@datagrok/bio 2.4.47 → 2.4.48

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.47",
+  "version": "2.4.48",
   "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/package.ts

@@ -57,6 +57,7 @@ import {BioPackage, BioPackageProperties} from './package-types';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {ObjectPropertyBag} from 'datagrok-api/dg';
 import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
+import {getCompositionAnalysisWidget} from './widgets/composition-analysis-widget';
 
 export const _package = new BioPackage();
 
@@ -218,6 +219,14 @@ export function macroMolColumnPropertyPanel(molColumn: DG.Column): DG.Widget {
   return getMacromoleculeColumnPropertyPanel(molColumn);
 }
 
+//name: Composition analysis
+//tags: panel, bio, widgets
+//input: semantic_value sequence { semType: Macromolecule }
+//output: widget result
+export function compositionAnalysisWidget(sequence: DG.SemanticValue): DG.Widget {
+  return getCompositionAnalysisWidget(sequence);
+}
+
 //name: separatorSequenceCellRenderer
 //tags: cellRenderer
 //meta.cellType: sequence

package/src/widgets/composition-analysis-widget.ts

@@ -0,0 +1,62 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import {TAGS as bioTAGS, ALPHABET, getPaletteByType} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
+import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
+import '../../css/composition-analysis.css';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+
+export function getCompositionAnalysisWidget(val: DG.SemanticValue) {
+  const host = ui.div();
+  host.classList.add('macromolecule-cell-comp-analysis-host');
+  const alphabet = val.cell.column.tags[bioTAGS.alphabet];
+  let palette: SeqPalette = UnknownSeqPalettes.Color;
+  switch (alphabet) {
+    case ALPHABET.DNA:
+    case ALPHABET.RNA:
+      palette = getPaletteByType(ALPHABET.DNA);
+      break;
+    case ALPHABET.PT:
+      palette = getPaletteByType(ALPHABET.PT);
+      break;
+    default:
+      break;
+  }
+
+  const counts = new Map<string, number>();
+  let max = 0;
+  const uh = UnitsHandler.getOrCreate(val.cell.column);
+  const splitter = uh.getSplitter();
+  const parts = splitter(val.value);
+  const len = parts.length;
+  parts.filter((p) => p && p !== '').forEach((c: string) => {
+    const count = counts.get(c) || 0;
+    counts.set(c, count + 1);
+    max = Math.max(max, count + 1);
+  });
+  max /= len;// percentage
+  // calculate frequencies
+  const compositionMap: {[key: string]: HTMLElement} = {};
+  const valueArray = Array.from(counts.entries());
+  valueArray.sort((a, b) => b[1] - a[1]);
+  valueArray.forEach(([key, value]) => {
+    const ratio = value / len;
+    const color = palette.get(key);
+    const barDiv = ui.div('', {classes: 'macromolecule-cell-comp-analysis-bar'});
+    barDiv.style.width = `${ratio / max * 50}px`;
+    const valueDiv = ui.div((ratio * 100).toFixed(2) + '%');
+    barDiv.style.backgroundColor = color;
+    compositionMap[key] = ui.div([barDiv, valueDiv], {classes: 'macromolecule-cell-comp-analysis-value'});
+  });
+
+  const table = ui.tableFromMap(compositionMap);
+  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;
+  });
+
+  host.appendChild(table);
+  return new DG.Widget(host);
+}