@datagrok/bio 2.11.24 → 2.11.26

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.24",
+  "version": "2.11.26",
   "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",
@@ -36,7 +36,7 @@
     "@biowasm/aioli": "^3.1.0",
     "@datagrok-libraries/bio": "^5.39.18",
     "@datagrok-libraries/chem-meta": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.3.68",
+    "@datagrok-libraries/ml": "^6.4.0",
     "@datagrok-libraries/tutorials": "^1.3.11",
     "@datagrok-libraries/utils": "^4.1.36",
     "@datagrok-libraries/math": "^1.0.7",

package/src/analysis/sequence-space.ts

@@ -1,12 +1,9 @@
 import * as DG from 'datagrok-api/dg';
-import {reduceDimensinalityWithNormalization} from '@datagrok-libraries/ml/src/sequence-space';
-import {BitArrayMetrics, StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import {ISequenceSpaceParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
-import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
+import * as grok from 'datagrok-api/grok';
+import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {mmDistanceFunctionArgs} from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {getMonomerSubstitutionMatrix} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import * as grok from 'datagrok-api/grok';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
 export interface ISequenceSpaceResult {
@@ -14,47 +11,6 @@ export interface ISequenceSpaceResult {
   coordinates: DG.ColumnList;
 }
 
-export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<ISequenceSpaceResult> {
-  // code deprecated since seqCol is encoded
-  /*    let preparedData: any;
-  if (!(spaceParams.seqCol!.tags[DG.TAGS.UNITS] === 'HELM')) {
-    const sep = spaceParams.seqCol.getTag(UnitsHandler.TAGS.separator);
-    const sepFinal = sep ? sep === '.' ? '\\\.' : sep : '-';
-    const regex = new RegExp(sepFinal, 'g');
-    if (Object.keys(AvailableMetrics['String']).includes(spaceParams.similarityMetric))
-      preparedData = spaceParams.seqCol.toList().map((v: string) => v.replace(regex, '')) as string[];
-    else
-      preparedData = spaceParams.seqCol.toList().map((v: string) => v.replace(regex, '')) as string[];
-  } else {
-    preparedData = spaceParams.seqCol.toList();
-  }  */
-
-  const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
-    spaceParams.seqCol.toList(),
-    spaceParams.methodName,
-    spaceParams.similarityMetric as StringMetrics | BitArrayMetrics,
-    spaceParams.options);
-  const cols: DG.Column[] = spaceParams.embedAxesNames.map(
-    (name: string, index: number) => DG.Column.fromFloat32Array(name, sequenceSpaceResult.embedding[index]));
-  return {distance: sequenceSpaceResult.distance, coordinates: new DG.ColumnList(cols)};
-}
-
-export async function sequenceSpaceByFingerprints(spaceParams: ISequenceSpaceParams): Promise<ISequenceSpaceResult> {
-  if (spaceParams.seqCol.version !== spaceParams.seqCol.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
-    //we expect only string columns here
-    await invalidateMols(spaceParams.seqCol as unknown as DG.Column<string>, false);
-
-  const result = await grok.functions.call('Chem:getChemSpaceEmbeddings', {
-    col: spaceParams.seqCol.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS],
-    methodName: spaceParams.methodName,
-    similarityMetric: spaceParams.similarityMetric,
-    xAxis: spaceParams.embedAxesNames[0],
-    yAxis: spaceParams.embedAxesNames[1],
-    options: spaceParams.options,
-  });
-  return result;
-}
-
 export async function getEncodedSeqSpaceCol(
   seqCol: DG.Column, similarityMetric: BitArrayMetrics | MmDistanceFunctionsNames, fingerprintType: string = 'Morgan'
 ): Promise<{seqList:string[], options: {[_:string]: any}}> {
@@ -118,32 +74,3 @@ export async function getEncodedSeqSpaceCol(
   }
   return {seqList, options};
 }
-
-export async function getSequenceSpace(spaceParams: ISequenceSpaceParams,
-  progressFunc?: (epochNum: number, epochsLength: number, embedding: number[][]) => void
-): Promise<ISequenceSpaceResult> {
-  const ncUH = UnitsHandler.getOrCreate(spaceParams.seqCol);
-  if (ncUH.isHelm())
-    return await sequenceSpaceByFingerprints(spaceParams);
-
-
-  const {seqList, options} = await getEncodedSeqSpaceCol(spaceParams.seqCol, spaceParams.similarityMetric);
-
-  spaceParams.options = spaceParams.options ?? {};
-  spaceParams.options.distanceFnArgs = options;
-  const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
-    seqList,
-    spaceParams.methodName,
-    spaceParams.similarityMetric,
-    spaceParams.options,
-    true, progressFunc);
-  const cols: DG.Column[] = spaceParams.embedAxesNames.map(
-    (name: string, index: number) => DG.Column.fromFloat32Array(name, sequenceSpaceResult.embedding[index]));
-  return {distance: sequenceSpaceResult.distance, coordinates: new DG.ColumnList(cols)};
-}
-
-export function getEmbeddingColsNames(df: DG.DataFrame) {
-  const axes = ['Embed_X', 'Embed_Y'];
-  const colNameInd = df.columns.names().filter((it: string) => it.includes(axes[0])).length + 1;
-  return axes.map((it) => `${it}_${colNameInd}`);
-}

package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts

@@ -10,9 +10,9 @@ import {getTreeHelper, ITreeHelper} from '@datagrok-libraries/bio/src/trees/tree
 import {getDendrogramService, IDendrogramService} from '@datagrok-libraries/bio/src/trees/dendrogram';
 import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {getClusterMatrixWorker} from '@datagrok-libraries/math';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 const dataFn: string = 'data/sample_FASTA_PT_activity.csv';
 
@@ -51,9 +51,10 @@ export async function demoBio01bUI() {
         delay: 2000,
       })
       .step('Find activity cliffs', async () => {
+        const seqEncodingFunc = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
         activityCliffsViewer = (await activityCliffs(
           df, df.getCol('Sequence'), df.getCol('Activity'),
-          80, dimRedMethod, MmDistanceFunctionsNames.LEVENSHTEIN)) as DG.ScatterPlotViewer;
+          80, dimRedMethod, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc, {})) as DG.ScatterPlotViewer;
         view.dockManager.dock(activityCliffsViewer, DG.DOCK_TYPE.RIGHT, null, 'Activity Cliffs', 0.35);
 
         // Show grid viewer with the cliffs

package/src/demo/bio05-helm-msa-sequence-space.ts

@@ -5,7 +5,6 @@ import * as DG from 'datagrok-api/dg';
 import {IWebLogoViewer} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {awaitStatus, DockerContainerStatus} from '@datagrok-libraries/bio/src/utils/docker';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
 import {Pepsea, pepseaMethods, runPepsea} from '../utils/pepsea';
@@ -13,6 +12,7 @@ import {sequenceSpaceTopMenu} from '../package';
 import {handleError} from './utils';
 
 import {_package} from '../package';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 const helmFn: string = 'samples/HELM.csv';
 

package/src/demo/utils.ts

@@ -3,10 +3,11 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {_package, sequenceSpaceTopMenu} from '../package';
-import {reduceDimensinalityWithNormalization} from '@datagrok-libraries/ml/src/sequence-space';
 import {StringMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {getNormalizedEmbeddings} from
+  '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/embeddings-space';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 enum EMBED_COL_NAMES {
   X = 'Embed_X',
@@ -38,8 +39,8 @@ export async function demoSequenceSpace(
 
       const t1: number = Date.now();
       _package.logger.debug('Bio: demoBio01aUI(), calc reduceDimensionality start...');
-      const redDimRes = await reduceDimensinalityWithNormalization( // TODO: Rename method typo
-        seqList, method, StringMetricsNames.Levenshtein, {});
+      const redDimRes = await getNormalizedEmbeddings( // TODO: Rename method typo
+        [seqList], method as any, [StringMetricsNames.Levenshtein], [1], 'MANHATTAN', {distanceFnArgs: [{}]});
       const t2: number = Date.now();
       _package.logger.debug('Bio: demoBio01aUI(), calc reduceDimensionality ' +
         `ET: ${((t2 - t1) / 1000)} s`);
@@ -47,7 +48,7 @@ export async function demoSequenceSpace(
       for (let embedI: number = 0; embedI < embedColNameList.length; embedI++) {
         const embedColName: string = embedColNameList[embedI];
         const embedCol: DG.Column = df.getCol(embedColName);
-        const embedColData: Float32Array = redDimRes.embedding[embedI];
+        const embedColData: Float32Array = redDimRes[embedI];
         // TODO: User DG.Column.setRawData()
         // embedCol.setRawData(embedColData);
         embedCol.init((rowI) => { return embedColData[rowI]; });

package/src/package.ts

@@ -3,23 +3,14 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-
-import {delay} from '@datagrok-libraries/utils/src/test';
-import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-utils';
 import {Options} from '@datagrok-libraries/utils/src/type-declarations';
-import {DimReductionMethods, ITSNEOptions, IUMAPOptions} from '@datagrok-libraries/ml/src/reduce-dimensionality';
-import {SequenceSpaceFunctionEditor} from '@datagrok-libraries/ml/src/functionEditors/seq-space-editor';
 import {DimReductionBaseEditor, PreprocessFunctionReturnType}
   from '@datagrok-libraries/ml/src/functionEditors/dimensionality-reduction-editor';
-import {reduceDimensionality} from '@datagrok-libraries/ml/src/functionEditors/dimensionality-reducer';
-import {ActivityCliffsFunctionEditor} from '@datagrok-libraries/ml/src/functionEditors/activity-cliffs-editor';
-import {
-  ISequenceSpaceParams, getActivityCliffs, SequenceSpaceFunc, CLIFFS_COL_ENCODE_FN
-} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
+import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetrics, KnownMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {
-  TAGS as bioTAGS, ALPHABET, NOTATION,
+  TAGS as bioTAGS,
 } from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
@@ -38,11 +29,9 @@ import {
 } from './utils/cell-renderer';
 import {VdRegionsViewer} from './viewers/vd-regions-viewer';
 import {SequenceAlignment} from './seq_align';
+import {getEncodedSeqSpaceCol} from './analysis/sequence-space';
 import {
-  ISequenceSpaceResult, getEmbeddingColsNames, getEncodedSeqSpaceCol, getSequenceSpace, sequenceSpaceByFingerprints
-} from './analysis/sequence-space';
-import {
-  createLinesGrid, createPropPanelElement, createTooltipElement, getChemSimilaritiesMatrix,
+  createLinesGrid, createPropPanelElement, createTooltipElement,
 } from './analysis/sequence-activity-cliffs';
 import {SequenceSimilarityViewer} from './analysis/sequence-similarity-viewer';
 import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
@@ -79,15 +68,17 @@ import {GetRegionApp} from './apps/get-region-app';
 import {GetRegionFuncEditor} from './utils/get-region-func-editor';
 import {sequenceToMolfile} from './utils/sequence-to-mol';
 import {detectMacromoleculeProbeDo} from './utils/detect-macromolecule-probe';
-
-import {SHOW_SCATTERPLOT_PROGRESS} from '@datagrok-libraries/ml/src/functionEditors/seq-space-base-editor';
-import {DIMENSIONALITY_REDUCER_TERMINATE_EVENT}
-  from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
+import {ActivityCliffsEditor} from '@datagrok-libraries/ml/src/functionEditors/activity-cliffs-function-editor';
 import BitArray from '@datagrok-libraries/utils/src/bit-array';
+import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
+import {getEmbeddingColsNames, multiColReduceDimensionality} from
+  '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/reduce-dimensionality';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
+import {ITSNEOptions, IUMAPOptions} from
+  '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/multi-column-dim-reducer';
 
 export const _package = new BioPackage();
 
-export const BYPASS_LARGE_DATA_WARNING = 'bypassLargeDataWarning';
 // /** Avoid reassigning {@link monomerLib} because consumers subscribe to {@link IMonomerLib.onChanged} event */
 // let monomerLib: MonomerLib | null = null;
 
@@ -256,16 +247,24 @@ export function SequenceSpaceEditor(call: DG.FuncCall) {
 //tags: editor
 //input: funccall call
 export function SeqActivityCliffsEditor(call: DG.FuncCall) {
-  const funcEditor = new ActivityCliffsFunctionEditor(DG.SEMTYPE.MACROMOLECULE);
+  const funcEditor = new ActivityCliffsEditor({semtype: DG.SEMTYPE.MACROMOLECULE});
   ui.dialog({title: 'Activity Cliffs'})
-    .add(funcEditor.paramsUI)
+    .add(funcEditor.getEditor())
     .onOK(async () => {
-      return call.func.prepare(funcEditor.funcParams).call(true);
-    })
-    .show();
+      const params = funcEditor.getParams();
+      return call.func.prepare({
+        table: params.table,
+        molecules: params.col,
+        activities: params.activities,
+        similarity: params.similarityThreshold,
+        methodName: params.methodName,
+        similarityMetric: params.similarityMetric,
+        preprocessingFunction: params.preprocessingFunction,
+        options: params.options,
+      }).call();
+    }).show();
 }
 
-
 // -- Package settings editor --
 
 // //name: packageSettingsEditor
@@ -405,74 +404,57 @@ export async function getRegionTopMenu(
 //input: double similarity = 80 [Similarity cutoff]
 //input: string methodName { choices:["UMAP", "t-SNE"] }
 //input: string similarityMetric { choices:["Hamming", "Levenshtein", "Monomer chemical distance"] }
+//input: func preprocessingFunction
 //input: object options {optional: true}
 //output: viewer result
 //editor: Bio:SeqActivityCliffsEditor
-export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<string>, activities: DG.Column,
+export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<string>, activities: DG.Column,
   similarity: number, methodName: DimReductionMethods,
-  similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics,
+  similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics, preprocessingFunction: DG.Func,
   options?: (IUMAPOptions | ITSNEOptions) & Options): Promise<DG.Viewer | undefined> {
-  if (!checkInputColumnUI(macroMolecule, 'Activity Cliffs'))
+  if (!checkInputColumnUI(molecules, 'Activity Cliffs'))
     return;
-  const axesNames = getEmbeddingColsNames(df);
+  const axesNames = getEmbeddingColsNames(table);
   const tags = {
-    'units': macroMolecule.getTag(DG.TAGS.UNITS),
-    'aligned': macroMolecule.getTag(bioTAGS.aligned),
-    'separator': macroMolecule.getTag(bioTAGS.separator),
-    'alphabet': macroMolecule.getTag(bioTAGS.alphabet),
+    'units': molecules.getTag(DG.TAGS.UNITS),
+    'aligned': molecules.getTag(bioTAGS.aligned),
+    'separator': molecules.getTag(bioTAGS.separator),
+    'alphabet': molecules.getTag(bioTAGS.alphabet),
   };
-  let cliffsEncodeFunction: (seqCol: DG.Column, similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics) => any =
-    getEncodedSeqSpaceCol;
-  const ncUH = UnitsHandler.getOrCreate(macroMolecule);
   const columnDistanceMetric: MmDistanceFunctionsNames | BitArrayMetrics = similarityMetric;
-  const seqCol = macroMolecule;
-
-  let sequenceSpaceFunc: SequenceSpaceFunc = getSequenceSpace;
-  if (ncUH.isHelm()) {
-    sequenceSpaceFunc = sequenceSpaceByFingerprints;
-    cliffsEncodeFunction = async (seqCol: DG.Column, similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics) => {
-      await invalidateMols(seqCol, false);
-      const molecularCol = seqCol.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS];
-      const fingerPrints: DG.Column =
-        await grok.functions.call('Chem:getMorganFingerprints', {molColumn: molecularCol});
-      const fingerPrintsBitArray = fingerPrints.toList().map((f: DG.BitSet) =>
-        BitArray.fromUint32Array(f.length, new Uint32Array(f.getBuffer().buffer)));
-      return {seqList: fingerPrintsBitArray, options: {}};
-    };
-  }
+  const seqCol = molecules;
 
   const runCliffs = async () => {
     const sp = await getActivityCliffs(
-      df,
+      table,
       seqCol,
-      null,
       axesNames,
       'Activity cliffs', //scatterTitle
       activities,
       similarity,
       columnDistanceMetric, //similarityMetric
       methodName,
+      {...(options ?? {})},
       DG.SEMTYPE.MACROMOLECULE,
       tags,
-      sequenceSpaceFunc,
-      getChemSimilaritiesMatrix,
+      preprocessingFunction,
       createTooltipElement,
       createPropPanelElement,
       createLinesGrid,
-      {...(options ?? {}), [CLIFFS_COL_ENCODE_FN]: cliffsEncodeFunction});
+    );
     return sp;
   };
 
   const allowedRowCount = methodName === DimReductionMethods.UMAP ? 200_000 : 20_000;
   const fastRowCount = methodName === DimReductionMethods.UMAP ? 5_000 : 2_000;
-  if (df.rowCount > allowedRowCount) {
+  if (table.rowCount > allowedRowCount) {
     grok.shell.warning(`Too many rows, maximum for sequence activity cliffs is ${allowedRowCount}`);
     return;
   }
 
   const pi = DG.TaskBarProgressIndicator.create(`Running sequence activity cliffs ...`);
   return new Promise<DG.Viewer | undefined>((resolve, reject) => {
-    if (df.rowCount > fastRowCount && !options?.[BYPASS_LARGE_DATA_WARNING]) {
+    if (table.rowCount > fastRowCount && !options?.[BYPASS_LARGE_DATA_WARNING]) {
       ui.dialog().add(ui.divText(`Activity cliffs analysis might take several minutes.
     Do you want to continue?`))
         .onOK(async () => {
@@ -495,7 +477,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<
 //meta.supportedSemTypes: Macromolecule
 //meta.supportedTypes: string
 //meta.supportedUnits: fasta,separator,helm
-//meta.supportedDistanceFunctions: Hamming,Levenshtein,Monomer chemical distance,Needlemann-Wunsch
+//meta.supportedDistanceFunctions: Levenshtein,Hamming,Monomer chemical distance,Needlemann-Wunsch
 //input: column col {semType: Macromolecule}
 //input: string metric
 //input: double gapOpen = 1 {caption: Gap open penalty; default: 1; optional: true}
@@ -506,6 +488,8 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<
 export async function macromoleculePreprocessingFunction(
   col: DG.Column, metric: MmDistanceFunctionsNames, gapOpen: number = 1, gapExtend: number = 0.6,
   fingerprintType = 'Morgan'): Promise<PreprocessFunctionReturnType> {
+  if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
+    return {entries: col.toList(), options: {}};
   const {seqList, options} = await getEncodedSeqSpaceCol(col, metric, fingerprintType);
   return {entries: seqList, options: {...options, gapOpen, gapExtend}};
 }
@@ -558,13 +542,15 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
     return;
   if (!preprocessingFunction)
     preprocessingFunction = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
-
-  const res = await reduceDimensionality(table, molecules, methodName,
-      similarityMetric as KnownMetrics, preprocessingFunction, plotEmbeddings, clusterEmbeddings ?? false, options, {
-        fastRowCount: 10000,
-        scatterPlotName: 'Sequence space',
-        bypassLargeDataWarning: options?.[BYPASS_LARGE_DATA_WARNING],
-      });
+  options ??= {};
+  const res = await multiColReduceDimensionality(table, [molecules], methodName,
+    [similarityMetric as KnownMetrics], [1], [preprocessingFunction], 'MANHATTAN',
+    plotEmbeddings, clusterEmbeddings ?? false,
+    {...options, preprocessingFuncArgs: [options.preprocessingFuncArgs ?? {}]}, {
+      fastRowCount: 10000,
+      scatterPlotName: 'Sequence space',
+      bypassLargeDataWarning: options?.[BYPASS_LARGE_DATA_WARNING],
+    });
   return res;
 }
 

package/src/tests/activity-cliffs-tests.ts

@@ -5,7 +5,6 @@ import {after, before, category, test} from '@datagrok-libraries/utils/src/test'
 
 import {readDataframe} from './utils';
 import {_testActivityCliffsOpen} from './activity-cliffs-utils';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
@@ -15,6 +14,7 @@ import {
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {_package} from '../package-test';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 
 category('activityCliffs', async () => {
@@ -24,8 +24,8 @@ category('activityCliffs', async () => {
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
   let userLibSettings: LibSettings;
-
-
+  const seqEncodingFunc = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
+  const helmEncodingFunc = DG.Func.find({name: 'helmPreprocessingFunction', package: 'Bio'})[0];
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
@@ -57,7 +57,7 @@ category('activityCliffs', async () => {
     const cliffsNum = DG.Test.isInBenchmark ? 6 : 3;
 
     await _testActivityCliffsOpen(actCliffsDf, DimReductionMethods.UMAP,
-      'sequence', 'Activity', 90, cliffsNum, MmDistanceFunctionsNames.LEVENSHTEIN);
+      'sequence', 'Activity', 90, cliffsNum, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc);
   });
 
   test('activityCliffsWithEmptyRows', async () => {
@@ -67,14 +67,14 @@ category('activityCliffs', async () => {
     viewList.push(actCliffsTableViewWithEmptyRows);
 
     await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, DimReductionMethods.UMAP,
-      'sequence', 'Activity', 90, 3, MmDistanceFunctionsNames.LEVENSHTEIN);
+      'sequence', 'Activity', 90, 3, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc);
   });
 
   test('Helm', async () => {
     const df = await _package.files.readCsv('data/sample_HELM_50.csv');
-    const view = grok.shell.addTableView(df);
+    const _view = grok.shell.addTableView(df);
 
     await _testActivityCliffsOpen(df, DimReductionMethods.UMAP,
-      'HELM', 'Activity', 65, 4, BitArrayMetricsNames.Tanimoto);
+      'HELM', 'Activity', 65, 20, BitArrayMetricsNames.Tanimoto, helmEncodingFunc);
   });
 });

package/src/tests/activity-cliffs-utils.ts

@@ -2,19 +2,20 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {expect} from '@datagrok-libraries/utils/src/test';
-import {activityCliffs, BYPASS_LARGE_DATA_WARNING} from '../package';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
+import {activityCliffs} from '../package';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
+import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 export async function _testActivityCliffsOpen(df: DG.DataFrame, drMethod: DimReductionMethods,
   seqColName: string, activityColName: string, similarityThr: number, tgtNumberCliffs: number,
-  similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics
+  similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics, preprocessingFunction: DG.Func,
 ): Promise<void> {
   await grok.data.detectSemanticTypes(df);
   const scatterPlot = await activityCliffs(
     df, df.getCol(seqColName), df.getCol(activityColName),
-    similarityThr, drMethod, similarityMetric, {[`${BYPASS_LARGE_DATA_WARNING}`]: true});
+    similarityThr, drMethod, similarityMetric, preprocessingFunction, {[`${BYPASS_LARGE_DATA_WARNING}`]: true});
   // const scatterPlot = (await grok.functions.call('Bio:activityCliffs', {
   //   table: df, molecules: df.getCol(colName), activities: df.getCol('Activity'),
   //   similarity: 50, methodName: method

package/src/tests/msa-tests.ts

@@ -81,12 +81,12 @@ MWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHP
   test('isCorrectHelm', async () => {
     await awaitContainerStart();
     await _testMSAOnColumn(helmFromCsv, helmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {skipReason: 'GROK-13221'});
+  });
 
   test('isCorrectHelmLong', async () => {
     await awaitContainerStart();
     await _testMSAOnColumn(longHelmFromCsv, longHelmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {skipReason: 'GROK-13221'});
+  });
 
   test('isCorrectSeparator', async () => {
     await _testMSAOnColumn(

package/src/tests/pepsea-tests.ts

@@ -20,5 +20,5 @@ category('PepSeA', () => {
     const alignedTestCol = table.getCol('MSA');
     for (let i = 0; i < alignedCol!.length; ++i)
       expect(alignedCol!.get(i) == alignedTestCol.get(i), true);
-  }, {skipReason: 'GROK-13221'});
+  });
 });

package/src/tests/sequence-space-test.ts

@@ -5,7 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {category, test} from '@datagrok-libraries/utils/src/test';
 import {readDataframe} from './utils';
 import {_testSequenceSpaceReturnsResult} from './sequence-space-utils';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 category('sequenceSpace', async () => {
   let testFastaDf: DG.DataFrame;

package/src/tests/sequence-space-utils.ts

@@ -3,8 +3,8 @@ import * as grok from 'datagrok-api/grok';
 import {expect} from '@datagrok-libraries/utils/src/test';
 import {sequenceSpaceTopMenu} from '../package';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 
 export async function _testSequenceSpaceReturnsResult(
   df: DG.DataFrame, algorithm: DimReductionMethods, colName: string,

package/src/tests/utils.ts

@@ -35,9 +35,11 @@ export function _testTableIsNotEmpty(table: DG.DataFrame): void {
 /** Waits if container is not started
  * @param {number} ms - time to wait in milliseconds */
 export async function awaitContainerStart(ms: number = 10000): Promise<void> {
-  const pepseaContainer = await grok.dapi.docker.dockerContainers.filter('bio').first();
-  if (pepseaContainer.status !== 'started' && pepseaContainer.status !== 'checking')
+  const container = await grok.dapi.docker.dockerContainers.filter('bio').first();
+  if (container.status !== 'started' && container.status !== 'checking')
     await delay(ms);
+    // TODO: Enable with new JS API version
+    // await grok.dapi.docker.dockerContainers.run(container.id, true);
 }
 
 export async function awaitGrid(grid: DG.Grid, timeout: number = 5000): Promise<void> {

package/dist/23.js

@@ -1,2 +0,0 @@
-var bio;(()=>{"use strict";var e,r,t={5023:(e,r,t)=>{const o=e=>null==e;var n=t(6361),a=t(9657);onmessage=async e=>{const{values:r,startIdx:t,endIdx:s,threshold:i,fnName:c,opts:l}=e.data;try{const e=[],p=[],h=[],f=s-t;if((0,n.sQ)(c))for(let e=0;e<r.length;++e)o(r[e])||(r[e]=new a.Z(r[e]._data,r[e]._length));let u=0;const g=new n.UH(c).getMeasure(l),v=r.length-2-Math.floor(Math.sqrt(-8*t+4*r.length*(r.length-1)-7)/2-.5),b=t-r.length*v+Math.floor((v+1)*(v+2)/2);let d=v,w=b;for(;u<f;){const t=o(r[d])||o(r[w])?1:g(r[d],r[w]);1-t>=i&&(e.push(d),p.push(w),h.push(t)),u++,w++,w===r.length&&(d++,w=d+1)}const y=new Int32Array(e),m=new Int32Array(p),x=new Float32Array(h);postMessage({i:y,j:m,distance:x})}catch(e){postMessage({error:e})}}}},o={};function n(e){var r=o[e];if(void 0!==r)return r.exports;var a=o[e]={exports:{}};return t[e](a,a.exports,n),a.exports}n.m=t,n.x=()=>{var e=n.O(void 0,[378,361],(()=>n(5023)));return n.O(e)},e=[],n.O=(r,t,o,a)=>{if(!t){var s=1/0;for(p=0;p<e.length;p++){for(var[t,o,a]=e[p],i=!0,c=0;c<t.length;c++)(!1&a||s>=a)&&Object.keys(n.O).every((e=>n.O[e](t[c])))?t.splice(c--,1):(i=!1,a<s&&(s=a));if(i){e.splice(p--,1);var l=o();void 0!==l&&(r=l)}}return r}a=a||0;for(var p=e.length;p>0&&e[p-1][2]>a;p--)e[p]=e[p-1];e[p]=[t,o,a]},n.d=(e,r)=>{for(var t in r)n.o(r,t)&&!n.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},n.f={},n.e=e=>Promise.all(Object.keys(n.f).reduce(((r,t)=>(n.f[t](e,r),r)),[])),n.u=e=>e+".js",n.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),n.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;n.g.importScripts&&(e=n.g.location+"");var r=n.g.document;if(!e&&r&&(r.currentScript&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var o=t.length-1;o>-1&&!e;)e=t[o--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),n.p=e})(),(()=>{var e={23:1};n.f.i=(r,t)=>{e[r]||importScripts(n.p+n.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[o,a,s]=r;for(var i in a)n.o(a,i)&&(n.m[i]=a[i]);for(s&&s(n);o.length;)e[o.pop()]=1;t(r)}})(),r=n.x,n.x=()=>Promise.all([n.e(378),n.e(361)]).then(r);var a=n.x();bio=a})();
-//# sourceMappingURL=23.js.map

package/dist/23.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"23.js","mappings":"+BAAIA,ECAAC,E,kBCAG,MAAMC,EAASC,GAAMA,Q,wBCG5BC,UAAYC,MAAOC,IACf,MAAM,OAAEC,EAAM,SAAEC,EAAQ,OAAEC,EAAM,UAAEC,EAAS,OAAEC,EAAM,KAAEC,GAASN,EAAMO,KACpE,IAGI,MAAMC,EAAI,GACJC,EAAI,GACJC,EAAY,GACZC,EAAYR,EAASD,EAG3B,IAAI,QAAiBG,GACjB,IAAK,IAAIG,EAAI,EAAGA,EAAIP,EAAOW,SAAUJ,EAC7BZ,EAAMK,EAAOO,MAEjBP,EAAOO,GAAK,IAAI,IAASP,EAAOO,GAAGK,MAAOZ,EAAOO,GAAGM,UAG5D,IAAIC,EAAM,EACV,MAAMC,EAAa,IAAI,KAAQX,GAAQY,WAAWX,GAC5CY,EAAWjB,EAAOW,OAAS,EAAIO,KAAKC,MAAMD,KAAKE,MAAM,EAAInB,EAAW,EAAID,EAAOW,QAAUX,EAAOW,OAAS,GAAK,GAAK,EAAI,IACvHU,EAAWpB,EAAWD,EAAOW,OAASM,EAAWC,KAAKC,OAAOF,EAAW,IAAMA,EAAW,GAAK,GACpG,IAAIK,EAAKL,EACLM,EAAKF,EACT,KAAOP,EAAMJ,GAAW,CAEpB,MAAMc,EAAS7B,EAAMK,EAAOsB,KAAS3B,EAAMK,EAAOuB,IACT,EAArCR,EAAWf,EAAOsB,GAAKtB,EAAOuB,IAC9B,EAAIC,GAASrB,IACbI,EAAEkB,KAAKH,GACPd,EAAEiB,KAAKF,GACPd,EAAUgB,KAAKD,IAEnBV,IACAS,IACIA,IAAOvB,EAAOW,SACdW,IACAC,EAAKD,EAAK,EAElB,CACA,MAAMI,EAAS,IAAIC,WAAWpB,GACxBqB,EAAS,IAAID,WAAWnB,GACxBqB,EAAgB,IAAIC,aAAarB,GACvCsB,YAAY,CAAExB,EAAGmB,EAAQlB,EAAGoB,EAAQI,SAAUH,GAClD,CACA,MAAOI,GACHF,YAAY,CAAEG,MAAOD,GACzB,E,GCjDAE,EAA2B,CAAC,EAGhC,SAASC,EAAoBC,GAE5B,IAAIC,EAAeH,EAAyBE,GAC5C,QAAqBE,IAAjBD,EACH,OAAOA,EAAaE,QAGrB,IAAIC,EAASN,EAAyBE,GAAY,CAGjDG,QAAS,CAAC,GAOX,OAHAE,EAAoBL,GAAUI,EAAQA,EAAOD,QAASJ,GAG/CK,EAAOD,OACf,CAGAJ,EAAoBO,EAAID,EAGxBN,EAAoBxC,EAAI,KAGvB,IAAIgD,EAAsBR,EAAoBS,OAAEN,EAAW,CAAC,IAAI,MAAM,IAAOH,EAAoB,QAEjG,OADsBA,EAAoBS,EAAED,EAClB,EJjCvBnD,EAAW,GACf2C,EAAoBS,EAAI,CAACC,EAAQC,EAAUC,EAAIC,KAC9C,IAAGF,EAAH,CAMA,IAAIG,EAAeC,IACnB,IAAS5C,EAAI,EAAGA,EAAId,EAASkB,OAAQJ,IAAK,CAGzC,IAFA,IAAKwC,EAAUC,EAAIC,GAAYxD,EAASc,GACpC6C,GAAY,EACP5C,EAAI,EAAGA,EAAIuC,EAASpC,OAAQH,MACpB,EAAXyC,GAAsBC,GAAgBD,IAAaI,OAAOC,KAAKlB,EAAoBS,GAAGU,OAAOC,GAASpB,EAAoBS,EAAEW,GAAKT,EAASvC,MAC9IuC,EAASU,OAAOjD,IAAK,IAErB4C,GAAY,EACTH,EAAWC,IAAcA,EAAeD,IAG7C,GAAGG,EAAW,CACb3D,EAASgE,OAAOlD,IAAK,GACrB,IAAImD,EAAIV,SACET,IAANmB,IAAiBZ,EAASY,EAC/B,CACD,CACA,OAAOZ,CAnBP,CAJCG,EAAWA,GAAY,EACvB,IAAI,IAAI1C,EAAId,EAASkB,OAAQJ,EAAI,GAAKd,EAASc,EAAI,GAAG,GAAK0C,EAAU1C,IAAKd,EAASc,GAAKd,EAASc,EAAI,GACrGd,EAASc,GAAK,CAACwC,EAAUC,EAAIC,EAqBjB,EKzBdb,EAAoBuB,EAAI,CAACnB,EAASoB,KACjC,IAAI,IAAIJ,KAAOI,EACXxB,EAAoByB,EAAED,EAAYJ,KAASpB,EAAoByB,EAAErB,EAASgB,IAC5EH,OAAOS,eAAetB,EAASgB,EAAK,CAAEO,YAAY,EAAMC,IAAKJ,EAAWJ,IAE1E,ECNDpB,EAAoB6B,EAAI,CAAC,EAGzB7B,EAAoBH,EAAKiC,GACjBC,QAAQC,IAAIf,OAAOC,KAAKlB,EAAoB6B,GAAGI,QAAO,CAACC,EAAUd,KACvEpB,EAAoB6B,EAAET,GAAKU,EAASI,GAC7BA,IACL,KCNJlC,EAAoBmC,EAAKL,GAEZA,EAAU,MCHvB9B,EAAoBoC,EAAI,WACvB,GAA0B,iBAAfC,WAAyB,OAAOA,WAC3C,IACC,OAAOC,MAAQ,IAAIC,SAAS,cAAb,EAChB,CAAE,MAAO1C,GACR,GAAsB,iBAAX2C,OAAqB,OAAOA,MACxC,CACA,CAPuB,GCAxBxC,EAAoByB,EAAI,CAACgB,EAAKC,IAAUzB,OAAO0B,UAAUC,eAAeC,KAAKJ,EAAKC,G,MCAlF,IAAII,EACA9C,EAAoBoC,EAAEW,gBAAeD,EAAY9C,EAAoBoC,EAAEY,SAAW,IACtF,IAAIC,EAAWjD,EAAoBoC,EAAEa,SACrC,IAAKH,GAAaG,IACbA,EAASC,gBACZJ,EAAYG,EAASC,cAAcC,MAC/BL,GAAW,CACf,IAAIM,EAAUH,EAASI,qBAAqB,UAC5C,GAAGD,EAAQ7E,OAEV,IADA,IAAIJ,EAAIiF,EAAQ7E,OAAS,EAClBJ,GAAK,IAAM2E,GAAWA,EAAYM,EAAQjF,KAAKgF,GAExD,CAID,IAAKL,EAAW,MAAM,IAAIQ,MAAM,yDAChCR,EAAYA,EAAUS,QAAQ,OAAQ,IAAIA,QAAQ,QAAS,IAAIA,QAAQ,YAAa,KACpFvD,EAAoBwD,EAAIV,C,WCdxB,IAAIW,EAAkB,CACrB,GAAI,GAgBLzD,EAAoB6B,EAAE1D,EAAI,CAAC2D,EAASI,KAE/BuB,EAAgB3B,IAElBiB,cAAc/C,EAAoBwD,EAAIxD,EAAoBmC,EAAEL,GAE9D,EAGD,IAAI4B,EAAqBC,KAAsB,gBAAIA,KAAsB,iBAAK,GAC1EC,EAA6BF,EAAmBrE,KAAKwE,KAAKH,GAC9DA,EAAmBrE,KAvBCnB,IACnB,IAAKyC,EAAUmD,EAAaC,GAAW7F,EACvC,IAAI,IAAI+B,KAAY6D,EAChB9D,EAAoByB,EAAEqC,EAAa7D,KACrCD,EAAoBO,EAAEN,GAAY6D,EAAY7D,IAIhD,IADG8D,GAASA,EAAQ/D,GACdW,EAASpC,QACdkF,EAAgB9C,EAASqD,OAAS,EACnCJ,EAA2B1F,EAAK,C,KVnB7BZ,EAAO0C,EAAoBxC,EAC/BwC,EAAoBxC,EAAI,IAChBuE,QAAQC,IAAI,CAClBhC,EAAoBH,EAAE,KACtBG,EAAoBH,EAAE,OACpBoE,KAAK3G,GWJT,IAAIkD,EAAsBR,EAAoBxC,I","sources":["webpack://bio/webpack/runtime/chunk loaded","webpack://bio/webpack/runtime/startup chunk dependencies","webpack://bio/./node_modules/@datagrok-libraries/ml/src/distance-matrix/utils.js","webpack://bio/./node_modules/@datagrok-libraries/ml/src/distance-matrix/sparse-matrix-worker.js","webpack://bio/webpack/bootstrap","webpack://bio/webpack/runtime/define property getters","webpack://bio/webpack/runtime/ensure chunk","webpack://bio/webpack/runtime/get javascript chunk filename","webpack://bio/webpack/runtime/global","webpack://bio/webpack/runtime/hasOwnProperty shorthand","webpack://bio/webpack/runtime/publicPath","webpack://bio/webpack/runtime/importScripts chunk loading","webpack://bio/webpack/startup"],"sourcesContent":["var deferred = [];\n__webpack_require__.O = (result, chunkIds, fn, priority) => {\n\tif(chunkIds) {\n\t\tpriority = priority || 0;\n\t\tfor(var i = deferred.length; i > 0 && deferred[i - 1][2] > priority; i--) deferred[i] = deferred[i - 1];\n\t\tdeferred[i] = [chunkIds, fn, priority];\n\t\treturn;\n\t}\n\tvar notFulfilled = Infinity;\n\tfor (var i = 0; i < deferred.length; i++) {\n\t\tvar [chunkIds, fn, priority] = deferred[i];\n\t\tvar fulfilled = true;\n\t\tfor (var j = 0; j < chunkIds.length; j++) {\n\t\t\tif ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {\n\t\t\t\tchunkIds.splice(j--, 1);\n\t\t\t} else {\n\t\t\t\tfulfilled = false;\n\t\t\t\tif(priority < notFulfilled) notFulfilled = priority;\n\t\t\t}\n\t\t}\n\t\tif(fulfilled) {\n\t\t\tdeferred.splice(i--, 1)\n\t\t\tvar r = fn();\n\t\t\tif (r !== undefined) result = r;\n\t\t}\n\t}\n\treturn result;\n};","var next = __webpack_require__.x;\n__webpack_require__.x = () => {\n\treturn Promise.all([\n\t\t__webpack_require__.e(378),\n\t\t__webpack_require__.e(361)\n\t]).then(next);\n};","export const isNil = (x) => x === null || x === undefined;\nexport function insertSmaller(distancesAr, indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1]) {\n        return;\n    }\n    const newPosition = distancesAr.findIndex((v) => num < v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n    if (num < distancesAr[distancesAr.length - 1]) {\n        return;\n    }\n    const newPosition = distancesAr.findIndex((v) => num > v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\n//# sourceMappingURL=data:application/json;base64,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","import { isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, threshold, fnName, opts } = event.data;\n    try {\n        // if (startIdx != -1)\n        //   throw new Error('Error in sparse matrix worker'); // TODO: remove this line\n        const i = [];\n        const j = [];\n        const distances = [];\n        const chunkSize = endIdx - startIdx;\n        //const mi = startRow;\n        //const mj = startCol;\n        if (isBitArrayMetric(fnName)) {\n            for (let i = 0; i < values.length; ++i) {\n                if (isNil(values[i]))\n                    continue;\n                values[i] = new BitArray(values[i]._data, values[i]._length);\n            }\n        }\n        let cnt = 0;\n        const distanceFn = new Measure(fnName).getMeasure(opts);\n        const startRow = values.length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values.length * (values.length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values.length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n        let mi = startRow;\n        let mj = startCol;\n        while (cnt < chunkSize) {\n            //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n            const value = !isNil(values[mi]) && !isNil(values[mj]) ?\n                distanceFn(values[mi], values[mj]) : 1;\n            if (1 - value >= threshold) {\n                i.push(mi);\n                j.push(mj);\n                distances.push(value);\n            }\n            cnt++;\n            mj++;\n            if (mj === values.length) {\n                mi++;\n                mj = mi + 1;\n            }\n        }\n        const iArray = new Int32Array(i);\n        const jArray = new Int32Array(j);\n        const distanceArray = new Float32Array(distances);\n        postMessage({ i: iArray, j: jArray, distance: distanceArray });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# sourceMappingURL=data:application/json;base64,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","// The module cache\nvar __webpack_module_cache__ = {};\n\n// The require function\nfunction __webpack_require__(moduleId) {\n\t// Check if module is in cache\n\tvar cachedModule = __webpack_module_cache__[moduleId];\n\tif (cachedModule !== undefined) {\n\t\treturn cachedModule.exports;\n\t}\n\t// Create a new module (and put it into the cache)\n\tvar module = __webpack_module_cache__[moduleId] = {\n\t\t// no module.id needed\n\t\t// no module.loaded needed\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n// expose the modules object (__webpack_modules__)\n__webpack_require__.m = __webpack_modules__;\n\n// the startup function\n__webpack_require__.x = () => {\n\t// Load entry module and return exports\n\t// This entry module depends on other loaded chunks and execution need to be delayed\n\tvar __webpack_exports__ = __webpack_require__.O(undefined, [378,361], () => (__webpack_require__(5023)))\n\t__webpack_exports__ = __webpack_require__.O(__webpack_exports__);\n\treturn __webpack_exports__;\n};\n\n","// define getter functions for harmony exports\n__webpack_require__.d = (exports, definition) => {\n\tfor(var key in definition) {\n\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n\t\t}\n\t}\n};","__webpack_require__.f = {};\n// This file contains only the entry chunk.\n// The chunk loading function for additional chunks\n__webpack_require__.e = (chunkId) => {\n\treturn Promise.all(Object.keys(__webpack_require__.f).reduce((promises, key) => {\n\t\t__webpack_require__.f[key](chunkId, promises);\n\t\treturn promises;\n\t}, []));\n};","// This function allow to reference async chunks and sibling chunks for the entrypoint\n__webpack_require__.u = (chunkId) => {\n\t// return url for filenames based on template\n\treturn \"\" + chunkId + \".js\";\n};","__webpack_require__.g = (function() {\n\tif (typeof globalThis === 'object') return globalThis;\n\ttry {\n\t\treturn this || new Function('return this')();\n\t} catch (e) {\n\t\tif (typeof window === 'object') return window;\n\t}\n})();","__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))","var scriptUrl;\nif (__webpack_require__.g.importScripts) scriptUrl = __webpack_require__.g.location + \"\";\nvar document = __webpack_require__.g.document;\nif (!scriptUrl && document) {\n\tif (document.currentScript)\n\t\tscriptUrl = document.currentScript.src;\n\tif (!scriptUrl) {\n\t\tvar scripts = document.getElementsByTagName(\"script\");\n\t\tif(scripts.length) {\n\t\t\tvar i = scripts.length - 1;\n\t\t\twhile (i > -1 && !scriptUrl) scriptUrl = scripts[i--].src;\n\t\t}\n\t}\n}\n// When supporting browsers where an automatic publicPath is not supported you must specify an output.publicPath manually via configuration\n// or pass an empty string (\"\") and set the __webpack_public_path__ variable from your code to use your own logic.\nif (!scriptUrl) throw new Error(\"Automatic publicPath is not supported in this browser\");\nscriptUrl = scriptUrl.replace(/#.*$/, \"\").replace(/\\?.*$/, \"\").replace(/\\/[^\\/]+$/, \"/\");\n__webpack_require__.p = scriptUrl;","// no baseURI\n\n// object to store loaded chunks\n// \"1\" means \"already loaded\"\nvar installedChunks = {\n\t23: 1\n};\n\n// importScripts chunk loading\nvar installChunk = (data) => {\n\tvar [chunkIds, moreModules, runtime] = data;\n\tfor(var moduleId in moreModules) {\n\t\tif(__webpack_require__.o(moreModules, moduleId)) {\n\t\t\t__webpack_require__.m[moduleId] = moreModules[moduleId];\n\t\t}\n\t}\n\tif(runtime) runtime(__webpack_require__);\n\twhile(chunkIds.length)\n\t\tinstalledChunks[chunkIds.pop()] = 1;\n\tparentChunkLoadingFunction(data);\n};\n__webpack_require__.f.i = (chunkId, promises) => {\n\t// \"1\" is the signal for \"already loaded\"\n\tif(!installedChunks[chunkId]) {\n\t\tif(true) { // all chunks have JS\n\t\t\timportScripts(__webpack_require__.p + __webpack_require__.u(chunkId));\n\t\t}\n\t}\n};\n\nvar chunkLoadingGlobal = self[\"webpackChunkbio\"] = self[\"webpackChunkbio\"] || [];\nvar parentChunkLoadingFunction = chunkLoadingGlobal.push.bind(chunkLoadingGlobal);\nchunkLoadingGlobal.push = installChunk;\n\n// no HMR\n\n// no HMR manifest","// run startup\nvar __webpack_exports__ = __webpack_require__.x();\n"],"names":["deferred","next","isNil","x","onmessage","async","event","values","startIdx","endIdx","threshold","fnName","opts","data","i","j","distances","chunkSize","length","_data","_length","cnt","distanceFn","getMeasure","startRow","Math","floor","sqrt","startCol","mi","mj","value","push","iArray","Int32Array","jArray","distanceArray","Float32Array","postMessage","distance","e","error","__webpack_module_cache__","__webpack_require__","moduleId","cachedModule","undefined","exports","module","__webpack_modules__","m","__webpack_exports__","O","result","chunkIds","fn","priority","notFulfilled","Infinity","fulfilled","Object","keys","every","key","splice","r","d","definition","o","defineProperty","enumerable","get","f","chunkId","Promise","all","reduce","promises","u","g","globalThis","this","Function","window","obj","prop","prototype","hasOwnProperty","call","scriptUrl","importScripts","location","document","currentScript","src","scripts","getElementsByTagName","Error","replace","p","installedChunks","chunkLoadingGlobal","self","parentChunkLoadingFunction","bind","moreModules","runtime","pop","then"],"sourceRoot":""}

package/dist/282.js

@@ -1,2 +0,0 @@
-var bio;(()=>{"use strict";var e,r,t={1282:(e,r,t)=>{const n=e=>null==e;function o(e,r,t,n){if(t>e[e.length-1])return;const o=e.findIndex((e=>t<e));e.pop(),e.splice(o,0,t),r.pop(),r.splice(o,0,n)}var a=t(6361),i=t(9657);onmessage=async e=>{const{values:r,startIdx:t,endIdx:l,fnName:s,opts:c,nNeighbours:p}=e.data;try{const e=new Array(r.length).fill(null).map((()=>new Array(p).fill(-1))),f=new Array(r.length).fill(null).map((()=>new Array(p).fill(999999))),h=l-t;if((0,a.sQ)(s))for(let e=0;e<r.length;++e)n(r[e])||(r[e]=new i.Z(r[e]._data,r[e]._length));let u=0;const g=new a.UH(s).getMeasure(c),v=r.length-2-Math.floor(Math.sqrt(-8*t+4*r.length*(r.length-1)-7)/2-.5),b=t-r.length*v+Math.floor((v+1)*(v+2)/2);let d=v,w=b;for(;u<h;){const t=n(r[d])||n(r[w])?1:g(r[d],r[w]);o(f[d],e[d],t,w),o(f[w],e[w],t,d),u++,w++,w===r.length&&(d++,w=d+1)}postMessage({knnDistances:f,knnIndexes:e})}catch(e){postMessage({error:e})}}}},n={};function o(e){var r=n[e];if(void 0!==r)return r.exports;var a=n[e]={exports:{}};return t[e](a,a.exports,o),a.exports}o.m=t,o.x=()=>{var e=o.O(void 0,[378,361],(()=>o(1282)));return o.O(e)},e=[],o.O=(r,t,n,a)=>{if(!t){var i=1/0;for(p=0;p<e.length;p++){for(var[t,n,a]=e[p],l=!0,s=0;s<t.length;s++)(!1&a||i>=a)&&Object.keys(o.O).every((e=>o.O[e](t[s])))?t.splice(s--,1):(l=!1,a<i&&(i=a));if(l){e.splice(p--,1);var c=n();void 0!==c&&(r=c)}}return r}a=a||0;for(var p=e.length;p>0&&e[p-1][2]>a;p--)e[p]=e[p-1];e[p]=[t,n,a]},o.d=(e,r)=>{for(var t in r)o.o(r,t)&&!o.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},o.f={},o.e=e=>Promise.all(Object.keys(o.f).reduce(((r,t)=>(o.f[t](e,r),r)),[])),o.u=e=>e+".js",o.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),o.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;o.g.importScripts&&(e=o.g.location+"");var r=o.g.document;if(!e&&r&&(r.currentScript&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var n=t.length-1;n>-1&&!e;)e=t[n--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),o.p=e})(),(()=>{var e={282:1};o.f.i=(r,t)=>{e[r]||importScripts(o.p+o.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[n,a,i]=r;for(var l in a)o.o(a,l)&&(o.m[l]=a[l]);for(i&&i(o);n.length;)e[n.pop()]=1;t(r)}})(),r=o.x,o.x=()=>Promise.all([o.e(378),o.e(361)]).then(r);var a=o.x();bio=a})();
-//# sourceMappingURL=282.js.map