@datagrok/bio 2.13.2 → 2.13.5

package/src/utils/monomer-lib/library-file-manager/file-validator.ts

@@ -14,7 +14,8 @@ export class MonomerLibFileValidator {
   constructor(
     private helmMonomerSchema: JSONSchemaType<any>
   ) {
-    const ajv = new Ajv2020({allErrors: true, strictTuples: false});
+    // HELMMonomerSchema.json / #/properties/id uses a union type (string added by Maria Dolotova)
+    const ajv = new Ajv2020({allErrors: true, strictTuples: false, allowUnionTypes: true});
     addErrors(ajv);
     this.validateMonomerSchema = ajv.compile(this.helmMonomerSchema);
   }

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -139,12 +139,9 @@ class LibraryControlsManager {
     const logPrefix = `${this.toLog()}.createLibInput()`;
     _package.logger.debug(`${logPrefix}, libFileName = '${libFileName}', start`);
     const isMonomerLibrarySelected = !this.userLibSettings.exclude.includes(libFileName);
-    const libInput = ui.boolInput(
-      libFileName,
-      isMonomerLibrarySelected,
-      (isSelected: boolean) => {
-        this.fileManager.eventManager.updateLibrarySelectionStatus(libFileName, isSelected);
-      });
+    const libInput = ui.input.bool(libFileName, {value: isMonomerLibrarySelected, onValueChanged: (input) => {
+      this.fileManager.eventManager.updateLibrarySelectionStatus(libFileName, input.value);
+    }});
     ui.tooltip.bind(libInput.root, `Include monomers from ${libFileName}`);
     const deleteIcon = ui.iconFA('trash-alt', () => this.promptForLibraryDeletion(libFileName));
     ui.tooltip.bind(deleteIcon, `Delete ${libFileName}`);

package/src/utils/multiple-sequence-alignment-ui.ts

@@ -38,18 +38,18 @@ export async function multipleSequenceAlignmentUI(
     }
 
     // UI for PepSea alignment
-    const methodInput = ui.choiceInput('Method', options.pepsea.method, pepseaMethods);
+    const methodInput = ui.input.choice('Method', {value: options.pepsea.method, items: pepseaMethods});
     methodInput.setTooltip('Alignment method');
 
     // UI for Kalign alignment
-    const terminalGapInput = ui.floatInput('Terminal gap', options?.kalign?.terminalGap ?? null);
+    const terminalGapInput = ui.input.float('Terminal gap', {value: options?.kalign?.terminalGap});
     terminalGapInput.setTooltip('Penalty for opening a gap at the beginning or end of the sequence');
     const kalignVersionDiv = ui.p(`Kalign version: ${kalignVersion}`, 'kalign-version');
 
     // shared UI
-    const gapOpenInput = ui.floatInput('Gap open', options.pepsea.gapOpen);
+    const gapOpenInput = ui.input.float('Gap open', {value: options.pepsea.gapOpen});
     gapOpenInput.setTooltip('Gap opening penalty at group-to-group alignment');
-    const gapExtendInput = ui.floatInput('Gap extend', options.pepsea.gapExtend);
+    const gapExtendInput = ui.input.float('Gap extend', {value: options.pepsea.gapExtend});
     gapExtendInput.setTooltip('Gap extension penalty to skip the alignment');
 
     const msaParamsDiv = ui.inputs([gapOpenInput, gapExtendInput, terminalGapInput]);
@@ -69,25 +69,24 @@ export async function multipleSequenceAlignmentUI(
     let performAlignment: (() => Promise<DG.Column<string> | null>) | undefined;
 
     let prevSeqCol = seqCol;
-    const colInput = ui.columnInput(
-      'Sequence', table, seqCol,
-      async (valueCol: DG.Column) => {
-        if (!valueCol || valueCol.semType !== DG.SEMTYPE.MACROMOLECULE) {
+    const colInput = ui.input.column(
+      'Sequence', {table: table, value: seqCol, onValueChanged: async (input: DG.InputBase<DG.Column<string>>): Promise<void> => {
+        if (!input.value || input.value.semType !== DG.SEMTYPE.MACROMOLECULE) {
           okBtn.disabled = true;
           await delay(0); // to
           colInput.value = prevSeqCol as DG.Column<string>;
           return;
         }
-        prevSeqCol = valueCol;
+        prevSeqCol = input.value;
         okBtn.disabled = false;
         performAlignment = await onColInputChange(
           colInput.value, table, pepseaInputRootStyles, kalignInputRootStyles,
           methodInput, clustersColInput, gapOpenInput, gapExtendInput, terminalGapInput,
         );
-      }, {filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE} as ColumnInputOptions
+      }, filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE} as ColumnInputOptions
     ) as DG.InputBase<DG.Column<string>>;
     colInput.setTooltip('Sequences column to use for alignment');
-    const clustersColInput = ui.columnInput('Clusters', table, options.clustersCol);
+    const clustersColInput = ui.input.column('Clusters', {table: table, value: options.clustersCol!});
     clustersColInput.nullable = true;
 
     const dlg = ui.dialog('MSA')

package/src/utils/multiple-sequence-alignment.ts

@@ -103,13 +103,13 @@ export async function runKalign(srcCol: DG.Column<string>, isAligned: boolean =
   }
 
   // units
-  const srcUnits = srcCol.getTag(DG.TAGS.UNITS);
+  const srcUnits = srcCol.meta.units;
   //aligned
   const tgtAligned = ALIGNMENT.SEQ_MSA;
   //alphabet
   const srcAlphabet = srcCol.getTag(bioTAGS.alphabet);
 
-  tgtCol.setTag(DG.TAGS.UNITS, srcUnits);
+  tgtCol.meta.units = srcUnits;
   tgtCol.setTag(bioTAGS.aligned, tgtAligned);
   tgtCol.setTag(bioTAGS.alphabet, srcAlphabet);
   tgtCol.semType = DG.SEMTYPE.MACROMOLECULE;

package/src/utils/pepsea.ts

@@ -91,7 +91,7 @@ export async function runPepsea(srcCol: DG.Column<string>, unUsedName: string,
   }
 
   const alignedSequencesCol: DG.Column<string> = DG.Column.fromStrings(unUsedName, alignedSequences);
-  alignedSequencesCol.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+  alignedSequencesCol.meta.units = NOTATION.SEPARATOR;
   alignedSequencesCol.setTag(bioTAGS.separator, C.PEPSEA.SEPARATOR);
   alignedSequencesCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
   alignedSequencesCol.setTag(bioTAGS.alphabet, ALPHABET.UN);

package/src/utils/save-as-fasta.ts

@@ -20,8 +20,8 @@ export function saveAsFastaUI() {
     .find((gcol: DG.GridColumn) => gcol.name.toLowerCase().indexOf('id') !== -1);
   const idDefaultValue = defaultIdGCol ? [defaultIdGCol.name] : [];
 
-  const idGColListInput = ui.multiChoiceInput('Seq id columns', idDefaultValue,
-    idGColList.map((gcol: DG.GridColumn) => gcol.name));
+  const idGColListInput = ui.input.multiChoice('Seq id columns', {value: idDefaultValue,
+    items: idGColList.map((gcol: DG.GridColumn) => gcol.name)});
 
   const seqGColList: DG.GridColumn[] = wu.count(0).take(grid.columns.length)/* range rom 0 to grid.columns.length */
     .map((colI: number) => grid.columns.byIndex(colI)!)
@@ -35,10 +35,10 @@ export function saveAsFastaUI() {
     }).toArray();
 
   const seqDefaultValue = seqGColList.length > 0 ? seqGColList[0].name : [];
-  const seqColInput = ui.choiceInput('Seq column', seqDefaultValue,
-    seqGColList.map((gCol: DG.GridColumn) => gCol.name));
+  const seqColInput = ui.input.choice('Seq column', {value: seqDefaultValue,
+    items: seqGColList.map((gCol: DG.GridColumn) => gCol.name)});
 
-  const lineWidthInput = ui.intInput('FASTA line width', FASTA_LINE_WIDTH);
+  const lineWidthInput = ui.input.int('FASTA line width', {value: FASTA_LINE_WIDTH});
 
   ui.dialog({title: 'Save as FASTA'})
     .add(ui.inputs([

package/src/viewers/vd-regions-viewer.ts

@@ -392,8 +392,8 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
     // this.mainLayout.style.height = '100%';
     // this.mainLayout.style.border = '1px solid black';
 
-    this.filterSourceInput = ui.choiceInput<FilterSources>('Data source', this.filterSource,
-      Object.values(FilterSources), this.filterSourceInputOnValueChanged.bind(this));
+    this.filterSourceInput = ui.input.choice<FilterSources>('Data source', {value: this.filterSource,
+      items: Object.values(FilterSources), onValueChanged: this.filterSourceInputOnValueChanged.bind(this)});
     this.filterSourceInput.root.style.position = 'absolute';
     this.filterSourceInput.root.style.right = '9px';
     this.filterSourceInput.root.style.top = '-4px';

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

@@ -128,7 +128,7 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
       }
       const sh = SeqHandler.forColumn(this.column!);
       this.columnName ??= this.column?.name;
-      this.notation ??= this.column?.getTag(DG.TAGS.UNITS);
+      this.notation ??= this.column?.meta.units!;
 
       this.bioFilter = this.notation === NOTATION.FASTA ?
         new FastaBioFilter() : this.notation === NOTATION.SEPARATOR ?
@@ -296,10 +296,10 @@ export class FastaBioFilter extends BioFilterBase<BioFilterProps> {
   constructor() {
     super();
 
-    this.substructureInput = ui.stringInput('', '', () => {
+    this.substructureInput = ui.input.string('', {value: '', onValueChanged: () => {
       this.props = new BioFilterProps(this.substructureInput.value);
       if (!this._propsChanging) this.onChanged.next();
-    }, {placeholder: 'Substructure'});
+    }, placeholder: 'Substructure'});
   }
 
   public applyProps() {
@@ -336,15 +336,15 @@ export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
   constructor(colSeparator: string) {
     super();
 
-    this.substructureInput = ui.stringInput('', '', () => {
+    this.substructureInput = ui.input.string('', {value: '', onValueChanged: () => {
       this.props = new SeparatorFilterProps(this.substructureInput.value, this.props.separator);
       if (!this._propsChanging) this.onChanged.next();
-    }, {placeholder: 'Substructure'});
-    this.separatorInput = ui.stringInput('', this.colSeparator = colSeparator, () => {
+    }, placeholder: 'Substructure'});
+    this.separatorInput = ui.input.string('', {value: this.colSeparator = colSeparator, onValueChanged: () => {
       const separator: string | undefined = !!this.separatorInput.value ? this.separatorInput.value : undefined;
       this.props = new SeparatorFilterProps(this.props.substructure, separator);
       if (!this._propsChanging) this.onChanged.next();
-    }, {placeholder: 'Separator'});
+    }, placeholder: 'Separator'});
   }
 
   applyProps(): void {

package/src/widgets/package-settings-editor-widget.ts

@@ -1,10 +1,9 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {MonomerWidthMode} from '../utils/cell-renderer-consts';
-
 import {_package} from '../package';
 
+
 export class PackageSettingsEditorWidget extends DG.Widget {
   maxMonomerLengthProp: DG.Property;
   tooltipWebLogo: DG.Property;
@@ -22,34 +21,35 @@ export class PackageSettingsEditorWidget extends DG.Widget {
   }
 
   async init(): Promise<void> {
-    const monomerWidthModeInput = ui.choiceInput('Monomer width mode',
-      _package.properties.MonomerWidthMode,
-      [MonomerWidthMode.short, MonomerWidthMode.long],
-      (value: MonomerWidthMode) => {
-        _package.properties.MonomerWidthMode = value;
-      });
-
-    const maxMonomerLengthInput = ui.intInput('Max monomer length',
-      _package.properties.MaxMonomerLength,
-      (value: number) => {
+    const maxMonomerLengthInput = ui.input.int('Max Monomer Length', {
+      value: _package.properties.maxMonomerLength!,
+      nullable: true, min: 0,
+      onValueChanged: () => {
         // Handle user changed value
-        _package.properties.MaxMonomerLength = value;
-      });
-
-    const tooltipWebLogoInput = ui.boolInput('Tooltip WebLogo',
-      _package.properties.TooltipWebLogo,
-      (value: boolean) => {
-        _package.properties.TooltipWebLogo = value;
-      });
-
-    const defaultSeparatorInput = ui.choiceInput('Default Separator',
-      _package.properties.DefaultSeparator, ['.', '/', '-'],
-      (value: string) => {
-        _package.properties.DefaultSeparator = value;
-      });
+        _package.properties.maxMonomerLength = maxMonomerLengthInput.value ?? null;
+      },
+      tooltipText: this.maxMonomerLengthProp.description,
+    });
+
+    const tooltipWebLogoInput = ui.input.bool('Tooltip WebLogo', {
+      value: _package.properties.tooltipWebLogo,
+      nullable: false,
+      onValueChanged: () => {
+        _package.properties.tooltipWebLogo = tooltipWebLogoInput.value!;
+      },
+      tooltipText: this.tooltipWebLogo.description,
+    });
+
+    const defaultSeparatorInput = ui.input.choice('Default Separator', {
+      value: _package.properties.defaultSeparator,
+      items: ['.', '/', '-'],
+      onValueChanged: () => {
+        _package.properties.defaultSeparator = defaultSeparatorInput.value!;
+      },
+      tooltipText: this.defaultSeparator.description,
+    });
 
     this.root.appendChild(ui.form([
-      monomerWidthModeInput,
       maxMonomerLengthInput,
       tooltipWebLogoInput,
       defaultSeparatorInput,

package/src/widgets/representations.ts

@@ -6,11 +6,11 @@ import {getMolfilesFromSingleSeq} from '@datagrok-libraries/bio/src/monomer-work
 import {TAGS as mmcrTAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
 import {
-  Tags as mmcrTags, Temps as mmcrTemps, MonomerWidthMode,
-  tempTAGS, rendererSettingsChangedState
+  Temps as mmcrTemps, rendererSettingsChangedState, Temps
 } from '../utils/cell-renderer-consts';
 
 import {_package} from '../package';
+import {max} from 'rxjs/operators';
 
 
 /**
@@ -25,81 +25,77 @@ export function getMacromoleculeColumnPropertyPanel(col: DG.Column): DG.Widget {
   const columnsSet = new Set(columnsList);
   columnsSet.delete(col.name);
 
-  const monomerWidthModeInput = ui.input.choice('Monomer width', {
-    value: (col?.temp[tempTAGS.monomerWidthMode] != null) ? col.temp[tempTAGS.monomerWidthMode] :
-      (_package.properties?.MonomerWidthMode ?? MonomerWidthMode.short),
-    items: [MonomerWidthMode.short, MonomerWidthMode.long],
+  let maxMonomerLength: number | null = (_package.properties ? _package.properties.maxMonomerLength : 4);
+  if (mmcrTAGS.maxMonomerLength in col.tags) {
+    const v = parseInt(col.getTag(mmcrTAGS.maxMonomerLength));
+    maxMonomerLength = !isNaN(v) ? v : maxMonomerLength;
+  }
+  if (Temps.maxMonomerLength in col.temp) {
+    const v = parseInt(col.temp[Temps.maxMonomerLength]);
+    maxMonomerLength = !isNaN(v) ? v : maxMonomerLength;
+  }
+  const maxMonomerLengthInput = ui.input.int('Max Monomer Length', {
+    value: maxMonomerLength!,
+    nullable: true, min: 1, max: 50, step: 1,
     onValueChanged: () => {
-      const s = monomerWidthModeInput.value;
-      col.temp[tempTAGS.monomerWidthMode] = s;
-      col.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.true);
-      col.dataFrame.fireValuesChanged();
-
-      maxMonomerLengthInput.enabled = monomerWidthModeInput.value === MonomerWidthMode.short;
+      if (maxMonomerLengthInput.value == 0)
+        setTimeout(() => { maxMonomerLengthInput.value = null!; }, 0);
+      else {
+        const value = maxMonomerLengthInput.value ?? '';
+        const tagValue = value == null ? '' : value.toString();
+        col.temp[Temps.maxMonomerLength] = tagValue;
+        col.temp[Temps.rendererSettingsChanged] = rendererSettingsChangedState.true;
+        col.dataFrame.fireValuesChanged();
+      }
     },
+    tooltipText: `The max length of monomer symbol displayed without shortening, empty to no limit`
   });
-  monomerWidthModeInput.setTooltip(
-    `In short mode, only the 'Max monomer length' characters are displayed, followed by .. if there are more`);
-
-  const tagMaxMonomerLength: number = parseInt(col.getTag(mmcrTAGS.maxMonomerLength));
-  const maxMonomerLengthInput = ui.input.slider('Max monomer length', {
-    value: !isNaN(tagMaxMonomerLength) ? tagMaxMonomerLength :
-      (_package.properties?.MaxMonomerLength ?? 4),
-    min: 1, max: 16, step: 1,
+
+  const gapLengthInput = ui.input.int('Monomer Margin', {
+    value: col.temp[mmcrTemps.gapLength] ?? 0,
     onValueChanged: () => {
-      const value = maxMonomerLengthInput.value;
-      maxMonomerLengthValueDiv.innerText = maxMonomerLengthInput.stringValue;
-      col.setTag(mmcrTAGS.maxMonomerLength, value.toString());
-      col.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.true);
+      col.temp[mmcrTemps.gapLength] = gapLengthInput.value;
+      col.temp[mmcrTemps.rendererSettingsChanged] = rendererSettingsChangedState.true;
       col.dataFrame.fireValuesChanged();
     },
+    tooltipText: 'The size of margin between monomers (in pixels)'
   });
-  const maxMonomerLengthValueDiv = ui.divText(maxMonomerLengthInput.stringValue, 'ui-input-description');
-  maxMonomerLengthInput.addOptions(maxMonomerLengthValueDiv);
-  maxMonomerLengthInput.setTooltip(
-    `The max length of monomer name displayed without shortening ` +
-    ` in '${MonomerWidthMode.short}' monomer width mode.`);
-  maxMonomerLengthInput.enabled = monomerWidthModeInput.value === MonomerWidthMode.short;
-
-  const gapLengthInput = ui.intInput('Monomer margin', col.temp[mmcrTemps.gapLength] ?? 0,
-    (value: number) => {
-      col.temp[mmcrTemps.gapLength] = value;
-      col.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.true);
-      col.dataFrame.fireValuesChanged();
-    });
-  gapLengthInput.setTooltip('The size of margin between monomers (in pixels)');
 
-  const colorCode = ui.boolInput('Color code',
-    (col?.temp['color-code'] != null) ? col.temp['color-code'] : true,
-    (v: boolean) => {
-      col.temp['color-code'] = v;
+  const colorCodeInput = ui.input.bool('Color Code', {
+    value: (col?.temp['color-code'] != null) ? col.temp['color-code'] : true,
+    onValueChanged: () => {
+      col.temp['color-code'] = colorCodeInput.value;
       col.dataFrame.fireValuesChanged();
-    });
-  colorCode.setTooltip('Color code');
+    },
+    tooltipText: 'Color code'
+  });
 
-  const referenceSequence = ui.stringInput('Reference sequence',
-    (col?.temp['reference-sequence'] != null) ? col?.temp['reference-sequence'] : '', (v: string) => {
-      col.temp['reference-sequence'] = v;
+  const referenceSequenceInput = ui.input.string('Reference Sequence', {
+    value: (col?.temp['reference-sequence'] != null) ? col?.temp['reference-sequence'] : '',
+    nullable: true,
+    onValueChanged: () => {
+      col.temp['reference-sequence'] = referenceSequenceInput.value;
       col.dataFrame.fireValuesChanged();
-    });
-  referenceSequence.setTooltip('Reference sequence is not empty, then the sequence will be render ' + '\n' +
-    'as a difference from the reference sequence');
-
-  const compareWithCurrent = ui.boolInput('Compare with current',
-    (col?.temp['compare-with-current'] != null) ? col.temp['compare-with-current'] : true,
-    (v: boolean) => {
-      col.temp['compare-with-current'] = v;
+    },
+    tooltipText: 'Reference sequence is not empty, then the sequence will be render ' + '\n' +
+      'as a difference from the reference sequence'
+  });
+
+  const compareWithCurrentInput = ui.input.bool('Compare with current', {
+    value: (col?.temp['compare-with-current'] != null) ? col.temp['compare-with-current'] : true,
+    onValueChanged: () => {
+      col.temp['compare-with-current'] = compareWithCurrentInput.value;
       col.dataFrame.fireValuesChanged();
-    });
-  compareWithCurrent.setTooltip('When on, all sequences get rendered in the "diff" mode');
+    },
+    tooltipText: 'When on, all sequences get rendered in the "diff" mode'
+  });
 
   const rdKitInputs = ui.inputs([
-    monomerWidthModeInput,
     maxMonomerLengthInput,
     gapLengthInput,
-    referenceSequence,
-    colorCode,
-    compareWithCurrent,
+    referenceSequenceInput,
+    colorCodeInput,
+    compareWithCurrentInput,
   ]);
 
   return new DG.Widget(rdKitInputs);

package/tsconfig.json

@@ -4,9 +4,9 @@
 
     /* Basic Options */
     // "incremental": true,                         /* Enable incremental compilation */
-    "target": "es2020",                             /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
-    "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
-    "lib": ["ES2022", "ES2022.String", "dom"],      /* Specify library files to be included in the compilation. */
+    "target": "ES2022",                             /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
+    "module": "ES2022",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
+    "lib": ["ES2022", "ES2022.String", "DOM"],      /* Specify library files to be included in the compilation. */
     // "allowJs": true,                             /* Allow javascript files to be compiled. */
     // "checkJs": true,                             /* Report errors in .js files. */
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
@@ -65,7 +65,7 @@
     "emitDecoratorMetadata": true,                  /* Enables experimental support for emitting type metadata for decorators. */
     "typeRoots": ["./node_modules/@webgpu/types", "./node_modules/@types"],
     /* Advanced Options */
-    "skipLibCheck": false,                          /* Skip type checking of declaration files. */
+    "skipLibCheck": true,                           /* Skip type checking of declaration files. */
     "forceConsistentCasingInFileNames": true,       /* Disallow inconsistently-cased references to the same file. */
     //"jsx": "react"
   }

package/webpack.config.js

@@ -31,7 +31,7 @@ module.exports = {
   plugins: [
     new FuncGeneratorPlugin({outputPath: './src/package.g.ts'}),
   ],
-  devtool: mode !== 'production' ? 'inline-source-map' : 'source-map',
+  devtool: 'source-map',
   externals: {
     'datagrok-api/dg': 'DG',
     'datagrok-api/grok': 'grok',

package/dist/23.js

@@ -1,2 +0,0 @@
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function insertSmaller(distancesAr, indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1])\n        return;\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    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 getAggregationFunction(aggregationMethod, weights) {\n    switch (aggregationMethod) {\n        case DistanceAggregationMethods.MANHATTAN:\n            return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n        default:\n            return (vs) => {\n                // euclidean\n                const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n                return Math.sqrt(sum);\n            };\n    }\n}\n//# 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{ getAggregationFunction, 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, fnNames, opts, aggregationMethod, weights } = 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        const aggregate = getAggregationFunction(aggregationMethod, weights);\n        values.forEach((v, colIdx) => {\n            if (isBitArrayMetric(fnNames[colIdx])) {\n                for (let i = 0; i < v.length; ++i) {\n                    if (isNil(v[i]))\n                        continue;\n                    values[colIdx][i] = new BitArray(values[colIdx][i]._data, values[colIdx][i]._length);\n                }\n            }\n        });\n        let cnt = 0;\n        const distanceFns = new Array(fnNames.length).fill(null).map((_, i) => new Measure(fnNames[i]).getMeasure(opts[i]));\n        const startRow = values[0].length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values[0].length * (values[0].length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values[0].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 distanceValues = distanceFns.map((fn, idx) => !isNil(values[idx][mi]) && !isNil(values[idx][mj]) ?\n                fn(values[idx][mi], values[idx][mj]) : 1);\n            const value = distanceValues.length === 1 ? distanceValues[0] : aggregate(distanceValues);\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[0].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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