@datagrok/bio 2.21.2 → 2.21.4

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.21.2",
+  "version": "2.21.4",
   "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",

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

@@ -73,6 +73,8 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
         let prevTimer: any = null;
         const _ = resDf.onCurrentRowChanged.subscribe((_: any) => {
           prevTimer && clearTimeout(prevTimer);
+          if ((resDf.currentRowIdx ?? -1) < 0)
+            return;
           this.dataFrame.currentRowIdx = resDf.col('indexes')!.get(resDf.currentRowIdx);
           prevTimer = setTimeout(() => { this.createPropertyPanel(resDf); }, 300);
           this.gridSelect = true;

package/src/substructure-search/substructure-search.ts

@@ -96,7 +96,7 @@ export class SubstructureSearchDialog {
       ]))
       .onOK(async () => {
         let substructure = this.units === NOTATION.HELM ? df.get(SUBSTR_HELM_COL_NAME, 0) : this.substructureInput.value;
-        if (this.units === NOTATION.SEPARATOR && this.separatorInput.value !== this.separator && this.separatorInput.value !== '')
+        if (this.units === NOTATION.SEPARATOR && this.separatorInput.value !== this.separator && !!this.separatorInput.value)
           substructure = substructure.replaceAll(this.separatorInput.value, this.separator);
         let matches: DG.BitSet;
         if (this.units === NOTATION.HELM)

package/src/utils/monomer-cell-renderer.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as DG from 'datagrok-api/dg';
 import {GridCell} from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
@@ -25,8 +26,8 @@ export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase
   ): void {
     g.save();
     try {
-      if (gridCell.gridRow < 0) return;
-      const applyToBackground = gridCell.cell?.column && gridCell.cell.column.getTag(MONOMER_RENDERER_TAGS.applyToBackground) === 'true';
+      if (!gridCell.isTableCell) return;
+      const applyToBackground = gridCell.cell?.column && gridCell.cell.column?.dart && gridCell.cell.column.getTag(MONOMER_RENDERER_TAGS.applyToBackground) === 'true';
 
       g.font = `12px monospace`;
       g.textBaseline = 'middle';
@@ -44,9 +45,8 @@ export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase
           const colors = this.monomerLib.getMonomerColors(biotype, symbol);
           textcolor = colors?.textcolor ?? textcolor;
           backgroundcolor = colors?.backgroundcolor ?? backgroundcolor;
-        } else {
+        } else
           textcolor = this.monomerLib.getMonomerTextColor(biotype, symbol);
-        }
       }
 
       //cell width of monomer should dictate how many characters can be displayed

package/src/widgets/bio-substructure-filter.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-lines */
 /**
  * Macromolecules substructure filter that uses Datagrok's collaborative filtering.
  * 1. On onRowsFiltering event, only FILTER OUT rows that do not satisfy this filter's criteria
@@ -9,23 +10,21 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import wu from 'wu';
-import $ from 'cash-dom';
-import {fromEvent, Observable, Subject, Unsubscribable} from 'rxjs';
+
+import {Observable, Subject, Unsubscribable} from 'rxjs';
 
 import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
-import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {IRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
-import {helmSubstructureSearch, linearSubstructureSearch} from '../substructure-search/substructure-search';
-import {updateDivInnerHTML} from '../utils/ui-utils';
-import {BioFilterBase, BioFilterProps, IBioFilter, IFilterProps} from '@datagrok-libraries/bio/src/substructure-filter/bio-substructure-filter-types';
+import {linearSubstructureSearch} from '../substructure-search/substructure-search';
+import {BioFilterBase, BioFilterProps, IBioFilter, IFilterProps}
+  from '@datagrok-libraries/bio/src/substructure-filter/bio-substructure-filter-types';
 import {HelmBioFilter} from './bio-substructure-filter-helm';
-import { _package } from '../package';
+import {_package} from '../package';
 
 const FILTER_SYNC_EVENT: string = 'bio-substructure-filter';
 
@@ -334,14 +333,18 @@ export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
     this.substructureInput = ui.input.string('', {
       value: '', onValueChanged: (value) => {
         this.props = new SeparatorFilterProps(value, this.props.separator, _package.logger);
-        if (!this._propsChanging) this.onChanged.next();
+        setTimeout(() => {
+          if (!this._propsChanging) this.onChanged.next();
+        });
       }, placeholder: 'Substructure'
     });
     this.separatorInput = ui.input.string('', {
       value: this.colSeparator = colSeparator, onValueChanged: (value) => {
-        const separator: string | undefined = !!value ? value : undefined;
+        const separator: string | undefined = !!value ? value : '';
         this.props = new SeparatorFilterProps(this.props.substructure, separator, _package.logger);
-        if (!this._propsChanging) this.onChanged.next();
+        setTimeout(() => {
+          if (!this._propsChanging) this.onChanged.next();
+        });
       }, placeholder: 'Separator'
     });
   }
@@ -356,7 +359,7 @@ export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
   }
 
   get filterSummary(): string {
-    const sep: string = this.props.separator ? this.props.separator : this.colSeparator;
+    const _sep: string = this.props.separator ? this.props.separator : this.colSeparator;
     return `${this.props.substructure}, {sep}`;
   };