@datagrok/bio 2.11.23 → 2.11.26

package/src/widgets/bio-substructure-filter.ts

@@ -6,17 +6,21 @@
 
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-
 import * as grok from 'datagrok-api/grok';
+
 import wu from 'wu';
-import {helmSubstructureSearch, linearSubstructureSearch} from '../substructure-search/substructure-search';
-import {Subject, Subscription} from 'rxjs';
-import {updateDivInnerHTML} from '../utils/ui-utils';
+import {fromEvent, Subject, Subscription, Unsubscribable} from 'rxjs';
+import {debounceTime} from 'rxjs/operators';
+
 import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {errInfo, errStack} from '@datagrok-libraries/bio/src/utils/err-info';
 import {delay} from '@datagrok-libraries/utils/src/test';
-import {debounceTime} from 'rxjs/operators';
+import {IHelmWebEditor} from '@datagrok-libraries/bio/src/types/editor';
 
-import {_package} from '../package-test';
+import {helmSubstructureSearch, linearSubstructureSearch} from '../substructure-search/substructure-search';
+import {updateDivInnerHTML} from '../utils/ui-utils';
+
+import {_package} from '../package';
 
 export class BioSubstructureFilter extends DG.Filter {
   bioFilter: BioFilterBase | null = null;
@@ -84,6 +88,7 @@ export class BioSubstructureFilter extends DG.Filter {
   }
 
   detach() {
+    if (this.bioFilter) this.bioFilter.detach();
     super.detach();
   }
 
@@ -147,18 +152,16 @@ abstract class BioFilterBase {
     return new HTMLElement();
   }
 
-  get substructure() {
-    return '';
-  }
-
-  set substructure(s: string) {
-  }
+  abstract get substructure(): string;
+  abstract set substructure(s: string);
 
   async substructureSearch(_column: DG.Column): Promise<DG.BitSet | null> {
     return null;
   }
 
   abstract resetFilter(): void;
+
+  abstract detach(): void;
 }
 
 class FastaFilter extends BioFilterBase {
@@ -191,6 +194,8 @@ class FastaFilter extends BioFilterBase {
   resetFilter(): void {
     this.substructureInput.value = '';
   }
+
+  detach(): void { }
 }
 
 export class SeparatorFilter extends FastaFilter {
@@ -227,10 +232,12 @@ export class SeparatorFilter extends FastaFilter {
   async substructureSearch(column: DG.Column): Promise<DG.BitSet | null> {
     return linearSubstructureSearch(this.substructure, column, this.colSeparator);
   }
+
+  detach(): void { }
 }
 
 export class HelmFilter extends BioFilterBase {
-  helmEditor: any;
+  helmEditor: IHelmWebEditor;
   _filterPanel = ui.div('', {style: {cursor: 'pointer'}});
   helmSubstructure = '';
 
@@ -239,14 +246,18 @@ export class HelmFilter extends BioFilterBase {
     this.init();
   }
 
+  viewSubs: Unsubscribable[] = [];
+
   async init() {
-    this.helmEditor = await grok.functions.call('HELM:helmWebEditor');
+    this.helmEditor = await grok.functions.call('Helm:helmWebEditor');
     await ui.tools.waitForElementInDom(this._filterPanel);
     this.updateFilterPanel();
-    this._filterPanel.addEventListener('click', (_event: MouseEvent) => {
-      const {editorDiv, webEditor} = this.helmEditor.createWebEditor(this.helmSubstructure);
-      //@ts-ignore
-      ui.dialog({showHeader: false, showFooter: true})
+    let editorDiv: HTMLDivElement | undefined;
+    let webEditor: any | undefined;
+    // TODO: Unsubscribe 'click' and 'sizeChanged'
+    this.viewSubs.push(fromEvent(this._filterPanel, 'click').subscribe(() => {
+      ({editorDiv, webEditor} = this.helmEditor.createWebEditor(this.helmSubstructure));
+      const dlg = ui.dialog({showHeader: false, showFooter: true})
         .add(editorDiv)
         .onOK(() => {
           const helmString = webEditor.canvas.getHelm(true)
@@ -255,12 +266,24 @@ export class HelmFilter extends BioFilterBase {
           this.updateFilterPanel(this.substructure);
           setTimeout(() => { this.onChanged.next(); }, 10);
         }).show({modal: true, fullScreen: true});
-    });
-    ui.onSizeChanged(this._filterPanel).subscribe((_) => {
-      const helmString = this.helmEditor
-        .webEditor.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
-      this.updateFilterPanel(helmString);
-    });
+      const onCloseSub = dlg.onClose.subscribe(() => {
+        onCloseSub.unsubscribe();
+        editorDiv = undefined;
+        webEditor = undefined;
+      });
+    }));
+    this.viewSubs.push(ui.onSizeChanged(this._filterPanel).subscribe((_) => {
+      try {
+        if (!!webEditor) {
+          const helmString = webEditor.canvas.getHelm(true)
+            .replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
+          this.updateFilterPanel(helmString);
+        }
+      } catch (err: any) {
+        const [errMsg, errStack] = errInfo(err);
+        _package.logger.error(errMsg, undefined, errStack);
+      }
+    }));
   }
 
   get filterPanel() {
@@ -302,4 +325,8 @@ export class HelmFilter extends BioFilterBase {
     this.helmSubstructure = '';
     this.updateFilterPanel(this.substructure);
   }
+
+  detach(): void {
+    for (const sub of this.viewSubs) sub.unsubscribe();
+  }
 }

package/dist/23.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=23.js.map

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priority];\n\t\treturn;\n\t}\n\tvar notFulfilled = Infinity;\n\tfor (var i = 0; i < deferred.length; i++) {\n\t\tvar [chunkIds, fn, priority] = deferred[i];\n\t\tvar fulfilled = true;\n\t\tfor (var j = 0; j < chunkIds.length; j++) {\n\t\t\tif ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {\n\t\t\t\tchunkIds.splice(j--, 1);\n\t\t\t} else {\n\t\t\t\tfulfilled = false;\n\t\t\t\tif(priority < notFulfilled) notFulfilled = priority;\n\t\t\t}\n\t\t}\n\t\tif(fulfilled) {\n\t\t\tdeferred.splice(i--, 1)\n\t\t\tvar r = fn();\n\t\t\tif (r !== undefined) result = r;\n\t\t}\n\t}\n\treturn result;\n};","var next = __webpack_require__.x;\n__webpack_require__.x = () => {\n\treturn Promise.all([\n\t\t__webpack_require__.e(378),\n\t\t__webpack_require__.e(361)\n\t]).then(next);\n};","export const isNil = (x) => x === null || x === undefined;\nexport function insertSmaller(distancesAr, indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1]) {\n        return;\n    }\n    const newPosition = distancesAr.findIndex((v) => num < v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n    if (num < distancesAr[distancesAr.length - 1]) {\n        return;\n    }\n    const newPosition = distancesAr.findIndex((v) => num > v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\n//# 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{ isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, threshold, fnName, opts } = event.data;\n    try {\n        // if (startIdx != -1)\n        //   throw new Error('Error in sparse matrix worker'); // TODO: remove this line\n        const i = [];\n        const j = [];\n        const distances = [];\n        const chunkSize = endIdx - startIdx;\n        //const mi = startRow;\n        //const mj = startCol;\n        if (isBitArrayMetric(fnName)) {\n            for (let i = 0; i < values.length; ++i) {\n                if (isNil(values[i]))\n                    continue;\n                values[i] = new BitArray(values[i]._data, values[i]._length);\n            }\n        }\n        let cnt = 0;\n        const distanceFn = new Measure(fnName).getMeasure(opts);\n        const startRow = values.length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values.length * (values.length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values.length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n        let mi = startRow;\n        let mj = startCol;\n        while (cnt < chunkSize) {\n            //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n            const value = !isNil(values[mi]) && !isNil(values[mj]) ?\n                distanceFn(values[mi], values[mj]) : 1;\n            if (1 - value >= threshold) {\n                i.push(mi);\n                j.push(mj);\n                distances.push(value);\n            }\n            cnt++;\n            mj++;\n            if (mj === values.length) {\n                mi++;\n                mj = mi + 1;\n            }\n        }\n        const iArray = new Int32Array(i);\n        const jArray = new Int32Array(j);\n        const distanceArray = new Float32Array(distances);\n        postMessage({ i: iArray, j: jArray, distance: distanceArray });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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{ insertSmaller, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, fnName, opts, nNeighbours } = event.data;\n    try {\n        const knnIndexes = new Array(values.length).fill(null).map(() => new Array(nNeighbours).fill(-1));\n        const knnDistances = new Array(values.length).fill(null).map(() => new Array(nNeighbours).fill(999999));\n        const chunkSize = endIdx - startIdx;\n        if (isBitArrayMetric(fnName)) {\n            for (let i = 0; i < values.length; ++i) {\n                if (isNil(values[i]))\n                    continue;\n                values[i] = new BitArray(values[i]._data, values[i]._length);\n            }\n        }\n        let cnt = 0;\n        const distanceFn = new Measure(fnName).getMeasure(opts);\n        const startRow = values.length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values.length * (values.length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values.length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n        let mi = startRow;\n        let mj = startCol;\n        while (cnt < chunkSize) {\n            //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n            const value = !isNil(values[mi]) && !isNil(values[mj]) ?\n                distanceFn(values[mi], values[mj]) : 1;\n            insertSmaller(knnDistances[mi], knnIndexes[mi], value, mj);\n            insertSmaller(knnDistances[mj], knnIndexes[mj], value, mi);\n            cnt++;\n            mj++;\n            if (mj === values.length) {\n                mi++;\n                mj = mi + 1;\n            }\n        }\n        postMessage({ knnDistances, knnIndexes });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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n+32*s+e}}return-1}}r._onBitCount=Int8Array.from([0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8]),r._firstOnBit=Int8Array.from([-1,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,7,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0]),r._lastOnBit=Int8Array.from([-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7])},1811:(t,e,n)=>{n.d(e,{T:()=>s});const r=new Uint32Array(65536),s=(t,e)=>{if(t.length<e.length){const n=e;e=t,t=n}return 0===e.length?t.length:t.length<=32?((t,e)=>{const n=t.length,s=e.length,h=1<<n-1;let i=-1,o=0,a=n,l=n;for(;l--;)r[t.charCodeAt(l)]|=1<<l;for(l=0;l<s;l++){let t=r[e.charCodeAt(l)];const n=t|o;t|=(t&i)+i^i,o|=~(t|i),i&=t,o&h&&a++,i&h&&a--,o=o<<1|1,i=i<<1|~(n|o),o&=n}for(l=n;l--;)r[t.charCodeAt(l)]=0;return a})(t,e):((t,e)=>{const n=e.length,s=t.length,h=[],i=[],o=Math.ceil(n/32),a=Math.ceil(s/32);for(let t=0;t<o;t++)i[t]=-1,h[t]=0;let l=0;for(;l<a-1;l++){let o=0,a=-1;const g=32*l,f=Math.min(32,s)+g;for(let e=g;e<f;e++)r[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=r[e.charCodeAt(t)],s=i[t/32|0]>>>t&1,l=h[t/32|0]>>>t&1,g=n|o,f=((n|l)&a)+a^a|n|l;let _=o|~(f|a),c=a&f;_>>>31^s&&(i[t/32|0]^=1<<t),c>>>31^l&&(h[t/32|0]^=1<<t),_=_<<1|s,c=c<<1|l,a=c|~(g|_),o=_&g}for(let e=g;e<f;e++)r[t.charCodeAt(e)]=0}let g=0,f=-1;const _=32*l,c=Math.min(32,s-_)+_;for(let e=_;e<c;e++)r[t.charCodeAt(e)]|=1<<e;let u=s;for(let 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