@datagrok/bio 2.11.20 → 2.11.22

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.20",
+  "version": "2.11.22",
   "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",
@@ -34,9 +34,9 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.14",
+    "@datagrok-libraries/bio": "^5.39.16",
     "@datagrok-libraries/chem-meta": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.3.67",
+    "@datagrok-libraries/ml": "^6.3.68",
     "@datagrok-libraries/tutorials": "^1.3.11",
     "@datagrok-libraries/utils": "^4.1.36",
     "cash-dom": "^8.0.0",

package/src/analysis/sequence-diversity-viewer.ts

@@ -7,8 +7,10 @@ import {SequenceSearchBaseViewer} from './sequence-search-base-viewer';
 import {getMonomericMols} from '../calculations/monomerLevelMols';
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
-import {calcMmDistanceMatrix, dmLinearIndex} from './workers/mm-distance-worker-creator';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {getEncodedSeqSpaceCol} from './sequence-space';
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {DistanceMatrixService, dmLinearIndex} from '@datagrok-libraries/ml/src/distance-matrix';
 
 export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   diverseColumnLabel: string | null; // Use postfix Label to prevent activating table column selection editor
@@ -58,7 +60,11 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   }
 
   private async computeByMM() {
-    const distanceMatrixData = await calcMmDistanceMatrix(this.moleculeColumn!);
+    const encodedSequences =
+        (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
+    const distanceMatrixService = new DistanceMatrixService(true, false);
+    const distanceMatrixData = await distanceMatrixService.calc(encodedSequences, MmDistanceFunctionsNames.LEVENSHTEIN);
+    distanceMatrixService.terminate();
     const len = this.moleculeColumn!.length;
     const linearizeFunc = dmLinearIndex(len);
     this.renderMolIds = getDiverseSubset(len, Math.min(len, this.limit),

package/src/analysis/sequence-similarity-viewer.ts

@@ -8,8 +8,10 @@ import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {calcMmDistanceMatrix, dmLinearIndex} from './workers/mm-distance-worker-creator';
-import {calculateMMDistancesArray} from './workers/mm-distance-array-service';
+import {alignSequencePair} from '@datagrok-libraries/bio/src/utils/macromolecule/alignment';
+import {KnnResult, SparseMatrixService} from '@datagrok-libraries/ml/src/distance-matrix/sparse-matrix-service';
+import {getEncodedSeqSpaceCol} from './sequence-space';
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
 export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   cutoff: number;
@@ -26,6 +28,8 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   computeCompleted = new Subject<boolean>();
   distanceMatrixComputed: boolean = false;
   mmDistanceMatrix: Float32Array;
+  knn?: KnnResult;
+  kPrevNeighbors: number = 0;
 
   constructor() {
     super('similarity');
@@ -48,7 +52,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
         this.targetMoleculeIdx = this.dataFrame!.currentRowIdx == -1 ? 0 : this.dataFrame!.currentRowIdx;
         const uh = UnitsHandler.getOrCreate(this.moleculeColumn!);
 
-        await (uh.isFasta() ? this.computeByMM() : this.computeByChem());
+        await (!uh.isHelm() ? this.computeByMM() : this.computeByChem());
         const similarColumnName: string = this.similarColumnLabel != null ? this.similarColumnLabel :
           `similar (${this.moleculeColumnName})`;
         this.molCol = DG.Column.string(similarColumnName,
@@ -93,29 +97,24 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   }
 
   private async computeByMM() {
-    let distanceArray = new Float32Array();
-    if (!this.distanceMatrixComputed && this.preComputeDistanceMatrix) {
-      this.mmDistanceMatrix = await calcMmDistanceMatrix(this.moleculeColumn!);
-      this.distanceMatrixComputed = true;
-    } else if (!this.preComputeDistanceMatrix) {
-      // use fast distance array calculation if matrix will take too much space
-      distanceArray = await calculateMMDistancesArray(this.moleculeColumn!, this.targetMoleculeIdx);
-    }
     const len = this.moleculeColumn!.length;
-    const linearizeFunc = dmLinearIndex(len);
-    // array that keeps track of the indexes and scores together
-    const indexWScore = Array(len).fill(0)
-      .map((_, i) => ({
-        idx: i, score: i === this.targetMoleculeIdx ? 1 :
-          this.preComputeDistanceMatrix ? 1 - this.mmDistanceMatrix[linearizeFunc(this.targetMoleculeIdx, i)] :
-            1 - distanceArray[i]
-      }));
+    const actualLimit = Math.min(this.limit, len - 1);
+    if (!this.knn || this.kPrevNeighbors !== actualLimit) {
+      const encodedSequences =
+        (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
+
+      this.kPrevNeighbors = actualLimit;
+      this.knn = await (new SparseMatrixService()
+        .getKNN(encodedSequences, MmDistanceFunctionsNames.LEVENSHTEIN, Math.min(this.limit, len - 1)));
+    }
+    const indexWScore = new Array(actualLimit).fill(0).map((_, i) => ({
+      idx: this.knn!.knnIndexes[this.targetMoleculeIdx][i],
+      score: 1 - this.knn!.knnDistances[this.targetMoleculeIdx][i],
+    }));
     indexWScore.sort((a, b) => b.score - a.score);
-    // get the most similar molecules
-    const actualLimit = Math.min(this.limit, len);
-    const mostSimilar = indexWScore.slice(0, actualLimit);
-    this.idxs = DG.Column.int('indexes', actualLimit).init((i) => mostSimilar[i].idx);
-    this.scores = DG.Column.float('score', actualLimit).init((i) => mostSimilar[i].score);
+    indexWScore.unshift({idx: this.targetMoleculeIdx, score: DG.FLOAT_NULL});
+    this.idxs = DG.Column.int('indexes', actualLimit + 1).init((i) => indexWScore[i].idx);
+    this.scores = DG.Column.float('score', actualLimit + 1).init((i) => indexWScore[i].score);
   }
 
   createPropertyPanel(resDf: DG.DataFrame) {
@@ -127,7 +126,8 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     const splitter = uh.getSplitter();
     const subParts1 = splitter(this.moleculeColumn!.get(this.targetMoleculeIdx));
     const subParts2 = splitter(resDf.get(molColName, resDf.currentRowIdx));
-    const canvas = createDifferenceCanvas(subParts1, subParts2, uh.units, molDifferences);
+    const alignment = alignSequencePair(Array.from(subParts1), Array.from(subParts2));
+    const canvas = createDifferenceCanvas(alignment.seq1Splitted, alignment.seq2Splitted, uh.units, molDifferences);
     propPanel.append(ui.div(canvas, {style: {width: '300px', overflow: 'scroll'}}));
     if (subParts1.length !== subParts2.length) {
       propPanel.append(ui.divV([

package/src/tests/similarity-diversity-tests.ts

@@ -48,7 +48,7 @@ async function _testSimilaritySearchViewer() {
 
   /* eslint-disable max-len */
   const str0: string = 'D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me';
-  const str1: string = 'meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me';
+  const str1: string = 'Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Chg/N/D-Orn/D-aThr//Phe_4Me';
   const simStr1: string = 'meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me';
   /* eslint-enable max-len */
 
@@ -57,8 +57,8 @@ async function _testSimilaritySearchViewer() {
   expect(similaritySearchViewer.scores!.get(0), DG.FLOAT_NULL);
   expect(similaritySearchViewer.idxs!.get(0), 0);
   expect(similaritySearchViewer.molCol!.get(0), str0);
-  expect(similaritySearchViewer.scores!.get(1), 0.4722222089767456);
-  expect(similaritySearchViewer.idxs!.get(1), 11);
+  expect((similaritySearchViewer.scores!.get(1) as number).toFixed(2), '0.73');
+  expect(similaritySearchViewer.idxs!.get(1), 4);
   expect(similaritySearchViewer.molCol!.get(1), str1);
   moleculesView.dataFrame.currentRowIdx = 1;
   await awaitCheck(() => similaritySearchViewer.targetMoleculeIdx === 1,

package/src/utils/macromolecule-column-widget.ts

@@ -12,7 +12,7 @@ import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 export class MacromoleculeColumnWidget extends DG.Widget {
   private viewed: boolean = false;
 
-  private seqCol: DG.Column<string>;
+  private readonly seqCol: DG.Column<string>;
 
   private wlViewer: WebLogoViewer;
 
@@ -44,4 +44,9 @@ export class MacromoleculeColumnWidget extends DG.Widget {
       this.root.style.width = '100%';
     }
   }
+
+  override detach() {
+    this.wlViewer.detach();
+    super.detach();
+  }
 }

package/src/viewers/web-logo-viewer.ts

@@ -2,6 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import $ from 'cash-dom';
 import wu from 'wu';
 import {fromEvent, Observable, Subject, Unsubscribable} from 'rxjs';
 
@@ -558,7 +559,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     this.viewSubs.push(
       fromEvent<WheelEvent>(this.canvas, 'wheel').subscribe(this.canvasOnWheel.bind(this)));
 
-    await this.render(WlRenderLevel.Freqs, 'buildView');
+    this.render(WlRenderLevel.Freqs, 'buildView');
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.buildView() end`);
   }
 
@@ -589,7 +590,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
           this.unitsHandler = UnitsHandler.getOrCreate(this.seqCol);
 
           this.palette = pickUpPalette(this.seqCol);
-          this.updatePositions();
+          this.render(WlRenderLevel.Freqs, 'updateSeqCol()');
           this.error = null;
         } catch (err: any) {
           this.seqCol = null;
@@ -608,36 +609,6 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     }
   }
 
-  /** Updates {@link positionNames} and calculates {@link startPosition} and {@link endPosition}.
-   * Calls {@link render}() with {@link WlRenderLevel.Freqs}
-   */
-  private updatePositions(): void {
-    if (!this.seqCol) return;
-
-    const dfFilter = this.getFilter();
-    const maxLength: number = dfFilter.trueCount === 0 ? this.unitsHandler!.maxLength :
-      wu.enumerate(this.unitsHandler!.splitted).map(([mList, rowI]) => {
-        return dfFilter.get(rowI) && !!mList ? mList.length : 0;
-      }).reduce((max, l) => Math.max(max, l), 0);
-
-    /** positionNames and positionLabel can be set up through the column's tags only */
-    const positionNamesTxt = this.seqCol.getTag(bioTAGS.positionNames);
-    const positionLabelsTxt = this.seqCol.getTag(bioTAGS.positionLabels);
-    this.positionNames = !!positionNamesTxt ? positionNamesTxt.split(positionSeparator).map((v) => v.trim()) :
-      [...Array(maxLength).keys()].map((jPos) => `${jPos + 1}`)/* fallback if tag is not provided */;
-    this.positionLabels = !!positionLabelsTxt ? positionLabelsTxt.split(positionSeparator).map((v) => v.trim()) :
-      undefined;
-
-    this.startPosition = (this.startPositionName && this.positionNames &&
-      this.positionNames.includes(this.startPositionName)) ?
-      this.positionNames.indexOf(this.startPositionName) : 0;
-    this.endPosition = (this.endPositionName && this.positionNames &&
-      this.positionNames.includes(this.endPositionName)) ?
-      this.positionNames.indexOf(this.endPositionName) : (maxLength - 1);
-
-    this.render(WlRenderLevel.Freqs, 'updatePositions');
-  }
-
   private getFilter(): DG.BitSet {
     let dfFilterRes: DG.BitSet;
     switch (this.filterSource) {
@@ -851,13 +822,13 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       case PROPS.shrinkEmptyTail:
       case PROPS.skipEmptyPositions:
       case PROPS.positionHeight: {
-        this.updatePositions();
+        this.render(WlRenderLevel.Freqs, `onPropertyChanged( ${property.name} )`);
         break;
       }
 
       case PROPS.valueColumnName:
       case PROPS.valueAggrType: {
-        this.render(WlRenderLevel.Freqs, `onPropertyChanged(${property.name})`);
+        this.render(WlRenderLevel.Freqs, `onPropertyChanged( ${property.name} )`);
         break;
       }
       // this.positionWidth obtains a new value
@@ -892,7 +863,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   }
 
   /** Remove all handlers when table is a detach  */
-  public override async detach() {
+  public override detach() {
     const logPrefix = `${this.viewerToLog()}.detach()`;
     _package.logger.debug(`${logPrefix}, in`);
 
@@ -984,6 +955,31 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.calculateFreqsInt(), start `);
       if (!this.host || !this.seqCol || !this.dataFrame) return;
 
+      // region updatePositions
+
+      const dfFilter = this.getFilter();
+      const maxLength: number = dfFilter.trueCount === 0 ? this.unitsHandler!.maxLength :
+        wu.enumerate(this.unitsHandler!.splitted).map(([mList, rowI]) => {
+          return dfFilter.get(rowI) && !!mList ? mList.length : 0;
+        }).reduce((max, l) => Math.max(max, l), 0);
+
+      /** positionNames and positionLabel can be set up through the column's tags only */
+      const positionNamesTxt = this.seqCol.getTag(bioTAGS.positionNames);
+      const positionLabelsTxt = this.seqCol.getTag(bioTAGS.positionLabels);
+      this.positionNames = !!positionNamesTxt ? positionNamesTxt.split(positionSeparator).map((v) => v.trim()) :
+        [...Array(maxLength).keys()].map((jPos) => `${jPos + 1}`)/* fallback if tag is not provided */;
+      this.positionLabels = !!positionLabelsTxt ? positionLabelsTxt.split(positionSeparator).map((v) => v.trim()) :
+        undefined;
+
+      this.startPosition = (this.startPositionName && this.positionNames &&
+        this.positionNames.includes(this.startPositionName)) ?
+        this.positionNames.indexOf(this.startPositionName) : 0;
+      this.endPosition = (this.endPositionName && this.positionNames &&
+        this.positionNames.includes(this.endPositionName)) ?
+        this.positionNames.indexOf(this.endPositionName) : (maxLength - 1);
+
+      // endregion updatePositions
+
       const length: number = this.startPosition <= this.endPosition ? this.endPosition - this.startPosition + 1 : 0;
       this.unitsHandler = UnitsHandler.getOrCreate(this.seqCol);
       const posCount: number = this.startPosition <= this.endPosition ? this.endPosition - this.startPosition + 1 : 0;
@@ -996,7 +992,6 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       }
 
       // 2022-05-05 askalkin instructed to show WebLogo based on filter (not selection)
-      const dfFilter = this.getFilter();
       const dfRowCount = this.dataFrame.rowCount;
       const splitted = this.unitsHandler.splitted;
 
@@ -1136,6 +1131,11 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   }
 
   private renderRequestOnDebounce(renderLevel: WlRenderLevel): void {
+    const logPrefix = `${this.viewerToLog()}.renderRequestOnDebounce()`;
+    if ($(this.root).offsetParent().get()[0]?.tagName === 'HTML') {
+      _package.logger.warning(`${logPrefix}, $(this.root).offsetParent() is the 'HTML' tag.`);
+      return;
+    }
     this.requestedRenderLevel = WlRenderLevel.None;
     this.renderInt(renderLevel)
       .catch((err: any) => {
@@ -1176,7 +1176,6 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   private dataFrameFilterOnChanged(_value: any): void {
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.dataFrameFilterChanged()`);
     try {
-      this.updatePositions();
       if (this.filterSource === FilterSources.Filtered)
         this.render(WlRenderLevel.Freqs, 'dataFrameFilterOnChanged');
     } catch (err: any) {

package/dist/44.js

@@ -1,2 +0,0 @@
-"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[44],{489:(t,e,n)=>{n.d(e,{U:()=>s.U,o:()=>s.o});var s=n(5540)},5540:(t,e,n)=>{n.d(e,{U:()=>s,o:()=>o});var s,r=n(779),i=n(458),h=n(6683);!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(s||(s={}));const o={[s.HAMMING]:r.j,[s.LEVENSHTEIN]:i.r,[s.NEEDLEMANN_WUNSCH]:h.n,[s.MONOMER_CHEMICAL_DISTANCE]:r.j}},9657:(t,e,n)=>{n.d(e,{Z:()=>s});class s{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=s._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,s){if(t<e||t>n)throw new Error(`Argument ${s} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let s=0;s<n;s++)e[s]=t[s]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${this._length} != ${t._length})`);this.copy(t._data,this._data,this.lengthInInts),this._version++}get length(){return this._length}get buffer(){return this._data}set buffer(t){this._data=t,this._version++}get version(){return this._version}set version(t){this._version=t}incrementVersion(t=!0){this._version++}get lengthInInts(){return Math.floor((this._length+31)/32)}get versionedName(){return this._version==this._versionedNameVersion?this._versionedName:""}set versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new s(t._length);n._length=t._length,n._data=s._createBuffer(n._length),n._version=0;const r=t.lengthInInts;for(let s=0;s<r;s++)n._data[s]=t._data[s]&e._data[s];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new s(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new s(t);for(let s=0;s<t;++s)n.setBit(s,e(s));return n._version=0,n}static fromString(t){return s.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new s(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new s(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let r=0,i=0;for(;e-i>=4;)n._data[r++]=255&t[i]|(255&t[i+1])<<8|(255&t[i+2])<<16|(255&t[i+3])<<24,i+=4;return e-i==3&&(n._data[r]=(255&t[i+2])<<16),e-i==2&&(n._data[r]|=(255&t[i+1])<<8),e-i==1&&(n._data[r]|=255&t[i]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new s(0,!1);return t._data=Uint32Array.from(this._data),t._length=this._length,t._version=this._version,t}init(t,e){this.setAll(!1,!1);for(let e=0;e<this._length;e++)t(e)&&(this._data[Math.floor(e/32)]|=1<<(e%32&31));return this.incrementVersion(e),this}invert(t=!0){for(let t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,s=this.lengthInInts;for(let t=0;t<s;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,s=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(s)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,s=!0,r=!0){if(n&&r&&this.setAll(!e,!1),r)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(s)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return s.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return n}setRange(t,e,n,s=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const r=Math.min(t,e),i=Math.max(t,e);if(n)for(let t=r;t<=i;t++)this.setTrue(t);else for(let t=r;t<=i;t++)this.setFalse(t);return this.incrementVersion(s),this}setRandom(t,e,n=!0){if(t<0||t>this._length)throw new Error("n must be >= 0 && <= Count");t>this._length/2&&this.setRandom(this._length-t,!e),this.setAll(!e);for(let n=0;n<t;){const t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]&=t._data[e];return this.incrementVersion(e),this}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]|=t._data[e];return this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const s=this._length;this.setLength(this._length+e);for(let n=s-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let s=t;s<t+e;s++)this.setBit(s,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let s=-1;-1!=(s=t.findNext(s,!e));)this.setFast(n++,this.getBit(s));this._length=n,this._version++}return this}getBit(t){return 0!=(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=s._onBitCount[255&t];let n=this._data[e];const r=31&this._length;for(0!=r&&(n&=~(4294967295<<r));0!=n;n>>>=8)this._selectedCount+=s._onBitCount[255&n];this._selectedCountVersion=this._version}return t?this._selectedCount:this._length-this._selectedCount}countWhere(t){let e=0;if(this.trueCount()==this._length)for(let n=0;n<this._length;n++)e+=t(n)?1:0;else for(let n=-1;-1!=(n=this.findNext(n,!0));)e+=t(n)?1:0;return e}andWithCountBits(t,e){if(0==this._length)return 0;let n=0;const r=this.lengthInInts;let i=0;for(;i<r-1;i++)for(let e=this._data[i]&t._data[i];0!=e;e>>>=8)n+=s._onBitCount[255&e];let h=this._data[i]&t._data[i];const o=31&this._length;for(0!=o&&(h&=~(4294967295<<o));0!=h;h>>>=8)n+=s._onBitCount[255&h];return e?n:this._length-n}clear(){this.setLength(0)}contains(t){return this.findNext(-1,t)>=0}get allTrue(){return this.countBits(!0)==this._length}get allFalse(){return this.countBits(!1)==this._length}get anyTrue(){return this.countBits(!0)>0}get anyFalse(){return this.countBits(!1)>0}findNext(t,e=!0){if(this.assureInRange(t,-1,this._length,"index"),t>=this._length-1)return-1;let n=31&(t=t<0?0:t+1);const r=this.lengthInInts;for(let i=Math.floor(t/32);i<r;i++){let r=e?this._data[i]:~this._data[i];if(0!=n)r&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==r)continue;for(let e=0;0!=r;e+=8,r>>>=8){const n=s._firstOnBit[255&r];if(n>=0)return(t=n+32*i+e)>=this._length?-1:t}}return-1}findPrev(t,e=!0){if(0==t)return-1;this.assureInRange(t,-1,this._length,"index");let n=1+(t=t<0?this._length-1:t-1)&31;for(let r=Math.floor(t/32);r>=0;r--){let t=e?this._data[r]:~this._data[r];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=s._lastOnBit[t>>>24];if(n>=0)return n+32*r+e}}return-1}}s._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]),s._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]),s._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])},3979:(t,e)=>{e.H$=void 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