@datagrok/peptides 1.22.0 → 1.22.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.22.0",
+  "version": "1.22.1",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"

package/src/model.ts

@@ -14,7 +14,6 @@ import {DistanceMatrix} from '@datagrok-libraries/ml/src/distance-matrix';
 import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {TAGS as _treeTAGS} from '@datagrok-libraries/bio/src/trees';
 import BitArray from '@datagrok-libraries/utils/src/bit-array';
-import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import wu from 'wu';
 import * as rxjs from 'rxjs';
 import $ from 'cash-dom';
@@ -790,7 +789,7 @@ export class PeptidesModel {
    * Sets tooltips to analysis grid
    */
   setTooltips(): void {
-    this.analysisView.grid.onCellTooltip((cell, x, y) => {
+    this.analysisView.grid.onCellTooltip((cell, _x, _y) => {
       if (cell.isColHeader && cell.tableColumn?.semType === C.SEM_TYPES.MONOMER)
         return true;
 
@@ -862,7 +861,7 @@ export class PeptidesModel {
       }
     }
 
-    return DG.BitSet.fromBytes(combinedSelection.buffer.buffer, combinedSelection.length);
+    return DG.BitSet.fromBytes(combinedSelection.buffer.buffer as ArrayBuffer, combinedSelection.length);
   }
 
 

package/src/utils/cell-renderer.ts

@@ -13,7 +13,6 @@ import {MonomerPositionStats, MonomerPositionStatsCache, PositionStats} from './
 import {CLUSTER_TYPE} from '../viewers/logo-summary';
 import {MonomerPosition, MostPotentResidues, SARViewer} from '../viewers/sar-viewer';
 import {MONOMER_RENDERER_TAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {PeptideUtils} from '../peptideUtils';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 

package/src/utils/tooltips.ts

@@ -59,7 +59,7 @@ export function showTooltipAt(df: DG.DataFrame, activityCol: DG.Column<number>,
       return null;
 
 
-    const mask = DG.BitSet.fromBytes(stats.mask.buffer.buffer, activityCol.length);
+    const mask = DG.BitSet.fromBytes(stats.mask.buffer.buffer as ArrayBuffer, activityCol.length);
     const hist = getActivityDistribution(getDistributionTable(activityCol, mask), true);
     const tableMap = getStatsTableMap(stats);
     if (options.fromViewer) {
@@ -82,7 +82,7 @@ export function showTooltipAt(df: DG.DataFrame, activityCol: DG.Column<number>,
       ;
     if (!stats)
       return null;
-    const mask = DG.BitSet.fromBytes(stats.mask.buffer.buffer, activityCol.length);
+    const mask = DG.BitSet.fromBytes(stats.mask.buffer.buffer as ArrayBuffer, activityCol.length);
     const hist = getActivityDistribution(getDistributionTable(activityCol, mask), true);
     const tableMap = getStatsTableMap(stats, {countName: 'Unique count'});
     if (options.fromViewer) {

package/src/viewers/logo-summary.ts

@@ -491,7 +491,7 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
         continue;
 
 
-      const bsMask = DG.BitSet.fromBytes(bitArray.buffer.buffer, filteredDfRowCount);
+      const bsMask = DG.BitSet.fromBytes(bitArray.buffer.buffer as ArrayBuffer, filteredDfRowCount);
 
       const stats: StatsItem = isDfFiltered ? getStats(activityColData, bitArray) :
         this.clusterStats[CLUSTER_TYPE.CUSTOM][customClustCol.name];
@@ -552,7 +552,7 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
         continue;
 
 
-      const bsMask = DG.BitSet.fromBytes(mask.buffer.buffer, filteredDfRowCount);
+      const bsMask = DG.BitSet.fromBytes(mask.buffer.buffer as ArrayBuffer, filteredDfRowCount);
       const stats = isDfFiltered ? getStats(activityColData, mask) :
         this.clusterStats[CLUSTER_TYPE.ORIGINAL][origLSTClustColCat[rowIdx]];
       for (let aggColIdx = 0; aggColIdx < aggStringColNames.length; ++aggColIdx) {
@@ -777,10 +777,6 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
         ctrlPressed: ev.ctrlKey,
       });
       grid.invalidate();
-
-      _package.files.readAsText('help/logo-summary-table.md').then((text) => {
-        grok.shell.windows.help.showHelp(ui.markdown(text));
-      }).catch((e) => grok.log.error(e));
     });
     grid.onCellTooltip((gridCell, x, y) => {
       if (!gridCell.isTableCell) {
@@ -1003,7 +999,7 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
       return null;
 
 
-    const mask = DG.BitSet.fromBytes(bitArray.buffer.buffer, rowCount);
+    const mask = DG.BitSet.fromBytes(bitArray.buffer.buffer as ArrayBuffer, rowCount);
     const distributionTable = getDistributionTable(activityCol, mask);
     const hist = getActivityDistribution(distributionTable, true);
     const tableMap = getStatsTableMap(stats);

package/src/viewers/sar-viewer.ts

@@ -572,7 +572,6 @@ export abstract class SARViewer extends DG.JsViewer implements ISARViewer {
   /** Processes attached table and sets viewer properties. */
   onTableAttached(): void {
     super.onTableAttached();
-    this.helpUrl = 'https://datagrok.ai/help/datagrok/solutions/domains/bio/peptides-sar';
     if (isApplicableDataframe(this.dataFrame)) {
       this.getProperty(`${SAR_PROPERTIES.SEQUENCE}${COLUMN_NAME}`)
         ?.set(this, this.dataFrame.columns.bySemType(DG.SEMTYPE.MACROMOLECULE)!.name);
@@ -1008,8 +1007,6 @@ export class MonomerPosition extends SARViewer {
         }
       }
       grid.invalidate();
-
-      this.showHelp();
     });
 
     setViewerGridProps(grid);
@@ -1031,13 +1028,6 @@ export class MonomerPosition extends SARViewer {
     return grid;
   }
 
-  /** Shows viewer context help. */
-  showHelp(): void {
-    _package.files.readAsText('help/monomer-position.md').then((text) => {
-      grok.shell.windows.help.showHelp(ui.markdown(text));
-    }).catch((e) => grok.log.error(e));
-  }
-
   /**
    * Gets monomer-position from MonomerPosition grid cell.
    * @param gridCell - MonomerPosition grid cell.
@@ -1074,7 +1064,6 @@ export class MonomerPosition extends SARViewer {
         invariantMapMode.value = false;
         mutationCliffsMode.value = true;
         this.mode = SELECTION_MODE.MUTATION_CLIFFS;
-        this.showHelp();
       });
       mutationCliffsMode.setTooltip('Statistically significant changes in activity');
       const invariantMapMode = ui.input.bool(SELECTION_MODE.INVARIANT_MAP, {value: this.mode === SELECTION_MODE.INVARIANT_MAP});
@@ -1082,7 +1071,6 @@ export class MonomerPosition extends SARViewer {
         mutationCliffsMode.value = false;
         invariantMapMode.value = true;
         this.mode = SELECTION_MODE.INVARIANT_MAP;
-        this.showHelp();
       });
       invariantMapMode.setTooltip('Number of sequences having monomer-position');
       const setDefaultProperties = (input: DG.InputBase): void => {
@@ -1136,7 +1124,6 @@ export class MostPotentResidues extends SARViewer {
   /** Processes attached table and sets viewer properties. */
   onTableAttached(): void {
     super.onTableAttached();
-    this.helpUrl = 'https://datagrok.ai/help/datagrok/solutions/domains/bio/peptides-sar';
     this.render();
   }
 
@@ -1361,10 +1348,6 @@ export class MostPotentResidues extends SARViewer {
 
       this.modifyInvariantMapSelection(monomerPosition, {shiftPressed: ev.shiftKey, ctrlPressed: ev.ctrlKey});
       grid.invalidate();
-
-      _package.files.readAsText('help/most-potent-residues.md').then((text) => {
-        grok.shell.windows.help.showHelp(ui.markdown(text));
-      }).catch((e) => grok.log.error(e));
     });
 
     setViewerGridProps(grid);

package/src/widgets/distribution.ts

@@ -146,7 +146,7 @@ function getSingleDistribution(table: DG.DataFrame, stats: StatsItem, options: D
   const hist = getActivityDistribution(getDistributionTable(options.activityCol, table.selection,
     options.peptideSelection));
   const aggregatedColMap = getAggregatedColumnValues(table, Object.entries(options.columns),
-    {filterDf: true, mask: DG.BitSet.fromBytes(stats.mask.buffer.buffer, stats.mask.length)});
+    {filterDf: true, mask: DG.BitSet.fromBytes(stats.mask.buffer.buffer as ArrayBuffer, stats.mask.length)});
   const tableMap = getStatsTableMap(stats);
   const resultMap: { [key: string]: any } = {...tableMap, ...aggregatedColMap};
   const distributionRoot = getDistributionPanel(hist, resultMap, labelMap);