@datagrok/bio 2.10.29 → 2.11.0

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.10.29",
+  "version": "2.11.0",
   "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",
@@ -34,7 +34,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.38.13",
+    "@datagrok-libraries/bio": "^5.39.0",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.50",
     "@datagrok-libraries/tutorials": "^1.3.6",

package/src/apps/web-logo-app.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
 
-import {IWebLogoViewer} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import {IWebLogoViewer, WebLogoProps} from '@datagrok-libraries/bio/src/viewers/web-logo';
 
 import {PROPS as wlPROPS} from '../viewers/web-logo-viewer';
 
@@ -14,7 +14,11 @@ export class WebLogoApp {
   df: DG.DataFrame;
   view: DG.TableView;
 
-  constructor(private readonly urlParams: URLSearchParams, private readonly funcName: string) {}
+  constructor(
+    private readonly urlParams: URLSearchParams,
+    private readonly funcName: string,
+    private readonly options: Partial<WebLogoProps> = {}
+  ) {}
 
   async init(df: DG.DataFrame): Promise<void> {
     this.df = df;
@@ -32,7 +36,7 @@ export class WebLogoApp {
     this.view = grok.shell.addTableView(this.df);
     this.view.path = this.view.basePath = `func/${_package.name}.${this.funcName}?${urlParamsTxt}`;
 
-    const options: { [p: string]: any } = {sequenceColumnName: 'sequence'};
+    const options: { [p: string]: any } = {...this.options, ...{sequenceColumnName: 'sequence'}};
     for (const [optName, optValue] of this.urlParams.entries()) {
       switch (optName) {
         // boolean

package/src/package.ts

@@ -976,6 +976,20 @@ export async function webLogoLargeApp(): Promise<void> {
   }
 }
 
+//name: webLogoAggApp
+export async function webLogoAggApp(): Promise<void> {
+  const pi = DG.TaskBarProgressIndicator.create('WebLogo ...');
+  try {
+    const urlParams = new URLSearchParams(window.location.search);
+    const app = new WebLogoApp(urlParams, 'webLogoAggApp');
+    const df: DG.DataFrame = await _package.files.readCsv('data/sample_FASTA_PT_activity.csv');
+    await grok.data.detectSemanticTypes(df);
+    await app.init(df);
+  } finally {
+    pi.close();
+  }
+}
+
 //name: getRegionApp
 export async function getRegionApp(): Promise<void> {
   const pi = DG.TaskBarProgressIndicator.create('getRegion ...');

package/src/tests/WebLogo-positions-test.ts

@@ -55,7 +55,7 @@ ATC-G-TTGC--
     for (let i = 0; i < positions.length; i++) {
       expect(positions[i].name, resAllDf1[i].name);
       for (const m of positions[i].getMonomers())
-        expect(positions[i].getFreq(m).count, resAllDf1[i].getFreq(m).count);
+        expect(positions[i].getFreq(m).rowCount, resAllDf1[i].getFreq(m).rowCount);
     }
   });
 
@@ -104,7 +104,7 @@ ATC-G-TTGC--
     for (let i = 0; i < positions.length; i++) {
       expect(positions[i].name, resAllDf1[i].name);
       for (const m of positions[i].getMonomers())
-        expect(positions[i].getFreq(m).count, resAllDf1[i].getFreq(m).count);
+        expect(positions[i].getFreq(m).rowCount, resAllDf1[i].getFreq(m).rowCount);
     }
   });
 
@@ -204,7 +204,7 @@ function expectPositionInfo(actualPos: PI, expectedPos: PI): void {
   expectArray(actualPos.getMonomers(), expectedPos.getMonomers());
   for (const key of actualPos.getMonomers()) {
     //
-    expect(actualPos.getFreq(key).count, expectedPos.getFreq(key).count);
+    expect(actualPos.getFreq(key).rowCount, expectedPos.getFreq(key).rowCount);
   }
 }
 

package/src/utils/agg.ts

@@ -0,0 +1,29 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+export type AggValueListType = (number | null)[] | Float32Array | Int32Array;
+export type AggFunc = (valueList: AggValueListType) => number | null;
+
+export function getAgg(agg: DG.AggregationType): AggFunc {
+  let res: AggFunc;
+
+  function buildCol(valueList: AggValueListType): DG.Column<number> {
+    let resCol: DG.Column<number>;
+    const resColName = `agg`;
+    if (valueList instanceof Float32Array)
+      resCol = DG.Column.fromFloat32Array(resColName, valueList as Float32Array);
+    else if (valueList instanceof Int32Array)
+      resCol = DG.Column.fromInt32Array(resColName, valueList as Int32Array);
+    else
+      resCol = DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, resColName, valueList as (number | null)[]);
+
+    return resCol;
+  }
+
+  return (valueList: AggValueListType): number | null => {
+    const aggCol = buildCol(valueList);
+    const res = aggCol.aggregate(agg);
+    return res;
+  };
+}