@datagrok/bio 2.21.11 → 2.22.0

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.21.11",
+  "version": "2.22.0",
   "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",
@@ -44,10 +44,10 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.53.2",
+    "@datagrok-libraries/bio": "^5.53.4",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
-    "@datagrok-libraries/ml": "^6.10.0",
+    "@datagrok-libraries/ml": "^6.10.2",
     "@datagrok-libraries/tutorials": "^1.6.1",
     "@datagrok-libraries/utils": "^4.5.7",
     "datagrok-api": "^1.25.0",

package/src/package.ts

@@ -82,7 +82,7 @@ export const _package = new BioPackage(/*{debug: true}/**/);
 // let monomerLib: MonomerLib | null = null;
 
 //name: getMonomerLibHelper
-//description:
+//description: Returns an instance of the monomer library helper
 //output: object result
 export async function getMonomerLibHelper(): Promise<IMonomerLibHelper> {
   return await MonomerLibManager.getInstance();
@@ -377,7 +377,6 @@ export function macromoleculeDifferenceCellRenderer(): MacromoleculeDifferenceCe
 
 //name: sequenceAlignment
 //input: string alignType {choices: ['Local alignment', 'Global alignment']}
-// eslint-disable-next-line max-len
 //input: string alignTable {choices: ['AUTO', 'NUCLEOTIDES', 'BLOSUM45', 'BLOSUM50', 'BLOSUM62','BLOSUM80','BLOSUM90','PAM30','PAM70','PAM250','SCHNEIDER','TRANS']}
 //input: double gap
 //input: string seq1
@@ -464,7 +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'))
@@ -595,7 +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 =
@@ -975,12 +974,12 @@ export async function manageMonomersView() {
   await monomerManager.getViewRoot();
 }
 
-//name: Monomers
+//name: Manage Monomer Libraries
 //tags: app
 //meta.browsePath: Peptides
 //meta.icon: files/icons/monomers.png
 //output: view v
-export async function manageLibrariesApp(): Promise<DG.View> {
+export async function manageMonomerLibrariesView(): Promise<DG.View> {
   return await showManageLibrariesView(false);
 }
 

package/src/utils/seq-helper/seq-handler.ts

@@ -415,7 +415,7 @@ export class SeqHandler implements ISeqHandler {
   public get maxLength(): number {
     if (this._maxLength === null) {
       this._maxLength = this.column.length === 0 ? 0 :
-        Math.max(...wu.count(0).take(this.column.length).map((rowIdx) => this.getSplitted(rowIdx).length));
+        wu.count(0).take(this.column.length).map((rowIdx) => this.getSplitted(rowIdx).length).reduce((a, b) => a > b ? a : b, 0);
     }
     return this._maxLength!;
   }

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;
-}