@datagrok/peptides 0.6.1 → 0.7.1

package/detectors.js

@@ -3,7 +3,7 @@ class PeptidesPackageDetectors extends DG.Package {
   //input: column col
   //output: string semType
   detectAligned(col) {
-    const regexp = new RegExp(/^([^-^\n]*-){7,49}(\w|\(|\))+$/);
+    const regexp = new RegExp(/^([^\-\n]*-){7,49}(\w|\(|\))+$/);
     return DG.Detector.sampleCategories(col, (s) => regexp.test(s.trim())) ? 'alignedSequence' : null;
   }
 }

package/package.json

@@ -1,20 +1,19 @@
 {
 	"name": "@datagrok/peptides",
-	"version": "0.6.1",
+	"version": "0.7.1",
 	"description": "",
 	"dependencies": {
-		"@keckelt/tsne": "^1.0.2",
 		"cash-dom": "latest",
 		"d3": "latest",
 		"datagrok-api": ">=0.104.0",
 		"dayjs": "latest",
-		"jaro-winkler-typescript": "^1.0.1",
 		"jstat": "^1.9.5",
 		"logojs-react": "^2.1.1",
 		"rxjs": "^6.5.5",
-		"umap-js": "^1.3.3",
 		"@datagrok-libraries/utils": ">=0.0.13",
 		"@datagrok-libraries/statistics": ">=0.1.5",
+		"@datagrok-libraries/ml": ">=0.0.1",
+		"@datagrok-libraries/bio": ">=0.0.4",
 		"@types/d3": "^7.0.0",
 		"@types/jquery": "^3.5.6"
 	},
@@ -36,10 +35,12 @@
 		"common/ngl_viewer/ngl.js"
 	],
 	"scripts": {
+		"link-api": "npm link datagrok-api",
 		"link-utils": "npm link @datagrok-libraries/utils",
 		"link-statistics": "npm link @datagrok-libraries/statistics",
-		"link-api": "npm link datagrok-api",
-		"link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/statistics",
+		"link-ml": "npm link @datagrok-libraries/ml",
+		"link-bio": "npm link @datagrok-libraries/bio",
+		"link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/statistics link @datagrok-libraries/ml @datagrok-libraries/bio",
 		"install-dependencies": "npm install",
 		"debug-peptides": "grok publish --rebuild",
 		"release-peptides": "grok publish --rebuild --release",
@@ -53,5 +54,7 @@
 		"release-peptides-local": "grok publish local --rebuild --release",
 		"lint": "eslint \"./src/**/*.ts\"",
 		"lint-fix": "eslint \"./src/**/*.ts\" --fix"
-	}
-}
+	},
+	"canEdit": [ "Developers" ],
+	"canView": [ "All users" ]
+}

package/src/describe.ts

@@ -53,29 +53,13 @@ const groupDescription: {[key: string]: {'description': string, 'aminoAcids': st
   }
 }*/
 
-//TODO: decomposition!
-export async function describe(
+function joinDataFrames(
+  activityColumnScaled: string,
   df: DG.DataFrame,
+  positionColumns: string[],
+  splitSeqDf: DG.DataFrame,
   activityColumn: string,
-  activityScaling: string,
-  sourceGrid: DG.Grid,
-  twoColorMode: boolean,
-  initialBitset: DG.BitSet | null,
-  grouping: boolean,
-): Promise<[DG.Grid, DG.Grid, DG.DataFrame, {[key: string]: string}]> {
-  //Split the aligned sequence into separate AARs
-  let splitSeqDf: DG.DataFrame | undefined;
-  let invalidIndexes: number[];
-  const col: DG.Column = df.columns.bySemType('alignedSequence');
-  [splitSeqDf, invalidIndexes] = splitAlignedPeptides(col);
-  splitSeqDf.name = 'Split sequence';
-
-  const positionColumns = splitSeqDf.columns.names();
-  const activityColumnScaled = `${activityColumn}Scaled`;
-  const renderColNames: string[] = splitSeqDf.columns.names();
-
-  splitSeqDf.columns.add(df.getCol(activityColumn));
-
+) {
   if (df.col(activityColumnScaled)) {
     df.columns.remove(activityColumnScaled);
   }
@@ -90,13 +74,9 @@ export async function describe(
   if (!positionColumns.every((col: string) => dfColsSet.has(col))) {
     df.join(splitSeqDf, [activityColumn], [activityColumn], df.columns.names(), positionColumns, 'inner', true);
   }
+}
 
-  for (const col of df.columns) {
-    if (splitSeqDf.col(col.name) && col.name != activityColumn) {
-      setAARRenderer(col, sourceGrid);
-    }
-  }
-
+function sortSourceGrid(sourceGrid: DG.Grid) {
   if (sourceGrid) {
     const colNames:string[] = [];
     for (let i = 0; i < sourceGrid.columns.length; i++) {
@@ -116,8 +96,16 @@ export async function describe(
     });
     sourceGrid?.columns.setOrder(colNames);
   }
+}
 
-  // scale activity
+async function scaleActivity(
+  activityScaling: string,
+  activityColumn: string,
+  activityColumnScaled: string,
+  sourceGrid: DG.Grid,
+  splitSeqDf: DG.DataFrame,
+) {
+  const df = sourceGrid.dataFrame!;
   switch (activityScaling) {
   case 'lg':
     await df.columns.addNewCalculated(activityColumnScaled, 'Log10(${' + activityColumn + '})');
@@ -138,32 +126,17 @@ export async function describe(
     sourceGrid.columns.setOrder([`${activityColumn}`]);
     break;
   }
-  splitSeqDf = splitSeqDf.clone(initialBitset);
-
-  const positionColName = 'Position';
-  const aminoAcidResidue = 'AAR';
-
-  //unpivot a table and handle duplicates
-  splitSeqDf = splitSeqDf.groupBy(positionColumns)
-    .add('med', activityColumnScaled, activityColumnScaled)
-    .aggregate();
-
-  const peptidesCount = splitSeqDf.getCol(activityColumnScaled).length;
-
-  let matrixDf = splitSeqDf.unpivot([activityColumnScaled], positionColumns, positionColName, aminoAcidResidue);
-
-  //TODO: move to chem palette
-  let groupMapping: {[key: string]: string} = {};
-  if (grouping) {
-    groupMapping = aarGroups;
-    const aarCol = matrixDf.getCol(aminoAcidResidue);
-    aarCol.init((index) => groupMapping[aarCol.get(index)[0]] ?? '-');
-    aarCol.compact();
-  } else {
-    Object.keys(aarGroups).forEach((value) => groupMapping[value] = value);
-  }
+}
 
-  //statistics for specific AAR at a specific position
+async function calculateStatistics(
+  matrixDf: DG.DataFrame,
+  positionColName: string,
+  aminoAcidResidue: string,
+  activityColumnScaled: string,
+  peptidesCount: number,
+  splitSeqDf: DG.DataFrame,
+  groupMapping: {[key: string]: string},
+) {
   matrixDf = matrixDf.groupBy([positionColName, aminoAcidResidue])
     .add('count', activityColumnScaled, 'Count')
     .aggregate();
@@ -177,39 +150,31 @@ export async function describe(
   await matrixDf.columns.addNewCalculated('Ratio', '${count}/'.concat(`${peptidesCount}`));
 
   //calculate p-values based on t-test
-  let position: string;
-  let aar: string;
-  let currentActivity: number[];
-  let otherActivity: number[];
-  let testResult;
-  let currentMeanDiff: number;
   let pvalues: Float32Array = new Float32Array(matrixDf.rowCount).fill(1);
-  let pvalue = 1.;
-
   const mdCol: DG.Column = matrixDf.columns.addNewFloat('Mean difference');
   const pValCol: DG.Column = matrixDf.columns.addNewFloat('pValue');
   for (let i = 0; i < matrixDf.rowCount; i++) {
-    position = matrixDf.get(positionColName, i);
-    aar = matrixDf.get(aminoAcidResidue, i);
+    const position = matrixDf.get(positionColName, i);
+    const aar = matrixDf.get(aminoAcidResidue, i);
 
     //@ts-ignore
     splitSeqDf.rows.select((row) => groupMapping[row[position]] === aar);
-    currentActivity = splitSeqDf
+    const currentActivity: number[] = splitSeqDf
       .clone(splitSeqDf.selection, [activityColumnScaled])
       .getCol(activityColumnScaled)
       .toList();
 
     //@ts-ignore
     splitSeqDf.rows.select((row) => groupMapping[row[position]] !== aar);
-    otherActivity = splitSeqDf
+    const otherActivity: number[] = splitSeqDf
       .clone(splitSeqDf.selection, [activityColumnScaled])
       .getCol(activityColumnScaled)
       .toList();
 
-    testResult = tTest(currentActivity, otherActivity);
+    const testResult = tTest(currentActivity, otherActivity);
     // testResult = uTest(currentActivity, otherActivity);
-    currentMeanDiff = testResult['Mean difference']!;
-    pvalue = testResult[currentMeanDiff >= 0 ? 'p-value more' : 'p-value less'];
+    const currentMeanDiff = testResult['Mean difference']!;
+    const pvalue = testResult[currentMeanDiff >= 0 ? 'p-value more' : 'p-value less'];
 
     mdCol.set(i, currentMeanDiff);
     pvalues[i] = pvalue;
@@ -223,17 +188,12 @@ export async function describe(
     pValCol.set(i, pvalues[i]);
   }
 
-  const statsDf = matrixDf.clone();
-
-  // SAR matrix table
-  //pivot a table to make it matrix-like
-  matrixDf = matrixDf.groupBy([aminoAcidResidue])
-    .pivot(positionColName)
-    .add('first', 'Mean difference', '')
-    .aggregate();
-  matrixDf.name = 'SAR';
+  return matrixDf.clone();
+}
 
-  // Setting category order
+async function setCategoryOrder(
+  twoColorMode: boolean, statsDf: DG.DataFrame, aminoAcidResidue: string, matrixDf: DG.DataFrame,
+) {
   const sortArgument = twoColorMode ? 'Absolute Mean difference' : 'Mean difference';
   if (twoColorMode) {
     await statsDf.columns.addNewCalculated('Absolute Mean difference', 'Abs(${Mean difference})');
@@ -248,8 +208,14 @@ export async function describe(
   aarList.sort((first, second) => getWeight(second) - getWeight(first));
 
   matrixDf.getCol(aminoAcidResidue).setCategoryOrder(aarList);
+}
 
-  // SAR vertical table (naive, choose best Mean difference from pVals <= 0.01)
+function createVerticalTable(
+  statsDf: DG.DataFrame,
+  aminoAcidResidue: string,
+  positionColName: string,
+  twoColorMode: boolean,
+) {
   // TODO: aquire ALL of the positions
   let sequenceDf = statsDf.groupBy(['Mean difference', aminoAcidResidue, positionColName, 'Count', 'Ratio', 'pValue'])
     .where('pValue <= 0.1')
@@ -268,9 +234,18 @@ export async function describe(
   sequenceDf = sequenceDf.clone(DG.BitSet.create(sequenceDf.rowCount, (i) => {
     return sequenceDf.get('Mean difference', i) === maxAtPos[sequenceDf.get(positionColName, i)];
   }));
-  renderColNames.push('Mean difference');
 
-  // !!! DRAWING PHASE !!!
+  return sequenceDf;
+}
+
+function createGrids(
+  matrixDf: DG.DataFrame,
+  aminoAcidResidue: string,
+  positionColumns: string[],
+  sequenceDf: DG.DataFrame,
+  positionColName: string,
+  grouping: boolean,
+) {
   const sarGrid = matrixDf.plot.grid();
   sarGrid.sort([aminoAcidResidue]);
   sarGrid.columns.setOrder([aminoAcidResidue].concat(positionColumns));
@@ -291,7 +266,19 @@ export async function describe(
     }
   }
 
-  //render column headers and AAR symbols centered
+  return [sarGrid, sarVGrid];
+}
+
+function setCellRendererFunc(
+  renderColNames: string[],
+  positionColName: string,
+  aminoAcidResidue: string,
+  statsDf: DG.DataFrame,
+  twoColorMode: boolean,
+  sarGrid: DG.Grid,
+  sarVGrid: DG.Grid,
+) {
+  const mdCol = statsDf.getCol('Mean difference');
   const cellRendererFunc = function(args: DG.GridCellRenderArgs) {
     args.g.save();
     args.g.beginPath();
@@ -360,8 +347,18 @@ export async function describe(
   };
   sarGrid.onCellRender.subscribe(cellRendererFunc);
   sarVGrid.onCellRender.subscribe(cellRendererFunc);
+}
 
-  // show all the statistics in a tooltip over cell
+function setTooltipFunc(
+  renderColNames: string[],
+  statsDf: DG.DataFrame,
+  aminoAcidResidue: string,
+  positionColName: string,
+  peptidesCount: number,
+  grouping: boolean,
+  sarGrid: DG.Grid,
+  sarVGrid: DG.Grid,
+) {
   const onCellTooltipFunc = function(cell: DG.GridCell, x: number, y: number) {
     if (
       !cell.isRowHeader &&
@@ -414,7 +411,17 @@ export async function describe(
   };
   sarGrid.onCellTooltip(onCellTooltipFunc);
   sarVGrid.onCellTooltip(onCellTooltipFunc);
+}
 
+function postProcessGrids(
+  sourceGrid: DG.Grid,
+  invalidIndexes: number[],
+  matrixDf: DG.DataFrame,
+  grouping: boolean,
+  aminoAcidResidue: string,
+  sarGrid: DG.Grid,
+  sarVGrid: DG.Grid,
+) {
   sourceGrid.onCellPrepare((cell: DG.GridCell) => {
     const currentRowIndex = cell.tableRowIndex;
     if (currentRowIndex && invalidIndexes.includes(currentRowIndex) && !cell.isRowHeader) {
@@ -433,6 +440,100 @@ export async function describe(
 
   sarGrid.props.allowEdit = false;
   sarVGrid.props.allowEdit = false;
+}
+
+export async function describe(
+  df: DG.DataFrame,
+  activityColumn: string,
+  activityScaling: string,
+  sourceGrid: DG.Grid,
+  twoColorMode: boolean,
+  initialBitset: DG.BitSet | null,
+  grouping: boolean,
+): Promise<[DG.Grid, DG.Grid, DG.DataFrame, {[key: string]: string}]> {
+  //Split the aligned sequence into separate AARs
+  let splitSeqDf: DG.DataFrame | undefined;
+  let invalidIndexes: number[];
+  const col: DG.Column = df.columns.bySemType('alignedSequence');
+  [splitSeqDf, invalidIndexes] = splitAlignedPeptides(col);
+  splitSeqDf.name = 'Split sequence';
+
+  const positionColumns = splitSeqDf.columns.names();
+  const activityColumnScaled = `${activityColumn}Scaled`;
+  const renderColNames: string[] = splitSeqDf.columns.names();
+  const positionColName = 'Position';
+  const aminoAcidResidue = 'AAR';
+
+  splitSeqDf.columns.add(df.getCol(activityColumn));
+
+  joinDataFrames(activityColumnScaled, df, positionColumns, splitSeqDf, activityColumn);
+
+  for (const col of df.columns) {
+    if (splitSeqDf.col(col.name) && col.name != activityColumn) {
+      setAARRenderer(col, sourceGrid);
+    }
+  }
+
+  sortSourceGrid(sourceGrid);
+
+  await scaleActivity(activityScaling, activityColumn, activityColumnScaled, sourceGrid, splitSeqDf);
+  splitSeqDf = splitSeqDf.clone(initialBitset);
+
+  //unpivot a table and handle duplicates
+  splitSeqDf = splitSeqDf.groupBy(positionColumns)
+    .add('med', activityColumnScaled, activityColumnScaled)
+    .aggregate();
+
+  const peptidesCount = splitSeqDf.getCol(activityColumnScaled).length;
+
+  let matrixDf = splitSeqDf.unpivot([activityColumnScaled], positionColumns, positionColName, aminoAcidResidue);
+
+  //TODO: move to chem palette
+  let groupMapping: {[key: string]: string} = {};
+  if (grouping) {
+    groupMapping = aarGroups;
+    const aarCol = matrixDf.getCol(aminoAcidResidue);
+    aarCol.init((index) => groupMapping[aarCol.get(index)[0]] ?? '-');
+    aarCol.compact();
+  } else {
+    Object.keys(aarGroups).forEach((value) => groupMapping[value] = value);
+  }
+
+  //statistics for specific AAR at a specific position
+  const statsDf = await calculateStatistics(
+    matrixDf, positionColName, aminoAcidResidue, activityColumnScaled, peptidesCount, splitSeqDf, groupMapping,
+  );
+
+  // SAR matrix table
+  //pivot a table to make it matrix-like
+  matrixDf = statsDf.groupBy([aminoAcidResidue])
+    .pivot(positionColName)
+    .add('first', 'Mean difference', '')
+    .aggregate();
+  matrixDf.name = 'SAR';
+
+  // Setting category order
+  await setCategoryOrder(twoColorMode, statsDf, aminoAcidResidue, matrixDf);
+
+  // SAR vertical table (naive, choose best Mean difference from pVals <= 0.01)
+  const sequenceDf = createVerticalTable(statsDf, aminoAcidResidue, positionColName, twoColorMode);
+  renderColNames.push('Mean difference');
+
+  const [sarGrid, sarVGrid] = createGrids(
+    matrixDf, aminoAcidResidue, positionColumns, sequenceDf, positionColName, grouping,
+  );
+
+  setCellRendererFunc(
+    renderColNames, positionColName, aminoAcidResidue, statsDf, twoColorMode, sarGrid, sarVGrid,
+  );
+
+  // show all the statistics in a tooltip over cell
+  setTooltipFunc(
+    renderColNames, statsDf, aminoAcidResidue, positionColName, peptidesCount, grouping, sarGrid, sarVGrid,
+  );
+
+  postProcessGrids(sourceGrid, invalidIndexes, matrixDf, grouping, aminoAcidResidue, sarGrid, sarVGrid);
 
+  //TODO: return class instead
   return [sarGrid, sarVGrid, statsDf, groupMapping];
 }

package/src/{viewers/model.ts → model.ts}

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {describe} from '../describe';
+import {describe} from './describe';
 import {Subject} from 'rxjs';
 
 /**

package/src/package.ts

@@ -15,7 +15,6 @@ import {PeptideSimilaritySpaceWidget} from './utils/peptide-similarity-space';
 import {manualAlignmentWidget} from './widgets/manual-alignment';
 import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
 import {peptideMoleculeWidget} from './widgets/peptide-molecule';
-import {SpiralPlot} from './viewers/spiral-plot';
 import {SubstViewer} from './viewers/subst-viewer';
 
 export const _package = new DG.Package();
@@ -182,16 +181,3 @@ export async function peptideSpacePanel(col: DG.Column): Promise<DG.Widget> {
   const widget = new PeptideSimilaritySpaceWidget(col, view ?? grok.shell.v);
   return await widget.draw();
 }
-
-//name: Spiral Plot
-////input: dataframe table
-////input: column activity
-//tags: viewer, panel
-//output: viewer result
-export async function spiralPlot(): Promise<DG.Viewer> {//(table: DG.DataFrame, activity: DG.Column) {
-// Read as dataframe
-  const table = await grok.data.files.openTable('Demo:TestJobs:Files:DemoFiles/bio/peptides.csv');
-  const activity = await table.columns.addNewCalculated('-log10(Activity)', '0-Log10(${Activity})');
-  view = grok.shell.addTableView(table);
-  return view.addViewer(SpiralPlot.fromTable(table, {valuesColumnName: activity.name}));
-}

package/src/peptides.ts

@@ -2,6 +2,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {createPeptideSimilaritySpaceViewer} from './utils/peptide-similarity-space';
 import {addViewerToHeader} from './viewers/stacked-barchart-viewer';
+import {model} from './model';
 // import $ from 'cash-dom';
 
 /**
@@ -11,6 +12,12 @@ import {addViewerToHeader} from './viewers/stacked-barchart-viewer';
  * @class Peptides
  */
 export class Peptides {
+  private static _model = model;
+
+  static async recalculate() {
+    await Peptides._model.updateDefault();
+  }
+
   /**
    * Class initializer
    *
@@ -47,7 +54,10 @@ export class Peptides {
     const substViewer = view.addViewer(
       'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
     );
-    view.dockManager.dock(substViewer, DG.DOCK_TYPE.RIGHT, null, 'Substitution Analysis');
+    const substNode = view.dockManager.dock(substViewer, DG.DOCK_TYPE.RIGHT, null, 'Substitution Analysis');
+
+    const layout1 = view.saveLayout();
+    view.dockManager.close(substNode);
 
     const sarViewer = view.addViewer('peptide-sar-viewer', options);
     const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
@@ -65,8 +75,8 @@ export class Peptides {
       `${activityColumnChoice}Scaled`,
     );
     const psNode = view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
-    // const sarDockNodes = [sarNode, sarVNode, psNode];
-    // const sarViewers = [sarViewer, sarViewerVertical, peptideSpaceViewer];
+
+    const layout2 = view.saveLayout();
 
     const StackedBarchartProm = currentDf.plot.fromType('StackedBarChartAA');
     addViewerToHeader(tableGrid, StackedBarchartProm);
@@ -99,42 +109,22 @@ export class Peptides {
       view.setRibbonPanels(ribbonPanels);
     }, 'Close viewers and restore dataframe');
 
-    // let substViewer: DG.Viewer | null = null;
-    // let substNode: DG.DockNode | null = null;
-    // let isSA = false;
-    // let viewLayout1: DG.ViewLayout | null = null;
-    // let viewLayout2: DG.ViewLayout | null = null;
-    // const switchViewers = ui.iconFA('toggle-on', () => {
-    //   if (isSA) {
-    //     viewLayout2 = view.saveLayout();
-    //     // view.dockManager.close(substNode!);
-    //     substViewer?.close();
-
-    //     view.loadLayout(viewLayout1!);
-
-    //     $(switchViewers).removeClass('fa-toggle-off');
-    //     $(switchViewers).addClass('fa-toggle-on');
-    //   } else {
-    //     viewLayout1 = view.saveLayout();
-    //     // sarDockNodes.forEach((node) => view.dockManager.close(node));
-    //     sarViewers.forEach((v) => v.close());
-
-    //     if (viewLayout2 === null) {
-    //       substViewer = view.addViewer(
-    //         'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
-    //       );
-    //       substNode = view.dockManager.dock(substViewer, DG.DOCK_TYPE.DOWN, null, 'Substitution Analysis');
-    //     } else {
-    //       view.loadLayout(viewLayout2);
-    //     }
-
-    //     $(switchViewers).removeClass('fa-toggle-on');
-    //     $(switchViewers).addClass('fa-toggle-off');
-    //   }
-    //   isSA = !isSA;
-    // });
+    let isSA = false;
+    const switchViewers = ui.iconFA('toggle-on', () => {
+      if (isSA) {
+        view.loadLayout(layout1);
+        $(switchViewers).removeClass('fa-toggle-off');
+        $(switchViewers).addClass('fa-toggle-on');
+      } else {
+        view.loadLayout(layout2);
+        $(switchViewers).removeClass('fa-toggle-on');
+        $(switchViewers).addClass('fa-toggle-off');
+      }
+      isSA = !isSA;
+    });
 
     const ribbonPanels = view.getRibbonPanels();
+    // view.setRibbonPanels([[hideIcon, switchViewers]]);
     view.setRibbonPanels([[hideIcon]]);
   }
 }

package/src/styles.css

@@ -35,3 +35,12 @@
   height: 50px;
   overflow: hidden;
 }
+
+#pep-hist-host #center {
+  height: 131px;
+}
+
+#pep-hist-host > #root {
+  height: unset;
+  width: 100%;
+}

package/src/utils/peptide-similarity-space.ts

@@ -3,40 +3,14 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {getSequenceMolecularWeight} from './molecular-measure';
-import {AlignedSequenceEncoder} from '@datagrok-libraries/utils/src/sequence-encoder';
-import {DimensionalityReducer} from '@datagrok-libraries/utils/src/reduce-dimensionality';
-import {Measurer} from '@datagrok-libraries/utils/src/string-measure';
+import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
+import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimensionality';
+import {
+  createDimensinalityReducingWorker,
+} from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
+import {StringMeasure} from '@datagrok-libraries/ml/src/string-measure';
 import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
-/**
- * A worker to perform dimensionality reduction.
- *
- * @param {any[]} columnData The data to process.
- * @param {string} method A method of dimensionality reduction.
- * @param {string} measure A distance metrics.
- * @param {number} cyclesCount Number of iterations to run.
- * @return {Promise<unknown>} Resulting embedding.
- */
-function createDimensinalityReducingWorker(
-  columnData: any[],
-  method: string,
-  measure: string,
-  cyclesCount: number,
-): Promise<unknown> {
-  return new Promise(function(resolve) {
-    const worker = new Worker(new URL('../workers/dimensionality-reducer.ts', import.meta.url));
-    worker.postMessage({
-      columnData: columnData,
-      method: method,
-      measure: measure,
-      cyclesCount: cyclesCount,
-    });
-    worker.onmessage = ({data: {embedding}}) => {
-      resolve(embedding);
-    };
-  });
-}
-
 /**
  * Finds a column with an activity.
  *
@@ -157,7 +131,7 @@ export class PeptideSimilaritySpaceWidget {
    */
   constructor(alignedSequencesColumn: DG.Column, view: DG.TableView) {
     this.availableMethods = DimensionalityReducer.availableMethods;
-    this.availableMetrics = Measurer.availableMeasures;
+    this.availableMetrics = StringMeasure.availableMeasures;
     this.method = this.availableMethods[0];
     this.metrics = this.availableMetrics[0];
     this.currentDf = alignedSequencesColumn.dataFrame;