@datagrok/bio 2.11.22 → 2.11.23

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.22",
+  "version": "2.11.23",
   "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",
@@ -39,6 +39,7 @@
     "@datagrok-libraries/ml": "^6.3.68",
     "@datagrok-libraries/tutorials": "^1.3.11",
     "@datagrok-libraries/utils": "^4.1.36",
+    "@datagrok-libraries/math": "^1.0.7",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
     "datagrok-api": "^1.16.0",

package/src/demo/bio01a-hierarchical-clustering-and-sequence-space.ts

@@ -3,13 +3,11 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {_package} from '../package';
-
-import * as lev from 'fastest-levenshtein';
-import {DistanceMatrix} from '@datagrok-libraries/ml/src/distance-matrix';
 import {getTreeHelper, ITreeHelper} from '@datagrok-libraries/bio/src/trees/tree-helper';
 import {getDendrogramService, IDendrogramService} from '@datagrok-libraries/bio/src/trees/dendrogram';
 import {demoSequenceSpace, handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
+import {getClusterMatrixWorker} from '@datagrok-libraries/math';
 
 const dataFn = 'data/sample_FASTA_PT_activity.csv';
 const seqColName = 'sequence';
@@ -55,13 +53,11 @@ export async function demoBio01aUI() {
         delay: 2000,
       })
       .step('Cluster sequences', async () => {
-        const seqCol: DG.Column<string> = df.getCol(seqColName);
-        const seqList = seqCol.toList();
-        const distance: DistanceMatrix = DistanceMatrix.calc(seqList, (aSeq: string, bSeq: string) => {
-          const levDistance = lev.distance(aSeq, bSeq);
-          return levDistance / ((aSeq.length + bSeq.length) / 2);
-        });
-        const treeRoot = await treeHelper.hierarchicalClusteringByDistance(distance, 'ward');
+        const distance = await treeHelper.calcDistanceMatrix(df, [seqColName]);
+        const clusterMatrix = await getClusterMatrixWorker(
+          distance!.data, df.rowCount, 1,
+        );
+        const treeRoot = treeHelper.parseClusterMatrix(clusterMatrix);
         dendrogramSvc.injectTreeForGrid(view.grid, treeRoot, undefined, 150, undefined);
       }, {
         description: `Perform hierarchical clustering to reveal relationships between sequences.`,

package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts

@@ -6,14 +6,13 @@ import {_package, activityCliffs} from '../package';
 import $ from 'cash-dom';
 
 import {TEMPS as acTEMPS} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
-import * as lev from 'fastest-levenshtein';
-import {DistanceMatrix} from '@datagrok-libraries/ml/src/distance-matrix';
 import {getTreeHelper, ITreeHelper} from '@datagrok-libraries/bio/src/trees/tree-helper';
 import {getDendrogramService, IDendrogramService} from '@datagrok-libraries/bio/src/trees/dendrogram';
 import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {getClusterMatrixWorker} from '@datagrok-libraries/math';
 
 const dataFn: string = 'data/sample_FASTA_PT_activity.csv';
 
@@ -67,13 +66,12 @@ export async function demoBio01bUI() {
       })
       .step('Cluster sequences', async () => {
         const progressBar = DG.TaskBarProgressIndicator.create(`Running sequence clustering...`);
-        const seqCol: DG.Column<string> = df.getCol('sequence');
-        const seqList = seqCol.toList();
-        const distance: DistanceMatrix = DistanceMatrix.calc(seqList, (aSeq: string, bSeq: string) => {
-          const levDistance = lev.distance(aSeq, bSeq);
-          return levDistance / ((aSeq.length + bSeq.length) / 2);
-        });
-        const treeRoot = await treeHelper.hierarchicalClusteringByDistance(distance, 'ward');
+
+        const distance = await treeHelper.calcDistanceMatrix(df, ['sequence']);
+        const clusterMatrix = await getClusterMatrixWorker(
+          distance!.data, df.rowCount, 1,
+        );
+        const treeRoot = treeHelper.parseClusterMatrix(clusterMatrix);
         progressBar.close();
         dendrogramSvc.injectTreeForGrid(view.grid, treeRoot, undefined, 150, undefined);
 

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

@@ -294,6 +294,10 @@ enum WlRenderLevel {
   Freqs = 2,
 }
 
+export const Debounces = new class {
+  render: number = 20;
+}();
+
 const POSITION_LABELS_HEIGHT: number = 12;
 
 export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
@@ -507,7 +511,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     const dataFrameTxt: string = this.dataFrame ? 'data' : 'null';
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.buildView( dataFrame = ${dataFrameTxt} ) start`);
     const dpr = window.devicePixelRatio;
-    this.viewSubs.push(DG.debounce(this.renderRequest)
+    this.viewSubs.push(DG.debounce(this.renderRequest, Debounces.render)
       .subscribe(this.renderRequestOnDebounce.bind(this)));
 
     this.helpUrl = '/help/visualize/viewers/web-logo.md';