@datagrok/bio 2.12.15 → 2.12.17

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.12.15",
+  "version": "2.12.17",
   "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",
@@ -34,12 +34,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.40.8",
+    "@datagrok-libraries/bio": "^5.41.0",
     "@datagrok-libraries/chem-meta": "^1.2.5",
-    "@datagrok-libraries/math": "^1.1.1",
-    "@datagrok-libraries/ml": "^6.6.0",
+    "@datagrok-libraries/math": "^1.1.5",
+    "@datagrok-libraries/ml": "^6.6.5",
     "@datagrok-libraries/tutorials": "^1.3.12",
-    "@datagrok-libraries/utils": "^4.2.0",
+    "@datagrok-libraries/utils": "^4.2.2",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -55,9 +55,9 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok/chem": "^1.9.0",
-    "@datagrok/dendrogram": "^1.2.27",
-    "@datagrok/helm": "^2.1.30",
+    "@datagrok/chem": "^1.9.2",
+    "@datagrok/dendrogram": "^1.2.29",
+    "@datagrok/helm": "^2.1.34",
     "@types/node": "^17.0.24",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",

package/src/package.ts

@@ -3,6 +3,8 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import '@datagrok-libraries/bio/src/types/helm';
+
 import {Options} from '@datagrok-libraries/utils/src/type-declarations';
 import {DimReductionBaseEditor, PreprocessFunctionReturnType}
   from '@datagrok-libraries/ml/src/functionEditors/dimensionality-reduction-editor';
@@ -55,13 +57,9 @@ import {SplitToMonomersFunctionEditor} from './function-edtiors/split-to-monomer
 import {splitToMonomersUI} from './utils/split-to-monomers';
 import {MonomerCellRenderer} from './utils/monomer-cell-renderer';
 import {BioPackage, BioPackageProperties} from './package-types';
-// import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
 import {getCompositionAnalysisWidget} from './widgets/composition-analysis-widget';
 import {MacromoleculeColumnWidget} from './utils/macromolecule-column-widget';
 import {addCopyMenuUI} from './utils/context-menu';
-import {getPolyToolDialog} from './utils/poly-tool/ui';
-import {PolyToolCsvLibHandler} from './utils/poly-tool/csv-to-json-monomer-lib-converter';
-import {_setPeptideColumn} from './utils/poly-tool/utils';
 import {getRegionDo} from './utils/get-region';
 import {GetRegionApp} from './apps/get-region-app';
 import {GetRegionFuncEditor} from './utils/get-region-func-editor';
@@ -77,7 +75,8 @@ import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimen
 import {
   ITSNEOptions, IUMAPOptions
 } from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/multi-column-dim-reducer';
-import {CyclizedNotationProvider} from './utils/poly-tool/cyclized';
+import {CyclizedNotationProvider} from './utils/cyclized';
+import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
 
 export const _package = new BioPackage();
 
@@ -685,19 +684,6 @@ export function convertDialog() {
   convert(col);
 }
 
-//top-menu: Bio | Convert | PolyTool
-//name: polyTool
-//description: Perform cyclization of polymers
-export async function polyTool(): Promise<void> {
-  let dialog: DG.Dialog;
-  try {
-    dialog = await getPolyToolDialog();
-    dialog.show();
-  } catch (err: any) {
-    grok.shell.warning('To run PolyTool, open a dataframe with macromolecules');
-  }
-}
-
 //name: monomerCellRenderer
 //tags: cellRenderer
 //meta.cellType: Monomer
@@ -1010,25 +996,6 @@ export async function demoBioHelmMsaSequenceSpace(): Promise<void> {
   await demoBio05UI();
 }
 
-//name: polyToolColumnChoice
-//input: dataframe df [Input data table]
-//input: column macroMolecule
-export async function polyToolColumnChoice(df: DG.DataFrame, macroMolecule: DG.Column): Promise<void> {
-  _setPeptideColumn(macroMolecule);
-  await grok.data.detectSemanticTypes(df);
-}
-
-//name: createMonomerLibraryForPolyTool
-//input: file file
-export async function createMonomerLibraryForPolyTool(file: DG.FileInfo) {
-  const fileContent = await file.readAsString();
-  const libHandler = new PolyToolCsvLibHandler(file.fileName, fileContent);
-  const libObject = await libHandler.getJson();
-  const jsonFileName = file.fileName.replace(/\.csv$/, '.json');
-  const jsonFileContent = JSON.stringify(libObject, null, 2);
-  DG.Utils.download(jsonFileName, jsonFileContent);
-}
-
 //name: SDF to JSON Library
 //input: dataframe table
 export async function sdfToJsonLib(table: DG.DataFrame) {
@@ -1048,6 +1015,17 @@ export async function detectMacromoleculeProbe(file: DG.FileInfo, colName: strin
   await detectMacromoleculeProbeDo(csv, colName, probeCount);
 }
 
+//name: getMolFromHelm
+//input: dataframe df
+//input: column helmCol
+//input: bool chiralityEngine
+//output: column result
+export async function getMolFromHelm(
+  df: DG.DataFrame, helmCol: DG.Column<string>, chiralityEngine?: boolean
+): Promise<DG.Column<string>> {
+  return getMolColumnFromHelm(df, helmCol, chiralityEngine);
+}
+
 // -- Custom notation providers --
 
 //name: applyNotationProviderForCyclized

package/src/tests/renderers-monomer-placer-tests.ts

@@ -95,7 +95,7 @@ id3,QHIRE--LT
       const monLength: number = 3;
       const charWidth: number = 7;
       const sepWidth: number = 12;
-      const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, () => {
+      const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, _package.logger, () => {
         const sh = SeqHandler.forColumn(seqCol);
         return {
           seqHandler: sh,

package/src/utils/cell-renderer.ts

@@ -23,6 +23,7 @@ import {ISeqSplitted, SeqSplittedBase} from '@datagrok-libraries/bio/src/utils/m
 import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {alphabetPolymerTypes, IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 import {
   Temps as mmcrTemps, Tags as mmcrTags,
@@ -63,27 +64,6 @@ type RendererGridCellTemp = {
   [mmcrTemps.monomerPlacer]: MonomerPlacer
 }
 
-function getRendererFridCellTempTemp(gridCell: DG.GridCell): RendererGridCellTemp {
-  /** Primarily store/get MonomerPlacer at GridColumn, fallback at (Table) Column for scatter plot tooltip  */
-  let temp: RendererGridCellTemp | null = null;
-
-  let gridCol: DG.GridColumn | null = null;
-  try { gridCol = gridCell.gridColumn; } catch { gridCol = null; }
-  temp = gridCol && gridCol.dart ? gridCol.temp as RendererGridCellTemp : null;
-
-  if (!temp) {
-    let tableCol: DG.Column | null = null;
-    try { tableCol = gridCell.cell.column; } catch { tableCol = null; }
-    if (!tableCol) {
-      const k = 42;
-    }
-    temp = tableCol ? tableCol.temp as RendererGridCellTemp : null;
-  }
-  if (temp === null)
-    throw new Error(`Monomer placer store (GridColumn or Column) not found.`);
-  return temp;
-}
-
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   private padding: number = 5;
 
@@ -105,9 +85,9 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
     //   return;
 
-    const tableCol: DG.Column = gridCell.cell.column;
-    //const tableColTemp: TempType = tableCol.temp;
-    const seqColTemp: MonomerPlacer = getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer];
+    const [_gridCol, tableCol, temp] =
+      getGridCellRendererBack<string, MonomerPlacer>(gridCell);
+    const seqColTemp: MonomerPlacer = temp['rendererBack'];
     if (!seqColTemp) return; // Can do nothing without precalculated data
 
     const gridCellBounds: DG.Rect = gridCell.bounds;
@@ -121,7 +101,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
     const left: number | null = seqColTemp.getPosition(gridCell.tableRowIndex!, argsX);
 
-    const seqCList: SeqSplittedBase = SeqHandler.forColumn(seqColTemp.col)
+    const seqCList: SeqSplittedBase = SeqHandler.forColumn(tableCol)
       .getSplitted(gridCell.tableRowIndex!).canonicals;
     if (left !== null && left < seqCList.length) {
       const monomerSymbol: string = seqCList[left];
@@ -190,9 +170,11 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         (!isNaN(tagMaxMonomerLength) ? tagMaxMonomerLength : _package.properties?.MaxMonomerLength) ?? 4;
     }
 
-    let seqColTemp: MonomerPlacer = getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer];
+    const [gridCol, _tc, temp] =
+      getGridCellRendererBack<string, MonomerPlacer>(gridCell);
+    let seqColTemp: MonomerPlacer = temp['rendererBack'];
     if (!seqColTemp) {
-      seqColTemp = new MonomerPlacer(grid, tableCol,
+      seqColTemp = new MonomerPlacer(gridCol, tableCol, _package.logger,
         () => {
           const sh = SeqHandler.forColumn(tableCol);
           return {
@@ -217,7 +199,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const _maxIndex = maxLengthWords.length;
 
     // Store updated seqColTemp to the col temp
-    if (seqColTemp.updated) getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer] = seqColTemp;
+    if (seqColTemp.updated) temp['rendererBack'] = seqColTemp;
 
     g.save();
     try {

package/src/utils/{poly-tool/cyclized.ts → cyclized.ts}

@@ -1,8 +1,5 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {GAP_SYMBOL, INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {GAP_SYMBOL, INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc}
+  from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {getSplitterWithSeparator, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -33,9 +30,8 @@ export class CyclizedSeqSplitted extends StringListSeqSplitted {
     if (!this._canonicals) {
       const len = this.length;
       this._canonicals = new Array<string>(len);
-      for (let posIdx = 0; posIdx < len; ++posIdx) {
+      for (let posIdx = 0; posIdx < len; ++posIdx)
         this._canonicals[posIdx] = this.getCanonical(posIdx);
-      }
     }
     return this._canonicals;
   }

package/src/utils/monomer-lib/monomer-lib.ts

@@ -116,6 +116,14 @@ export class MonomerLib implements IMonomerLib {
     this._onChanged.next();
   }
 
+  getSummary(): string {
+    const monTypeList: string[] = this.getPolymerTypes();
+    const resStr: string = monTypeList.length == 0 ? 'empty' : monTypeList.map((monType) => {
+      return `${monType} ${this.getMonomerSymbolsByType(monType).length}`;
+    }).join('\n');
+    return resStr;
+  }
+
   getTooltip(polymerType: string, monomerSymbol: string): HTMLElement {
     // getTooltip(monomer: Monomer): HTMLElement;
     // getTooltip(monomerOrPolymerType: string | Monomer, symbol?: string): HTMLElement {
@@ -163,8 +171,12 @@ export class MonomerLib implements IMonomerLib {
         label('Source'),
         ui.divText(monomer.lib?.source ?? 'unknown', {classes: 'ui-input-text'}),
       ], {classes: 'ui-input-root'}));
-    } else
-      res.append(ui.divText('Monomer not found'));
+    } else {
+      res.append(ui.divV([
+        ui.divText(`Monomer '${monomerSymbol}' of type '${polymerType}' not found.`),
+        ui.divText('Open the Context Panel, then expand Manage Libraries'),
+      ]));
+    }
     return res;
   }
 }

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

@@ -2,14 +2,15 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import * as org from 'org';
 import $ from 'cash-dom';
-import {fromEvent, Observable, Subject, Unsubscribable} from 'rxjs';
+import {fromEvent, Unsubscribable} from 'rxjs';
 
-import {IHelmWebEditor, IWebEditorApp} from '@datagrok-libraries/bio/src/helm/types';
+import {IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/utils/src/test';
 
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {helmSubstructureSearch} from '../substructure-search/substructure-search';
@@ -54,7 +55,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
       this.logger.warning('TEST: HelmBioFilter.init().sync() waitForElementInDom ready');
       this.updateFilterPanel();
       let webEditorHost: HTMLDivElement | null;
-      let webEditorApp: IWebEditorApp | null;
+      let webEditorApp: org.helm.IWebEditorApp | null;
       // TODO: Unsubscribe 'click' and 'sizeChanged'
       this.viewSubs.push(fromEvent(this._filterPanel, 'click').subscribe(() => {
         webEditorHost = ui.div();

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

@@ -16,7 +16,6 @@ import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macro
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {IHelmWebEditor, IWebEditorApp} from '@datagrok-libraries/bio/src/helm/types';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
@@ -197,7 +196,7 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
 
     this.filterSyncer.sync(logPrefix, async () => {
       if (state.props && this.bioFilter)
-        this.bioFilter.props = state.props;
+        this.bioFilter.props = DG.toJs(state.props ?? {});
     });
   }
 

package/webpack.config.js

@@ -41,6 +41,8 @@ module.exports = {
     'cash-dom': '$',
     'dayjs': 'dayjs',
     'wu': 'wu',
+    'scil': 'scil',
+    'org': 'org',
   },
   output: {
     filename: '[name].js',

package/dist/246.js

@@ -1,2 +0,0 @@
-var bio;(()=>{"use strict";var n,e,t={8960:(n,e,t)=>{var r;!function(n){n.EUCLIDEAN="EUCLIDEAN",n.MANHATTAN="MANHATTAN"}(r||(r={}));const a={[r.EUCLIDEAN]:function(n){return`\n        var sum = 0.0;\n        for (var i = 0u; i < ${n}; i = i + 1u) {\n            sum = sum + distances[i] * distances[i] * computeInfo.weights[i] * computeInfo.weights[i];\n        }\n        return sqrt(sum);\n    `},[r.MANHATTAN]:function(n){return`\n        var sum = 0.0;\n        for (var i = 0u; i < ${n}; i = i + 1u) {\n            sum = sum + abs(distances[i]) * computeInfo.weights[i];\n        }\n        return sum;\n    `}};var i;!function(n){n.HAMMING="Hamming",n.EUCLIDEAN="Euclidean",n.MANHATTAN="Manhattan",n.TANIMOTO="Tanimoto",n.LEVENSTEIN="Levenshtein",n.NEEDLEMAN_WUNSCH="Needlemann-Wunsch",n.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",n.SOKAL="Sokal",n.COSINE="Cosine",n.ASYMMETRIC="Asymmetric",n.Difference="Difference",n.OneHot="One-Hot"}(i||(i={}));const o={[i.HAMMING]:function(n,e){return`\n  let aLength: u32 = computeInfo.entrySizes[${e}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${e}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n  let sizeDiff: u32 = maxLength - minLength;\n  \n  let maxIntDistance = ceil(maxDistance * f32(maxLength)) - f32(sizeDiff);\n\n  var diff: f32 = 0.0;\n  for (var i = 0u; i < ${n}; i = i + 1u) {\n      diff = diff + f32(a[i] != b[i]);\n      if (diff > maxIntDistance) {\n            return 1.0;\n        }\n  }\n  diff += f32(sizeDiff);\n  return diff / ${n};\n  `},[i.EUCLIDEAN]:function(n,e){return`\n  var dist: f32 = 0.0;\n  for (var i = 0u; i < ${n}; i = i + 1u) {\n    dist = dist + f32(a[i] - b[i]) * f32(a[i] - b[i]);\n  }\n  return sqrt(dist);\n  `},[i.MANHATTAN]:function(n,e){return`\n  var dist: f32 = 0.0;\n  for (var i = 0u; i < ${n}; i = i + 1u) {\n    dist = dist + abs(f32(a[i] - b[i]));\n  }\n  return dist;\n  `},[i.TANIMOTO]:function(n,e){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n\n  if (onBitsa == 0u && onBitsb == 0u) {\n      return 0.0;\n  }\n\n  let totalOnBits = onBitsa + onBitsb;\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n\n  return 1.0 - f32(commonBits) / f32(totalOnBits - commonBits);\n  `},[i.LEVENSTEIN]:function(n,e){return`\n  let aLength: u32 = computeInfo.entrySizes[${e}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${e}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n\n  let maxIntDistance = ceil(maxDistance * f32(maxLength));\n\n  // we will store two arrays as matrix and swap the working indices per pass.\n  // this way we can reduce memory usage per computation to just O(aLength)\n  // the grid will have aLength + 1 columns and bLength + 1 rows\n  // this will be guaranteed by iteration, but the array sizes must be known at compile time, so we will use a fixed size of maxArraySize\n  var dynamicPassMat: array<array<f32, ${n+1}u>, 2>; // initialize to 0\n  \n  var prevIndex: u32 = 0;\n  var curIndex: u32 = 1; // we will swap these indices per pass\n\n  // initialize the first row\n  for (var i = 0u; i <= aLength; i = i + 1u) {\n      dynamicPassMat[prevIndex][i] = f32(i);\n  }\n\n  // iterate over the rows\n  for (var i = 1u; i <= bLength; i = i + 1u) {\n      dynamicPassMat[curIndex][0] = f32(i);\n      var minEntry: f32 = f32(maxLength);\n      let prevRow = &dynamicPassMat[prevIndex];\n      let curRow = &dynamicPassMat[curIndex];\n      let bMon = u32(b[i - 1]);\n      for (var j = 1u; j <= aLength; j = j + 1u) {\n          var cost: f32 = f32(a[j - 1] != bMon);\n          var res: f32 = min(\n              min(\n                (*prevRow)[j] + 1.0, // deletion\n                (*curRow)[j - 1] + 1.0, // insertion\n              ),\n              (*prevRow)[j - 1] + cost // substitution\n              );\n              (*curRow)[j] = res;\n          if (res < minEntry) {\n              minEntry = res;\n          }\n      }\n      // swap the indices\n      let temp: u32 = prevIndex;\n      prevIndex = curIndex;\n      curIndex = temp;\n      if (minEntry > maxIntDistance) {\n          return 1.0;\n      }\n  }\n\n  return dynamicPassMat[prevIndex][aLength] / f32(maxLength);\n  `},[i.NEEDLEMAN_WUNSCH]:function(n,e){return`\n      let aLength: u32 = computeInfo.entrySizes[${e}][aIndex];\n      let bLength: u32 = computeInfo.entrySizes[${e}][bIndex];\n      let maxLength: u32 = max(aLength, bLength);\n      let minLength: u32 = min(aLength, bLength);\n  \n      let maxIntDistance = ceil(maxDistance * f32(maxLength));\n      // we will store two arrays as matrix and swap the working indices per pass.\n      // this way we can reduce memory usage per computation to just O(aLength)\n      // the grid will have aLength + 1 columns and bLength + 1 rows\n      // this will be guaranteed by iteration, but the array sizes must be known at compile time, so we will use a fixed size of maxArraySize\n      var dynamicPassMat: array<array<f32, ${n+1}u>, 2>; // initialize to 0\n      \n      // we need to keep track of which operation led to the current cell\n      // i.e. whether we came from the left, top or diagonal to assign gap open/gap extend penalty\n      var verticalGaps: array<u32, ${n+1}u>;\n      var horizontalGaps: array<u32, ${n+1}u>;\n\n      let gapOpenPenalty: f32 = suppInfo.gapOpenPenalty${e};\n      let gapExtensionPenalty: f32 = suppInfo.gapExtensionPenalty${e};\n      var prevIndex: u32 = 0;\n      var curIndex: u32 = 1; // we will swap these indices per pass\n      // initialize the first row\n      for (var i = 0u; i <= aLength; i = i + 1u) {\n          dynamicPassMat[prevIndex][i] = gapOpenPenalty + f32(i - 1) * gapExtensionPenalty;\n          dynamicPassMat[curIndex][i] = 0.0;\n      }\n      dynamicPassMat[0][0] = 0.0;\n\n      let simMatrix = &suppInfo.similarityMatrix${e}; // using pointers make things faster\n      // iterate over the rows\n      for (var i = 1u; i <= bLength; i = i + 1u) {\n          let prevRow = &dynamicPassMat[prevIndex];\n          let curRow = &dynamicPassMat[curIndex];\n          (*curRow)[0] = gapOpenPenalty + f32(i - 1) * gapExtensionPenalty;\n          var minEntry: f32 = f32(maxLength);\n          let monB = u32(b[i - 1]);\n          for (var j = 1u; j <= aLength; j = j + 1u) {\n              let monA = u32(a[j - 1]);\n              \n              let cost: f32 = (*prevRow)[j - 1] + 1f - (*simMatrix)[monA][monB];\n              var top = (*prevRow)[j]; // deletion\n              if (verticalGaps[j] > 0) {\n                  top = top + gapExtensionPenalty;\n              } else {\n                  top = top + gapOpenPenalty;\n              }\n              var left = (*curRow)[j - 1]; // insertion\n              if (horizontalGaps[j - 1] > 0) {\n                  left = left + gapExtensionPenalty;\n              } else {\n                  left = left + gapOpenPenalty;\n              }\n              var res: f32 = min(\n                  min(\n                      top, // deletion\n                      left, // insertion\n                  ),\n                  cost // substitution\n                  );\n                  (*curRow)[j] = res;\n              if (res < minEntry) {\n                  minEntry = res;\n              }\n              // update the horizontal and vertical gaps\n              if (res == cost) {\n                  verticalGaps[j] = 0;\n                  horizontalGaps[j] = 0;\n              } else if (res == left) {\n                  verticalGaps[j] = 0;\n                  horizontalGaps[j] = 1;\n              } else {\n                  verticalGaps[j] = 1;\n                  horizontalGaps[j] = 0;\n              }\n          }\n          // swap the indices\n          let temp: u32 = prevIndex;\n          prevIndex = curIndex;\n          curIndex = temp;\n          if (minEntry > maxIntDistance) {\n              return 1.0;\n          }\n      }\n      return dynamicPassMat[prevIndex][aLength] / f32(maxLength);\n  \n  `},[i.MONOMER_CHEMICAL_DISTANCE]:function(n,e){return`\n  let aLength: u32 = computeInfo.entrySizes[${e}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${e}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n  let sizeDiff: u32 = maxLength - minLength;\n  \n  let maxIntDistance = ceil(maxDistance * f32(maxLength)) - f32(sizeDiff);\n\n  let simMatrix = &(suppInfo.similarityMatrix${e}); // using pointers make things faster\n  var diff: f32 = 0.0;\n  for (var i = 0u; i < ${n}; i = i + 1u) {\n      diff = diff + 1.0 - (*simMatrix)[u32(a[i])][u32(b[i])];\n      if (diff > maxIntDistance) {\n            return 1.0;\n        }\n  }\n  diff += f32(sizeDiff);\n  return diff / ${n};\n  `},[i.SOKAL]:function(n,e){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let total = onBitsa + onBitsb;\n  if (total == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / f32(total * 2 - commonBits * 3);\n  `},[i.COSINE]:function(n,e){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let total = onBitsa * onBitsb; // p.s. here total is taken by multiplying\n  if (total == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / sqrt(f32(total));\n  `},[i.ASYMMETRIC]:function(n,e){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let min = min(onBitsa, onBitsb);\n  if (min == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${n}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / f32(min);\n  `},[i.Difference]:function(n,e){return`\n    let range = suppInfo.range${e};\n    return f32(abs(f32(a[0]) - f32(b[0])) / range);\n  `},[i.OneHot]:function(n,e){return`\n  let aLength: u32 = computeInfo.entrySizes[${e}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${e}][bIndex];\n  if (aLength != bLength) {\n    return 1.0;\n  }\n  for (var i = 0u; i < aLength; i = i + 1u) {\n    if(a[i] != b[i]) {\n      return 1.0;\n    }\n  }\n  return 0.0;\n  `}},s={[i.HAMMING]:n=>Math.ceil(n/30),[i.EUCLIDEAN]:n=>Math.ceil(n/30),[i.MANHATTAN]:n=>Math.ceil(n/30),[i.TANIMOTO]:n=>Math.ceil(n/60),[i.SOKAL]:n=>Math.ceil(n/60),[i.COSINE]:n=>Math.ceil(n/60),[i.ASYMMETRIC]:n=>Math.ceil(n/60),[i.LEVENSTEIN]:n=>Math.ceil(n*n/60),[i.NEEDLEMAN_WUNSCH]:n=>Math.ceil(n*n/60),[i.MONOMER_CHEMICAL_DISTANCE]:n=>Math.ceil(n/25),[i.Difference]:n=>1,[i.OneHot]:n=>Math.ceil(n/40)},u={STRING:new Set([i.HAMMING,i.LEVENSTEIN,i.NEEDLEMAN_WUNSCH,i.MONOMER_CHEMICAL_DISTANCE,i.OneHot]),UINT32ARRAY:new Set([i.HAMMING,i.EUCLIDEAN,i.MANHATTAN,i.MONOMER_CHEMICAL_DISTANCE,i.LEVENSTEIN,i.NEEDLEMAN_WUNSCH,i.TANIMOTO,i.COSINE,i.SOKAL,i.ASYMMETRIC,i.OneHot,i.Difference]),INT32ARRAY:new Set([i.EUCLIDEAN,i.MANHATTAN,i.OneHot,i.Difference]),FLOAT32ARRAY:new Set([i.EUCLIDEAN,i.MANHATTAN,i.Difference]),NUMBER:new Set([i.EUCLIDEAN,i.MANHATTAN,i.Difference]),BITARRAY:new Set([i.TANIMOTO,i.COSINE,i.SOKAL,i.ASYMMETRIC])};var l=function(n,e,t,r){return new(t||(t=Promise))((function(a,i){function o(n){try{u(r.next(n))}catch(n){i(n)}}function s(n){try{u(r.throw(n))}catch(n){i(n)}}function u(n){var e;n.done?a(n.value):(e=n.value,e instanceof t?e:new t((function(n){n(e)}))).then(o,s)}u((r=r.apply(n,e||[])).next())}))},c=function(n,e,t,r){return new(t||(t=Promise))((function(a,i){function o(n){try{u(r.next(n))}catch(n){i(n)}}function s(n){try{u(r.throw(n))}catch(n){i(n)}}function u(n){var e;n.done?a(n.value):(e=n.value,e instanceof t?e:new t((function(n){n(e)}))).then(o,s)}u((r=r.apply(n,e||[])).next())}))};function f(n,e,t,r){return n.map(((n,r)=>`\n        fn distanceScript${r}(aIndex: u32, bIndex: u32) -> f32 {\n          let a = computeInfo.data${r}[aIndex];\n          let b = computeInfo.data${r}[bIndex];\n          let maxDistance: f32 = ${t};\n          ${o[n](e[r],r)}\n        }\n      `)).join("\n")+"\n"+`\n      fn combinedDistance(aIndex: u32, bIndex: u32) -> f32 {\n        var distances: array<f32, ${n.length}>;\n        ${n.map(((n,e)=>`distances[${e}] = distanceScript${e}(aIndex, bIndex);`)).join("\n")}\n        ${a[r](n.length)}\n      }\n    \n    `}var m=t(2590);async function d(n,e,t){const r=n.length,a=[],i=[];for(let o=0;o<r;o++)for(let s=o+1;s<r;s++){const r=n[o],u=n[s];e[r]?.[u]>=t&&(a.push(o),i.push(s))}return function(n,e,t){const r=new Float32Array(t.length).fill(0).map((()=>10*Math.random())),a=new Float32Array(t.length).fill(0).map((()=>10*Math.random())),i=new Float32Array(t.length).fill(0),o=new Float32Array(t.length).fill(0);for(let s=0;s<100;s++){const u=1-s/100;i.fill(0),o.fill(0);for(let t=0;t<n.length;t++){const s=n[t],l=e[t],c=r[s]-r[l],f=a[s]-a[l];Math.abs(c)>=1&&(i[s]-=u*c,i[l]+=u*c),Math.abs(f)>=1&&(o[s]-=u*f,o[l]+=u*f)}for(let n=0;n<t.length;n++){const e=Math.sqrt(i[n]*i[n]+o[n]*o[n]);e>0&&(r[n]+=i[n]/e*u,a[n]+=o[n]/e*u)}}let s=r[0],u=a[0],l=r[0],c=a[0];for(let n=1;n<t.length;n++)s=Math.min(s,r[n]),u=Math.min(u,a[n]),l=Math.max(l,r[n]),c=Math.max(c,a[n]);let f=l-s,m=c-u;0===f&&(f=l);for(let n=0;n<t.length;n++)r[n]=(r[n]-s)/f/2+.5;0===m&&(m=c);for(let n=0;n<t.length;n++)a[n]=(a[n]-u)/m/2+.5;return{embedX:r,embedY:a}}(a,i,n)}const p={expandFactor:2,maxIterations:5,inflateFactor:2,multFactor:1};class h{constructor(n={}){this._options={...p,...n}}async transform(n,e){let t=this.toObjectForm(n);if(this._options.maxIterations>0){this.addLoops(t,e),this.normalize(t);for(let n=0;n<this._options.maxIterations;n++)t=this.expand(t,e),this.inflate(t),this.normalize(t)}const{clusters:r,is:a,js:i}=this.assignClusters(t,e);this.correctClusters(r);const o=await this.layout(r,t,e);return{clusters:r,embedX:o.embedX,embedY:o.embedY,is:a,js:i}}correctClusters(n){const e={};for(const t of n)e[t]||(e[t]=0),e[t]++;const t=Object.keys(e).map(Number).sort(((n,t)=>e[n]-e[t])),r={};t.forEach(((n,e)=>r[n]=e+1));for(let e=0;e<n.length;e++)n[e]=r[n[e]]}async layout(n,e,t){const r=new Float32Array(t).fill(0),a=new Float32Array(t).fill(0),i={};n.forEach(((n,e)=>{i[n]||(i[n]=[]),i[n].push(e)}));let o=0;const s=Object.keys(i);s.sort(((n,e)=>i[e].length-i[n].length));let u=6,l=0;for(const n of s){const t=i[n],s=await d(t,e,.001);o===Math.ceil(u/1.5)&&(o=0,l+=5/u,u=Math.ceil(1.5*u));const c=o%u*5/u*1.5;for(let n=0;n<s.embedX.length;n++)r[t[n]]=5*s.embedX[n]/u+c,a[t[n]]=5*s.embedY[n]/u+l;o++}return{embedX:r,embedY:a}}mergeClusters(n,e,t){const r=n[e],a=n[t];for(let e=0;e<n.length;e++)n[e]===a&&(n[e]=r)}assignClusters(n,e){let t=0;const r=[],a=[],i=Math.floor(Math.max(Math.log10(e),2))+1,o=Math.pow(10,i),s=new Array(e).fill(-1);for(const e of Object.keys(n))for(const i of Object.keys(n[e]))Math.round(n[e][i]*o)/o>0&&n[e][i]!==Number(e)&&Number(i)>Number(e)&&(r.push(Number(e)),a.push(Number(i)),-1!==s[Number(e)]&&-1!==s[Number(i)]?s[Number(e)]!==s[Number(i)]&&this.mergeClusters(s,Number(e),Number(i)):-1!==s[Number(e)]?s[Number(i)]=s[Number(e)]:-1!==s[Number(i)]?s[Number(e)]=s[Number(i)]:(t++,s[Number(e)]=t,s[Number(i)]=t));for(let n=0;n<s.length;n++)-1===s[n]&&(t++,s[n]=t);return{clusters:s,is:new Uint32Array(r),js:new Uint32Array(a)}}toObjectForm(n){const e={};for(let t=0;t<n.i.length;t++)e[n.i[t]]||(e[n.i[t]]={}),e[n.i[t]][n.j[t]]=1-n.distance[t],e[n.j[t]]||(e[n.j[t]]={}),e[n.j[t]][n.i[t]]=1-n.distance[t];return e}addLoops(n,e){for(let t=0;t<e;t++)n[t]||(n[t]={}),n[t][t]=this._options.multFactor}normalize(n){for(const e of Object.keys(n)){const t=n[e];let r=0;for(const n of Object.keys(t))r+=t[n];if(0!==r)for(const a of Object.keys(t))n[e][a]/=r}}expand(n,e){const t={},r=Math.floor(Math.max(Math.log10(e),2))+1,a=Math.pow(10,r);for(let r=0;r<e;r++)if(n[r]){t[r]={};for(let i=r;i<e;i++){if(!n[r]?.[i])continue;const e=this.getExpandValue(n,r,i);Math.round(e*a)/a>0&&(t[r][i]=e,t[i]||(t[i]={}),t[i][r]=e)}}return t}inflate(n){for(const e of Object.keys(n)){const t=n[e];for(const r of Object.keys(t))n[e][r]=Math.pow(n[e][r],this._options.inflateFactor)}}getExpandValue(n,e,t){let r=0;const a=Object.keys(n[e]??{}),i=Object.keys(n[t]??{});for(const o of a)i.includes(o)&&(r+=n[e][o]*n[t][o]);return r}}onmessage=async n=>{const{data:e,threshold:t,weights:a,aggregationMethod:o,distanceFnArgs:d,distanceFns:p,maxIterations:g,useWebGPU:y}=n.data;console.time("sparse matrix");let A=null;if(y)try{A=await function(n,e=.8,t,a,o,m){return c(this,void 0,void 0,(function*(){const c=yield function(){return l(this,void 0,void 0,(function*(){const n=yield navigator.gpu.requestAdapter({powerPreference:"high-performance"});if(null==n)return null;const e=1e9,t=n.limits,r=t.maxBufferSize,a=t.maxStorageBufferBindingSize;try{return yield n.requestDevice({requiredLimits:{maxBufferSize:Math.min(r,e),maxStorageBufferBindingSize:Math.min(a,e)}})}catch(e){return console.error("Failed to create device with required limits",e),yield n.requestDevice()}}))}();if(!c)return null;const d=Object.values(i);if(t.some((n=>!d.includes(n))))throw new Error("Invalid distance metrics provided: "+t.join(", "));if(!Object.values(r).includes(a))throw new Error("Invalid aggregation function provided: "+a);const p=1-e;if(m.length!==n.length||m.length!==t.length||m.length!==o.length)throw new Error("Options, weigths and distance functions must be provided for each column");if(n.some((e=>e.length!==n[0].length)))throw new Error("All entry lists must be the same length");const h=n.length,g=n[0].length,y=n.map(((n,e)=>function(n,e=i.HAMMING,t,r={gapOpenPenalty:1,gapExtensionPenalty:.6}){var a,o;let l=null;const c=n.some((n=>"string"==typeof n))?(l="STRING",n.map((n=>new Uint32Array(n.split("").map((n=>n.charCodeAt(0))))))):n.some((n=>"number"==typeof n))?(l="NUMBER",n.map((n=>new Float32Array([n])))):"object"==typeof n[0]&&n.some((n=>"_data"in n&&"_length"in n))?(l="BITARRAY",n.map((n=>n._data))):n.some((n=>n instanceof Float32Array))?(l="FLOAT32ARRAY",n):n.some((n=>n instanceof Uint32Array))?(l="UINT32ARRAY",n):n.some((n=>n instanceof Int32Array))?(l="INT32ARRAY",n):void 0;if(!c||!l)throw new Error("Invalid entry type, could not determine entry type from input list");const f=c[0]instanceof Int32Array?"INT32ARRAY":c[0]instanceof Float32Array?"FLOAT32ARRAY":"UINT32ARRAY",m=new Uint32Array(c.map((n=>n.length)));if(!u[l]||!u[l].has(e))throw new Error(`Distance metric '${e}' not supported for entry type '${l}'`);const d=m.reduce(((n,e)=>Math.max(n,e)),0),p=s[e](d),h="INT32ARRAY"===f?Int32Array:"FLOAT32ARRAY"===f?Float32Array:Uint32Array,g=new h(c.length*d);c.forEach(((n,e)=>{g.set(n,e*d)}));let y="",A=0,b="FLOAT32ARRAY",E=null;if(e===i.NEEDLEMAN_WUNSCH||e===i.MONOMER_CHEMICAL_DISTANCE){let n=r.scoringMatrix&&r.alphabetIndexes?Object.keys(r.alphabetIndexes).reduce(((n,e)=>Math.max(n,e.charCodeAt(0))),0):-1;if(!r.alphabetIndexes||!r.scoringMatrix){for(let e=0;e<g.length;e++)g[e]>n&&(n=g[e]);r.scoringMatrix=new Array(n+1).fill(null).map((()=>new Array(n+1).fill(0))),r.alphabetIndexes={};for(let n=0;n<r.scoringMatrix.length;n++)r.scoringMatrix[n][n]=1,r.alphabetIndexes[String.fromCharCode(n)]=n}const e=(n+1)*(n+1),i=new Array(n+1).fill(null).map((()=>new Float32Array(n+1)));for(let e=0;e<n+1;e++)i[e][e]=1;const s=r.alphabetIndexes;for(const n of Object.keys(s))for(const e of Object.keys(s))n!==e&&(i[n.charCodeAt(0)][e.charCodeAt(0)]=r.scoringMatrix[s[n]][s[e]]);A=2+e,b="FLOAT32ARRAY",E=new Float32Array(A),E[0]=null!==(a=r.gapOpenPenalty)&&void 0!==a?a:1,E[1]=null!==(o=r.gapExtensionPenalty)&&void 0!==o?o:.6;let u=2;for(let n=0;n<i.length;n++)E.set(i[n],u),u+=i[n].length;y=`\n            gapOpenPenalty${t}: f32,\n            gapExtensionPenalty${t}: f32,\n            similarityMatrix${t}: array<array<f32, ${n+1}>, ${n+1}>`}else if(e===i.Difference){if(!r.range||"number"!=typeof r.range||r.range<=0){const n=g.reduce(((n,e)=>Math.min(n,e)),g[0]),e=g.reduce(((n,e)=>Math.max(n,e)),g[0]);r.range=e-n}if(r.range<=0)throw new Error("Invalid range for difference distance metric: "+r.range);A=1,b="FLOAT32ARRAY",E=new Float32Array([r.range]),y=`\n            range${t}: f32`}const w=g instanceof Int32Array?"i32":g instanceof Float32Array?"f32":"u32",I=`data${t}: array<array<${w}, ${d}>, ${c.length}>`;return{flatSourceArray:g,sourceArraySize:g.length,maxEntryLen:d,arraySizes:m,complexity:p,suppInfoBuffer:E,suppInfoSize:A,suppInfoType:b,suppInfoStructWgsl:y,entryType:l,dataTypeWGSL:w,dataStructWgsl:I,EncodedArrayConstructor:h}}(n,t[e],e,m[e])));if(0===h)throw new Error("No columns provided. Please provide at least one column of data.");1===h&&(a=r.MANHATTAN);let A=y.map((n=>n.suppInfoStructWgsl)).filter((n=>!!n&&""!=n)).join(",\n"),b=!1;A&&""!=A.trim()||(b=!0,A="\ndummy: f32\n");const E=y.map((n=>n.dataStructWgsl)).filter((n=>!!n&&""!=n)).join(",\n"),w=new Uint32Array(h*g);y.forEach(((n,e)=>{w.set(n.arraySizes,e*g)}));const I=1e4,x=100,M=y.reduce(((n,e)=>n+e.complexity),0),v=Math.ceil(1e4/M),N=Math.ceil(Math.sqrt(Math.ceil(100))),L=10*N,B=g*(g-1)/2,S=Math.ceil(B/I),T=c.createShaderModule({label:"Sparse matrix compute shader",code:`\n    // each thread will perform 100 iterations at one time, comparing 100 pairs of entries.\n    // in total, each thread will perform at most ${S} comparisons.\n    // first is the result struct, containing is, js, and distances. each array with length of 100,\n    // and also integer for how many pairs were found to be below threshold.\n    struct SparseResult {\n      i: array<array<u32, 100>, 10000>,\n      j: array<array<u32, 100>, 10000>,\n      distances: array<array<f32, 100>, 10000>,\n      found: array<u32, 10000>,\n      done: array<u32, 10000>\n    }\n    // struct for the data\n    struct ComputeInfo {\n      // start at cols and rows, and end at cols and rows for each thread, these will be calculated on cpu and passed to gpu.\n      startAtCols: array<u32, 10000>,\n      startAtRows: array<u32, 10000>,\n      endAtCols: array<u32, 10000>,\n      endAtRows: array<u32, 10000>,\n\n      // the ACTUALLY sizes of each entry\n      entrySizes: array<array<u32, ${g}>, ${h}>,\n      // the weights for each entry\n      weights: array<f32, ${h}>,\n      // the data for each entry\n      ${E} // an example of the dataWgsl would be:\n      //data0: array<array<u32,20>,100>,\n      //data1: array<array<u32,20>,100>\n    }\n\n    // struct for the supplementary information\n    struct SuppInfo {\n      // struct containing all the supplementary info, like scoring matrix, alphabet indexes, range, etc.\n      ${A}\n    };\n\n    @group(0) @binding(0) var<storage, read_write> computeInfo: ComputeInfo;\n    @group(0) @binding(1) var<storage, read_write> suppInfo: SuppInfo;\n    @group(0) @binding(2) var<storage, read_write> results: SparseResult;\n    @compute @workgroup_size(10, 10) fn calcSparseMatrix(\n      @builtin(global_invocation_id) id: vec3<u32>\n    ) {\n      ${b?"let otherDummy = suppInfo.dummy * 2;":""} // just to make sure that the suppInfo is not optimized out\n      let threadCol = id.x;\n      let threadRow = id.y;\n      let linearIndex = threadRow * ${L} + threadCol;\n      if (linearIndex >= 10000) {\n        return; // if we are out of bounds, return\n      }      \n      var startAtCol: u32 = computeInfo.startAtCols[linearIndex];\n      var startAtRow: u32 = computeInfo.startAtRows[linearIndex];\n      let endAtCol: u32 = min(computeInfo.endAtCols[linearIndex], ${g}u);\n      let endAtRow: u32 = min(computeInfo.endAtRows[linearIndex], ${g}u);\n      let is = &results.i[linearIndex];\n      let js = &results.j[linearIndex];\n      let distances = &results.distances[linearIndex];\n      results.found[linearIndex] = 0; // initialize the found counter\n      var found: u32 = 0;\n      if (results.done[linearIndex] > 0) {\n        return; // if we are done, return\n      }\n      for (var i = 0; i < ${v}; i++) {\n        if (startAtCol >= endAtCol && startAtRow >= endAtRow) {\n          results.done[linearIndex] = 1;\n          break;\n        }\n        if (found >= 100) {\n          break;\n        }\n        let dist = combinedDistance(startAtCol, startAtRow);\n        if (dist <= ${p}) {\n          (*is)[found] = startAtCol;\n          (*js)[found] = startAtRow;\n          (*distances)[found] = dist;\n          found = found + 1;\n        }\n        startAtCol = startAtCol + 1;\n        if (startAtCol >= ${g}u) {\n          startAtRow += 1;\n          startAtCol = startAtRow + 1;\n        }\n      }\n      results.found[linearIndex] = found;\n      // update the startAtCols and startAtRows\n      computeInfo.startAtCols[linearIndex] = startAtCol;\n      computeInfo.startAtRows[linearIndex] = startAtRow;\n\n    }\n\n    // this will generate the distance script for each distance metric and then combine them into one\n    ${f(t,y.map((n=>n.maxEntryLen)),p,a)}\n\n\n    `}),O=c.createComputePipeline({label:"sparse matrix compute pipeline",layout:"auto",compute:{module:T,entryPoint:"calcSparseMatrix"}}),R=new Uint32Array(I),C=new Uint32Array(I),U=new Uint32Array(I),P=new Uint32Array(I),$=Math.floor(B/I);let j=0,_=1;console.time("GPUthreadStarts");for(let n=0;n<I;n++){const e=9999===n?B-1:(n+1)*$,t=g-2-Math.floor(Math.sqrt(-8*e+4*g*(g-1)-7)/2-.5),r=e-g*t+Math.floor((t+1)*(t+2)/2);R[n]=_,C[n]=j,U[n]=r,P[n]=t,j=t,_=r}console.timeEnd("GPUthreadStarts");const D=4e4+g*h+h+y.reduce(((n,e)=>n+e.sourceArraySize),0),z=y.reduce(((n,e)=>n+e.suppInfoSize),0),Y=1e6,G=D*Uint32Array.BYTES_PER_ELEMENT;let k=G;const 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