
-            gCol.width = 400;
-          }, 300);
+            // Set column width
+            setTimeout(() => {
+              if (grid.isDetached) return;
+              gCol.width = 400;
+            }, 300);
+          }
 
           // Handle cell rendering
           grid.sub(grid.onCellRender.subscribe((e) => {
@@ -524,8 +527,9 @@ export function handleSequenceHeaderRendering() {
             initializeHeaders(monomerLib);
           })
           .catch((error) => {
-            console.error('Error loading monomerLib:', error);
-            initializeHeaders();
+            grok.shell.warning(`Failed to initialize monomer library`);
+            //initializeHeaders();
+            console.error('Failed to initialize monomer library:', error);
           });
       }
     }, 1000);