@datagrok/bio 2.12.11 → 2.12.13

package/src/utils/helm-to-molfile/converter/simple-polymer.ts

@@ -0,0 +1,89 @@
+import {HELM_MONOMER_TYPE, HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
+import {Bond} from './types';
+
+/** Wrapper over simple polymer substring of HELM, like RNA1{d(A)p}  */
+export class SimplePolymer {
+  constructor(private simplePolymer: string) {
+    this.polymerType = this.getPolymerType();
+    this.idx = this.getIdx();
+    const {monomers, monomerTypes} = this.getMonomerSymbolsAndTypes();
+    this.monomers = monomers;
+    this.monomerTypes = monomerTypes;
+  }
+
+  readonly polymerType: string;
+  readonly monomers: string[];
+  private idx: number;
+  private monomerTypes: HELM_MONOMER_TYPE[];
+
+  /** Simple polymer id in the form 'polymer type' + 'index'  */
+  get id(): string {
+    return this.polymerType + this.idx.toString();
+  }
+
+  private getPolymerType(): string {
+    const regex = new RegExp(
+      `(${HELM_POLYMER_TYPE.PEPTIDE}|${HELM_POLYMER_TYPE.RNA})[0-9]+{`
+    );
+    const match = this.simplePolymer.match(regex);
+    if (!match)
+      throw new Error(`Unsupported polymer type in ${this.simplePolymer}`);
+    const polymerType = match[1];
+    return polymerType;
+  }
+
+  private getIdx(): number {
+    const regex = new RegExp(`${this.polymerType}([0-9]+){`);
+    const match = this.simplePolymer.match(regex);
+    if (!match)
+      throw new Error(`Cannot parse simple polymer id from ${this.simplePolymer}`);
+    const id = parseInt(match[1]);
+    return id;
+  }
+
+  private getMonomerSymbolsAndTypes(): {monomers: string[], monomerTypes: HELM_MONOMER_TYPE[]} {
+    const helmWrapperRegex = new RegExp(`${this.polymerType}${this.idx}{|}`, 'g');
+    const monomerGroups = this.simplePolymer.replace(helmWrapperRegex, '').split('.');
+    const monomerList: string[] = [];
+    const monomerTypeList: HELM_MONOMER_TYPE[] = [];
+    monomerGroups.forEach((monomerGroup) => {
+      const splitted = monomerGroup.split(/\(|\)/)
+        .map((el) => el.replace(/[\[\]]/g, ''));
+      monomerList.push(...splitted);
+      // WARNING: only the groups of the form r(A)p, as in RNA, are supported
+      const monomerTypes = splitted.map(
+        (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
+      );
+      monomerTypeList.push(...monomerTypes);
+    });
+    return {monomers: monomerList, monomerTypes: monomerTypeList};
+  }
+
+  /** Get list of pairs for bonded monomers, monomers indexed locally
+   * (within the simple polymer)  */
+  getBondData(): Bond[][] {
+    const result: Bond[][] = [];
+    const backboneMonomerIndices = this.monomerTypes.map((type, idx) => {
+      if (type === HELM_MONOMER_TYPE.BACKBONE)
+        return idx;
+    }
+    ).filter((idx) => idx !== undefined) as number[];
+    const branchMonomerIndices = this.monomerTypes.map((type, idx) => {
+      if (type === HELM_MONOMER_TYPE.BRANCH)
+        return idx;
+    }
+    ).filter((idx) => idx !== undefined) as number[];
+    for (let i = 0; i < backboneMonomerIndices.length - 1; i++) {
+      const backboneIdx = backboneMonomerIndices[i];
+      const nextBackboneIdx = backboneMonomerIndices[i + 1];
+      result.push([{monomerIdx: backboneIdx, rGroupId: 2}, {monomerIdx: nextBackboneIdx, rGroupId: 1}]);
+    }
+    for (let i = 0; i < branchMonomerIndices.length; i++) {
+      const branchIdx = branchMonomerIndices[i];
+      const backboneIdx = branchIdx - 1;
+      result.push([{monomerIdx: backboneIdx, rGroupId: 3}, {monomerIdx: branchIdx, rGroupId: 1}]);
+    }
+    return result;
+  }
+}
+

package/src/utils/helm-to-molfile/converter/types.ts

@@ -0,0 +1,12 @@
+export type Bond = {
+  /** Global (for complex polymer) or local (for simple polymer) monomer index, starting from 0 */
+  monomerIdx: number,
+  /** RGroup id, starting from 1  */
+  rGroupId: number
+}
+
+/** Position of a node in the connection list / bond block  */
+export type PositionInBonds = {
+  bondLineIdx: number,
+  nodeIdx: number,
+}

package/src/utils/helm-to-molfile/utils.ts

@@ -0,0 +1,32 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
+import {HelmToMolfileConverter} from './converter';
+
+/** Translate HELM column into molfile column and append to the dataframe */
+export async function helm2mol(df: DG.DataFrame, helmCol: DG.Column<string>): Promise<void> {
+  const molCol = await getMolColumnFromHelm(df, helmCol);
+  df.columns.add(molCol, true);
+  await grok.data.detectSemanticTypes(df);
+}
+
+
+/** Translate HELM column into molfile column and append to the dataframe */
+export async function getMolColumnFromHelm(
+  df: DG.DataFrame, helmCol: DG.Column<string>, chiralityEngine?: boolean
+): Promise<DG.Column<string>> {
+  const converter = new HelmToMolfileConverter(helmCol, df);
+  const molCol = await converter.convertToRdKitBeautifiedMolfileColumn(chiralityEngine);
+  molCol.semType = DG.SEMTYPE.MOLECULE;
+  return molCol;
+}
+
+export async function getSmilesColumnFromHelm(
+  df: DG.DataFrame, helmCol: DG.Column<string>
+): Promise<DG.Column<string>> {
+  const converter = new HelmToMolfileConverter(helmCol, df);
+  const smilesCol = await converter.convertToSmiles();
+  smilesCol.semType = DG.SEMTYPE.MOLECULE;
+  return smilesCol;
+}

package/src/utils/poly-tool/const.ts

@@ -1,9 +1,5 @@
 import {HELM_REQUIRED_FIELD} from '@datagrok-libraries/bio/src/utils/const';
 
-export const enum HELM_WRAPPER {
-  LEFT = 'PEPTIDE1{',
-  RIGHT = '}$$$$',
-}
 export const ALL_MONOMERS = '<All>';
 
 export const enum TRANSFORMATION_TYPE {

package/src/utils/poly-tool/transformation.ts

@@ -6,12 +6,15 @@ import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
-import {HELM_WRAPPER} from './const';
-import {getMolColumnFromHelm} from '../helm-to-molfile';
+import {getMolColumnFromHelm} from '../helm-to-molfile/utils';
 
 export const RULES_PATH = 'System:AppData/Bio/polytool-rules/';
 export const RULES_STORAGE_NAME = 'Polytool';
 
+const enum HELM_WRAPPER {
+  LEFT = 'PEPTIDE1{',
+  RIGHT = '}$$$$',
+}
 
 type ConnectionData = {
   allPos1: number[],
@@ -43,19 +46,8 @@ class TransformationCommon {
     this.helmColumn = helmColumn;
   }
 
-  protected hasTerminals(helm: string): boolean {
-    let isLinkable = false;
-    if (helm.includes('(1)'))
-      isLinkable = true;
-    if (helm.includes('(2)'))
-      isLinkable = true;
-
-    return isLinkable;
-  }
-
-  protected getLinkedPositions(helm: string, rules: Rule[]): [number, number][] {
-    const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
-    const monomers = seq.split('.').map((m) => { return m.replace('[', '').replace(']', ''); });
+  protected getLinkedPositions(monomers: string[], rules: Rule[]): [number, number][] {
+    const monomersNames = monomers.map((m) => { return m.replace('[', '').replace(']', ''); });
     const result: [number, number][] = new Array<[number, number]>(rules.length);
 
     for (let i = 0; i < rules.length; i++) {
@@ -65,35 +57,35 @@ class TransformationCommon {
       let firstEntryIndex = -1;
       let secondEntryIndex = -1;
       const add = `(${rules[i].code})`;
-      for (let j = 0; j < monomers.length; j++) {
-        if (monomers[j].includes(add)) {
+      for (let j = 0; j < monomersNames.length; j++) {
+        if (monomersNames[j].includes(add)) {
           if (firstFound) {
-            if (firstIsFirst && monomers[j] == rules[i].secondMonomer + add) {
+            if (firstIsFirst && monomersNames[j] == rules[i].secondMonomer + add) {
               secondFound = true;
               secondEntryIndex = j;
               break;
-            } else if (!firstIsFirst && monomers[j] == rules[i].firstMonomer + add) {
+            } else if (!firstIsFirst && monomersNames[j] == rules[i].firstMonomer + add) {
               secondFound = true;
               secondEntryIndex = j;
               break;
-            } else {
+            } else
               continue;
-            }
+
             //result[i][1] = j;
             // secondFound = true;
             // break;
           } else {
-            if (monomers[j] == rules[i].firstMonomer + add) {
+            if (monomersNames[j] == rules[i].firstMonomer + add) {
               firstFound = true;
               firstIsFirst = true;
               firstEntryIndex = j;
-            } else if (monomers[j] == rules[i].secondMonomer + add) {
+            } else if (monomersNames[j] == rules[i].secondMonomer + add) {
               firstFound = true;
               firstIsFirst = false;
               firstEntryIndex = j;
-            } else {
+            } else
               continue;
-            }
+
             //result[i] = [j, 0];
           }
         }
@@ -141,22 +133,42 @@ class TransformationCommon {
     return rules;
   }
 
-  protected getTransformedHelm(helm: string, rules: Rule[]): string {
-    const ruleCount = rules.length;
-    const positions = this.getLinkedPositions(helm, rules);
+  protected getDimeric(helm: string): [string[], [number, number][]] {
+    const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
+    const monomers = seq.split('.');
+    const duplicates: [number, number][] = [];
+
+    for (let i = 0; i < monomers.length; i++) {
+      if (monomers[i].includes('(#2)')) {
+        monomers[i] = monomers[i].replace('(#2)', '');
+        const duplicateStart = i + 1;
+        let duplicateFinish = 0;
+        for (let j = duplicateStart + 1; j < monomers.length; j++) {
+          if (monomers[j].includes('}')) {
+            duplicateFinish = j; break;
+          }
+        }
+        monomers[duplicateStart] = monomers[duplicateStart].replace('{', '');
+        monomers[duplicateFinish] = monomers[duplicateFinish].replace('}', '');
+        duplicates.push([duplicateStart, duplicateFinish]);
+      }
+    }
+
+    return [monomers, duplicates];
+  }
 
+  protected getAllCycles(rules: Rule[], monomers: string [], positions: [number, number][]) :
+  [string [], number [], number [], number [], number []] {
     const allPos1: number [] = [];
     const allPos2: number [] = [];
     const allAttaches1: number [] = [];
     const allAttaches2: number [] = [];
+    const ruleCount = rules.length;
 
     for (let i = 0; i < ruleCount; i++) {
       if (positions[i][0] == -1)
         continue;
 
-      //helm = helm.replaceAll(`(${i + 1})`, '');
-      const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
-      const monomers = seq.split('.');
       const firstMonomer = monomers[positions[i][0]].replace('[', '').replace(']', '');
       const secondMonomer = monomers[positions[i][1]].replace('[', '').replace(']', '');
 
@@ -167,31 +179,97 @@ class TransformationCommon {
       allPos2.push(positions[i][1] + 1);
       allAttaches1.push(rules[i].firstR);
       allAttaches2.push(rules[i].secondR);
+    }
 
-      helm = HELM_WRAPPER.LEFT;
-      for (let i = 0; i < monomers.length; i++) {
-        if (i != monomers.length - 1)
-          helm = helm + monomers[i] + '.';
-        else
-          helm = helm + monomers[i];
-      }
-      helm = helm + HELM_WRAPPER.RIGHT;
+    return [monomers, allPos1, allPos2, allAttaches1, allAttaches2];
+  }
+
+  protected getHelmCycle(source: ConnectionData, polFirst: number, poSecond: number): string {
+    let cycled = '';
+
+    for (let i = 0; i < source.allPos1.length; i++) {
+      if (i == 0)
+        cycled += `PEPTIDE${polFirst},PEPTIDE${poSecond},`;
+      else
+        cycled += `|PEPTIDE${polFirst},PEPTIDE${poSecond},`;
+      cycled += `${source.allPos1[i]}:R${source.allAttaches1[i]}-${source.allPos2[i]}:R${source.allAttaches2[i]}`;
     }
+    return cycled;
+  }
+
+  //"PEPTIDE1{[(#2)Succ].[{R].F.[Dab(2)].T.G.H.F.G.A.A.Y.P.[E(2)].[NH2}]}$$$$"
+  protected getTransformedHelm(helm: string, rules: Rule[]): string {
+    const [monomers, duplicates] = this.getDimeric(helm);
+    const positions = this.getLinkedPositions(monomers, rules);
+    const [monomersCycled, allPos1, allPos2, allAttaches1, allAttaches2] =
+      this.getAllCycles(rules, monomers, positions);
+
+    helm = 'PEPTIDE1{';
+    for (let i = 0; i < monomersCycled.length; i++)
+      helm += i != monomersCycled.length - 1 ? monomersCycled[i] + '.' : monomersCycled[i];
+
+    helm += '}';
+
+    const dimerCodes = new Array<string>(duplicates.length);
+    const cycleCodes = new Array<string>(duplicates.length);
+    for (let i = 0; i < duplicates.length; i++) {
+      let helmAdd = `|PEPTIDE${i + 2}{`;
+      const lengthAdd = duplicates[i][1] - duplicates[i][0];
+      //const monomersAdd = new Array<string>(lengthAdd);
+      const allPosAdd1: number [] = [];
+      const allPosAdd2: number [] = [];
+      const allAttachesAdd1: number [] = [];
+      const allAttachesAdd2: number [] = [];
+
+      for (let j = 0; j <= lengthAdd; j ++) {
+        const index = j + duplicates[i][0];
+        helmAdd += j != lengthAdd ? monomersCycled[index] + '.' : monomersCycled[index];
+      }
 
+      helmAdd += '}';
 
-    const cycledHelm = getHelmCycle(helm, {allPos1, allPos2, allAttaches1, allAttaches2});
+      for (let j = 0; j < allPos1.length; j++) {
+        if (allPos1[j] - 1 >= duplicates[i][0] && allPos1[j] - 1 <= duplicates[i][1]) {
+          allPosAdd1.push(allPos1[j] - duplicates[i][0]);
+          allPosAdd2.push(allPos2[j] - duplicates[i][0]);
+          allAttachesAdd1.push(allAttaches1[j]);
+          allAttachesAdd2.push(allAttaches1[j]);
+        }
+      }
 
-    return cycledHelm;
+      const addCyclysation = this.getHelmCycle({
+        allPos1: allPosAdd1,
+        allPos2: allPosAdd2,
+        allAttaches1: allAttachesAdd1,
+        allAttaches2: allAttachesAdd2}, i + 2, i + 2);
+
+      dimerCodes[i] = helmAdd;
+      cycleCodes[i] = this.getHelmCycle({
+        allPos1: [duplicates[i][0]],
+        allPos2: [1],
+        allAttaches1: [1],
+        allAttaches2: [1]}, 1, i + 2);
+      cycleCodes.push(addCyclysation);
+    }
+
+    for (let i = 0; i < dimerCodes.length; i++)
+      helm += dimerCodes[i];
+
+    helm += '$';
+    const mainCyclysation = this.getHelmCycle({allPos1, allPos2, allAttaches1, allAttaches2}, 1, 1);
+    helm += mainCyclysation;
+    for (let i = 0; i < cycleCodes.length; i++) {
+      helm += '|';
+      helm += cycleCodes[i];
+    }
+    helm += '$$$';
+    return helm;
   }
 
   transform(rulesTables: DG.DataFrame[]): string[] {
     const rules = this.getRules(rulesTables);
     const resultList = this.helmColumn.toList().map((helm: string) => {
-      if (this.hasTerminals(helm))
-        return this.getTransformedHelm(helm, rules);
-
-      console.log(helm);
-      return helm;
+      return this.getTransformedHelm(helm, rules);
     });
     return resultList;
   }
@@ -205,21 +283,6 @@ class PolymerTransformation {
   }
 }
 
-function getHelmCycle(helm: string, source: ConnectionData): string {
-  let cycled = helm.replace(HELM_WRAPPER.RIGHT, '}$');
-
-  for (let i = 0; i < source.allPos1.length; i++) {
-    if (i == 0)
-      cycled += 'PEPTIDE1,PEPTIDE1,';
-    else
-      cycled += '|PEPTIDE1,PEPTIDE1,';
-    cycled += `${source.allPos1[i]}:R${source.allAttaches1[i]}-${source.allPos2[i]}:R${source.allAttaches2[i]}`;
-  }
-
-  cycled += '$$$';
-  return cycled;
-}
-
 export async function addTransformedColumn(
   molColumn: DG.Column<string>, addHelm: boolean, ruleFiles: string[], chiralityEngine?: boolean
 ): Promise<void> {
@@ -249,8 +312,9 @@ export async function addTransformedColumn(
 
   if (addHelm) {
     targetHelmCol.setTag('cell.renderer', 'helm');
-    targetHelmCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    //targetHelmCol.semType = DG.SEMTYPE.MACROMOLECULE;
     df.columns.add(targetHelmCol);
   }
   df.columns.add(molCol, true);
+  await grok.data.detectSemanticTypes(df);
 }

package/src/utils/sequence-to-mol.ts

@@ -4,7 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
-import {helm2mol} from './helm-to-molfile';
+import {helm2mol} from './helm-to-molfile/utils';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {checkInputColumnUI} from './check-input-column';
 import {getMonomerLibHelper} from '../package';

package/webpack.config.js

@@ -2,11 +2,12 @@ const path = require('path');
 const FuncGeneratorPlugin = require('datagrok-tools/plugins/func-gen-plugin');
 const packageName = path.parse(require('./package.json').name).name.toLowerCase().replace(/-/g, '');
 
+const mode = 'development';
 module.exports = {
   cache: {
     type: 'filesystem',
   },
-  mode: 'development',
+  mode: mode,
   entry: {
     package: ['./src/package.ts'],
     test: {
@@ -29,12 +30,12 @@ module.exports = {
   plugins: [
     new FuncGeneratorPlugin({outputPath: './src/package.g.ts'}),
   ],
-  devtool: 'source-map',
+  devtool: mode === 'development' ? 'source-map' : 'inline-source-map',
   externals: {
     'datagrok-api/dg': 'DG',
     'datagrok-api/grok': 'grok',
     'datagrok-api/ui': 'ui',
-    'openchemlib/full.js': 'OCL',
+    'openchemlib/full': 'OCL',
     'rxjs': 'rxjs',
     'rxjs/operators': 'rxjs.operators',
     'cash-dom': '$',

package/dist/709.js

@@ -1,2 +0,0 @@
-var bio;(()=>{"use strict";var t,e,r={2357:(t,e,r)=>{var o=r(2590);async function n(t,e,r){const o=t.length,n=[],s=[];for(let a=0;a<o;a++)for(let l=a+1;l<o;l++){const o=t[a],i=t[l];e[o]?.[i]>=r&&(n.push(a),s.push(l))}return function(t,e,r){const o=new Float32Array(r.length).fill(0).map((()=>10*Math.random())),n=new Float32Array(r.length).fill(0).map((()=>10*Math.random())),s=new Float32Array(r.length).fill(0),a=new Float32Array(r.length).fill(0);for(let l=0;l<100;l++){const i=1-l/100;s.fill(0),a.fill(0);for(let r=0;r<t.length;r++){const l=t[r],c=e[r],f=o[l]-o[c],h=n[l]-n[c];Math.abs(f)>=1&&(s[l]-=i*f,s[c]+=i*f),Math.abs(h)>=1&&(a[l]-=i*h,a[c]+=i*h)}for(let t=0;t<r.length;t++){const e=Math.sqrt(s[t]*s[t]+a[t]*a[t]);e>0&&(o[t]+=s[t]/e*i,n[t]+=a[t]/e*i)}}let l=o[0],i=n[0],c=o[0],f=n[0];for(let t=1;t<r.length;t++)l=Math.min(l,o[t]),i=Math.min(i,n[t]),c=Math.max(c,o[t]),f=Math.max(f,n[t]);let h=c-l,u=f-i;0===h&&(h=c);for(let t=0;t<r.length;t++)o[t]=(o[t]-l)/h/2+.5;0===u&&(u=f);for(let t=0;t<r.length;t++)n[t]=(n[t]-i)/u/2+.5;return{embedX:o,embedY:n}}(n,s,t)}const s={expandFactor:2,maxIterations:5,inflateFactor:2,multFactor:1};class a{constructor(t={}){this._options={...s,...t}}async transform(t,e){let r=this.toObjectForm(t);if(this._options.maxIterations>0){this.addLoops(r,e),this.normalize(r);for(let t=0;t<this._options.maxIterations;t++)r=this.expand(r,e),this.inflate(r),this.normalize(r)}const{clusters:o,is:n,js:s}=this.assignClusters(r,e);this.correctClusters(o);const a=await this.layout(o,r,e);return{clusters:o,embedX:a.embedX,embedY:a.embedY,is:n,js:s}}correctClusters(t){const e={};for(const r of t)e[r]||(e[r]=0),e[r]++;const r=Object.keys(e).map(Number).sort(((t,r)=>e[t]-e[r])),o={};r.forEach(((t,e)=>o[t]=e+1));for(let e=0;e<t.length;e++)t[e]=o[t[e]]}async layout(t,e,r){const o=new Float32Array(r).fill(0),s=new Float32Array(r).fill(0),a={};t.forEach(((t,e)=>{a[t]||(a[t]=[]),a[t].push(e)}));let l=0;const i=Object.keys(a);i.sort(((t,e)=>a[e].length-a[t].length));let c=6,f=0;for(const t of i){const r=a[t],i=await n(r,e,.001);l===Math.ceil(c/1.5)&&(l=0,f+=5/c,c=Math.ceil(1.5*c));const h=l%c*5/c*1.5;for(let t=0;t<i.embedX.length;t++)o[r[t]]=5*i.embedX[t]/c+h,s[r[t]]=5*i.embedY[t]/c+f;l++}return{embedX:o,embedY:s}}mergeClusters(t,e,r){const o=t[e],n=t[r];for(let e=0;e<t.length;e++)t[e]===n&&(t[e]=o)}assignClusters(t,e){let r=0;const o=[],n=[],s=Math.floor(Math.max(Math.log10(e),2))+1,a=Math.pow(10,s),l=new Array(e).fill(-1);for(const e of Object.keys(t))for(const s of Object.keys(t[e]))Math.round(t[e][s]*a)/a>0&&t[e][s]!==Number(e)&&Number(s)>Number(e)&&(o.push(Number(e)),n.push(Number(s)),-1!==l[Number(e)]&&-1!==l[Number(s)]?l[Number(e)]!==l[Number(s)]&&this.mergeClusters(l,Number(e),Number(s)):-1!==l[Number(e)]?l[Number(s)]=l[Number(e)]:-1!==l[Number(s)]?l[Number(e)]=l[Number(s)]:(r++,l[Number(e)]=r,l[Number(s)]=r));for(let 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