@datagrok/bio 2.10.9 → 2.10.11

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.10.9",
+  "version": "2.10.11",
   "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/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts

@@ -65,6 +65,7 @@ export async function demoBio01bUI() {
         delay: 2000,
       })
       .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) => {
@@ -72,6 +73,7 @@ export async function demoBio01bUI() {
           return levDistance / ((aSeq.length + bSeq.length) / 2);
         });
         const treeRoot = await treeHelper.hierarchicalClusteringByDistance(distance, 'ward');
+        progressBar.close();
         dendrogramSvc.injectTreeForGrid(view.grid, treeRoot, undefined, 150, undefined);
 
         // adjust for visual

package/src/utils/cell-renderer.ts

@@ -34,8 +34,8 @@ type TempType = { [tagName: string]: any };
 const undefinedColor = 'rgb(100,100,100)';
 const monomerToShortFunction: MonomerToShortFunc = monomerToShort;
 
-function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number): number {
-  return grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number, dpr: number): number {
+  return !!grid ? Math.max(Math.min(grid.canvas.width / dpr - x, w)) : Math.max(g.canvas.width / dpr - x, 0);
 }
 
 export function processSequence(subParts: ISeqSplitted): [string[], boolean] {
@@ -182,11 +182,12 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     g.save();
     try {
+      const dpr = window.devicePixelRatio;
       const grid = gridCell.gridRow !== -1 ? gridCell.grid : null;
       const value: any = gridCell.cell.value;
       const paletteType = tableCol.getTag(bioTAGS.alphabet);
       const minDistanceRenderer = 50;
-      w = getUpdatedWidth(grid, g, x, w);
+      w = getUpdatedWidth(grid, g, x, w, dpr);
       g.beginPath();
       g.rect(x + this.padding, y + this.padding, w - this.padding - 1, h - this.padding * 2);
       g.clip();
@@ -263,13 +264,14 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
     _cellStyle: DG.GridCellStyle): void {
+    const dpr = window.devicePixelRatio;
     const grid = gridCell.grid;
     const cell = gridCell.cell;
     const tableCol = gridCell.tableColumn as DG.Column<string>;
     const s: string = cell.value ?? '';
     const separator = tableCol.tags[bioTAGS.separator];
     const units: string = tableCol.tags[DG.TAGS.UNITS];
-    w = getUpdatedWidth(grid, g, x, w);
+    w = getUpdatedWidth(grid, g, x, w, dpr);
     //TODO: can this be replaced/merged with splitSequence?
     const [s1, s2] = s.split('#');
     const splitter = getSplitter(units, separator);

package/src/viewers/vd-regions-viewer.ts

@@ -192,7 +192,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
       case PROPS.positionHeight:
         for (let orderI = 0; orderI < this.logos.length; ++orderI) {
           for (const chain of this.chains)
-            this.logos[orderI][chain].setOptions({[wlPROPS.positionWidth]: this.positionWidth});
+            this.logos[orderI][chain].setOptions({[wlPROPS.positionHeight]: this.positionHeight});
         }
         this.calcSize();
         break;