npm - @datagrok-libraries/bio - Versions diffs - 5.41.1 → 5.41.3 - Mend

@datagrok-libraries/bio 5.41.1 → 5.41.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (18) hide show

package/CHANGELOG.md +11 -0
package/package.json +1 -1
package/src/tests/monomer-lib-tests.js +1 -1
package/src/tests/monomer-lib-tests.js.map +1 -1
package/src/types/index.d.ts +4 -1
package/src/types/index.d.ts.map +1 -1
package/src/types/index.js.map +1 -1
package/src/utils/cell-renderer-async-base.d.ts +1 -0
package/src/utils/cell-renderer-async-base.d.ts.map +1 -1
package/src/utils/cell-renderer-async-base.js +11 -4
package/src/utils/cell-renderer-async-base.js.map +1 -1
package/src/utils/cell-renderer-back-base.d.ts.map +1 -1
package/src/utils/cell-renderer-back-base.js +2 -2
package/src/utils/cell-renderer-back-base.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +1 -0
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +23 -25
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,16 @@
 # bio changelog
+## 5.41.3 (2024-05-15)
+Fix cell renderer monomer placer hit test
+## 5.41.2 (2024-05-13)
+### Bug fixes
+Fix MonomerLib.getSummary for backward compatibility
+Fix cell renderer async base for sync rendering
 ## 5.41.1 (2024-05-13)
 ### Features

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.41.1",
+  "version": "5.41.3",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",

package/src/tests/monomer-lib-tests.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { expectObject } from '@datagrok-libraries/utils/src/test';
 export const defaultMonomerLibSummary = { 'PEPTIDE': 322, 'RNA': 383, 'CHEM': 0 };
 export function expectMonomerLib(lib, summary) {
     const exp = summary ?? defaultMonomerLibSummary;
-    const act = lib.getSummary();
+    const act = lib.getSummaryObj();
     for (const pt in exp)
         if (!exp[pt])
             delete exp[pt];

package/src/tests/monomer-lib-tests.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/types/index.d.ts CHANGED Viewed

@@ -49,8 +49,11 @@ export interface IMonomerLib {
     getPolymerTypes(): PolymerType[];
     update(lib: IMonomerLib): void;
     get onChanged(): Observable<any>;
+    /** Summary string with lib monomer count by type
+     * @deprecated Keep for backward compatibility */
+    getSummary(): string;
     /** Summary with lib monomer count by type */
-    getSummary(): MonomerLibSummaryType;
+    getSummaryObj(): MonomerLibSummaryType;
     /** Gets dataframe with columns 'polymerType', 'count'. */
     getSummaryDf(): DG.DataFrame;
     getTooltip(polymerType: PolymerType, monomerSymbol: string): HTMLElement;

package/src/types/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/types/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-async-base.d.ts CHANGED Viewed

@@ -50,6 +50,7 @@ export declare abstract class RenderServiceBase<TProps extends PropsBase, TAux>
      * @return             {@link consumerId} or assigned new if null
      */
     render(consumerId: number | null, task: RenderTask<TProps, TAux>, key?: keyof any, tryCount?: number): number;
+    isBusy(consumerId: number): boolean;
     protected getTask(): RenderQueueItem<TProps, TAux> | undefined;
     private _processQueue;
     /** Sweep queue for stalled tasks */

package/src/utils/cell-renderer-async-base.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-async-base.js CHANGED Viewed

@@ -62,11 +62,14 @@ export class RenderServiceBase {
         if (!this._busy) {
             this._sweepToggle(this._busy = true);
             // TODO: Use requestAnimationFrame()
-            this.logger.debug(`${logPrefix}, window.setTimeout() -> this._processQueue() `);
-            window.setTimeout(() => { this._processQueue(); }, 0 /* next event cycle */);
+            this.logger.debug(`${logPrefix}, window.requestAnimationFrame() -> this._processQueue() `);
+            window.requestAnimationFrame(() => { this._processQueue(); });
         }
         return consumerId;
     }
+    isBusy(consumerId) {
+        return this._queue.some((item) => item.consumerId === consumerId);
+    }
     getTask() {
         if (this._queue.length == 0)
             return undefined;
@@ -108,8 +111,8 @@ export class RenderServiceBase {
                 renderSub.unsubscribe(); // renderSub can be undefined for a sync render service (?)
             if (this._queue.length > 0) {
                 // Schedule processQueue the next item only afterRender has asynchronously completed for the previous one
-                this.logger.debug(`${logPrefixR}, ` + 'window.setTimeout() -> this._processQueue() ');
-                window.setTimeout(() => { this._processQueue(); }, 0 /* next event cycle */);
+                this.logger.debug(`${logPrefixR}, ` + 'window.requestAnimationFrame() -> this._processQueue() ');
+                window.requestAnimationFrame(() => { this._processQueue(); });
             }
             else {
                 // release flag allowing _processQueue on add queue item
@@ -295,6 +298,10 @@ export class CellRendererBackAsyncBase extends CellRendererBackBase {
                 this.logger.debug('PdbRenderer.render(), ' + `from imageCache[${rowIdx}]`);
                 this.renderOnGrid(g, bd, gridCell, cellImageData);
             }
+            if (!this.consumerId || !service.isBusy(this.consumerId)) {
+                // No async render task enqueued, fire onRendered as completed
+                this._onRendered.next();
+            }
         }
         catch (err) {
             const errMsg = err instanceof Error ? err.message : err.toString();

package/src/utils/cell-renderer-async-base.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/utils/cell-renderer-back-base.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-back-base.js CHANGED Viewed

@@ -85,12 +85,12 @@ export class CellRendererBackBase {
     invalidate(caller) {
         this.invalidateGrid();
     }
-    async awaitRendered(timeout = 10000, reason = `await rendered ${timeout} timeout`) {
+    async awaitRendered(timeout = 10000, reason = `${timeout} timeout`) {
         const logPrefix = `${this.toLog()}.awaitRendered()`;
         this.logger.debug(`${logPrefix}, start, testEvent before`);
         await testEvent(this._onRendered, () => { }, () => {
             this.invalidate();
-        }, timeout, reason);
+        }, timeout, `${logPrefix}, ${reason}`);
         // Rethrow stored syncer error (for test purposes)
         if (this.errors.length > 0) {
             const err = this.errors[0];

package/src/utils/cell-renderer-back-base.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.d.ts CHANGED Viewed

@@ -10,6 +10,7 @@ type MonomerPlacerProps = {
     monomerToShort: MonomerToShortFunc;
     monomerLengthLimit: number;
 };
+export declare function hitBounds(bounds: number[], x: number): number | null;
 export declare class MonomerPlacer extends CellRendererBackBase<string> {
     private readonly propsProvider;
     private _monomerLengthList;

package/src/utils/cell-renderer-monomer-placer.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.js CHANGED Viewed

@@ -3,6 +3,28 @@ import wu from 'wu';
 import { SeqHandler } from './seq-handler';
 import { CellRendererBackBase } from './cell-renderer-back-base';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
+export function hitBounds(bounds, x) {
+    let iterationCount = 100;
+    let leftI = 0;
+    let rightI = bounds.length - 1;
+    let midI;
+    while (leftI <= rightI) {
+        midI = Math.floor((rightI + leftI) / 2);
+        const logVal = { x, leftI, left: bounds[leftI], midI, mid: bounds[midI], rightI, right: bounds[rightI] };
+        console.debug(`bio lib: hitTestBounds(), ${JSON.stringify(logVal)}`);
+        if (bounds[midI] <= x && x < bounds[midI + 1])
+            return midI;
+        else if (x < bounds[midI])
+            rightI = midI - 1;
+        else /* if (bounds[midI + 1] <= x) */
+            leftI = midI + 1;
+        if (--iterationCount <= 0) {
+            throw new Error(`Get position for pointer x = ${x} searching has not converged ` +
+                `on ${JSON.stringify(bounds)}. `);
+        }
+    }
+    return null;
+}
 export class MonomerPlacer extends CellRendererBackBase {
     get updated() { return this._updated; }
     /** View is required to subscribe and handle for data frame changes */
@@ -136,31 +158,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         const seqMonList = wu(sh.getSplitted(rowIdx).originals).toArray();
         if (seqMonList.length === 0)
             return null;
-        let iterationCount = 100;
-        let left = null;
-        let right = seqMonList.length;
-        let found = false;
-        let mid = 0;
-        if (monomerMaxLengthSumList[0] <= x && x < monomerMaxLengthSumList.slice(-1)[0]) {
-            while (!found) {
-                mid = Math.floor((right + (left ?? 0)) / 2);
-                if (x >= monomerMaxLengthSumList[mid] && x <= monomerMaxLengthSumList[mid + 1]) {
-                    left = mid;
-                    found = true;
-                }
-                else if (x < monomerMaxLengthSumList[mid])
-                    right = mid - 1;
-                else if (x > monomerMaxLengthSumList[mid + 1])
-                    left = mid + 1;
-                if (left == right)
-                    found = true;
-                if (--iterationCount <= 0) {
-                    throw new Error(`Get position for pointer x = ${x} searching has not converged ` +
-                        `on ${JSON.stringify(monomerMaxLengthSumList)}. `);
-                }
-            }
-        }
-        return left;
+        return hitBounds(monomerMaxLengthSumList, x);
     }
     setMonomerLengthLimit(limit) {
         this.props.monomerLengthLimit = limit;

package/src/utils/cell-renderer-monomer-placer.js.map CHANGED Viewed

	@@ -1 +1 @@
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