@datagrok/peptides 0.5.6 → 0.8.4

package/src/peptides.ts

@@ -2,6 +2,8 @@ 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';
 
 /**
  * Peptides controller class.
@@ -10,6 +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
    *
@@ -27,7 +35,6 @@ export class Peptides {
     currentDf: DG.DataFrame,
     options: {[key: string]: string},
     col: DG.Column,
-    activityColumnChoice: string,
   ) {
     for (let i = 0; i < tableGrid.columns.length; i++) {
       const aarCol = tableGrid.columns.byIndex(i);
@@ -40,13 +47,23 @@ export class Peptides {
       }
     }
 
+    const initialFiter = currentDf.filter.clone();
     const originalDfColumns = (currentDf.columns as DG.ColumnList).names();
+    const originalDfName = currentDf.name;
+
+    // const substViewer = view.addViewer(
+    //   'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
+    // );
+    // 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');
 
     const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
-    view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
+    const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
 
     const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
       currentDf,
@@ -55,12 +72,17 @@ export class Peptides {
       'Levenshtein',
       100,
       view,
-      `${activityColumnChoice}Scaled`,
+      `${options['activityColumnChoice']}Scaled`,
     );
-    view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
+    const psNode = view.dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
+
+    const layout2 = view.saveLayout();
+
+    const nodeList = [sarNode, sarVNode, psNode];
 
     const StackedBarchartProm = currentDf.plot.fromType('StackedBarChartAA');
     addViewerToHeader(tableGrid, StackedBarchartProm);
+    tableGrid.props.allowEdit = false;
 
     const hideIcon = ui.iconFA('window-close', () => { //undo?, times?
       const viewers = [];
@@ -83,11 +105,62 @@ export class Peptides {
 
       tableGrid.setOptions({'colHeaderHeight': 20});
       tableGrid.columns.setVisible(originalDfColumns);
+      tableGrid.props.allowEdit = true;
+      currentDf.name = originalDfName;
 
       view.setRibbonPanels(ribbonPanels);
     }, 'Close viewers and restore dataframe');
 
+    let isSA = false;
+    //TODO: fix layouts
+    // 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');
+    //     $(switchViewers).addClass('fa-toggle-off');
+    //   }
+    //   isSA = !isSA;
+    // });
+    const switchViewers = ui.iconFA('toggle-on', async () => {
+      currentDf.filter.copyFrom(initialFiter);
+      currentDf.selection.setAll(false);
+      nodeList.forEach((node) => view.dockManager.close(node));
+      nodeList.length = 0;
+      if (isSA) {
+        const sarViewer = view.addViewer('peptide-sar-viewer', options);
+        const sarNode = view.dockManager.dock(sarViewer, DG.DOCK_TYPE.DOWN, null, 'SAR Viewer');
+
+        const sarViewerVertical = view.addViewer('peptide-sar-viewer-vertical');
+        const sarVNode = view.dockManager.dock(sarViewerVertical, DG.DOCK_TYPE.RIGHT, sarNode, 'SAR Vertical Viewer');
+
+        const peptideSpaceViewer = await createPeptideSimilaritySpaceViewer(
+          currentDf, col, 't-SNE', 'Levenshtein', 100, view, `${options['activityColumnChoice']}Scaled`);
+        const psNode = view.dockManager.dock(
+          peptideSpaceViewer, DG.DOCK_TYPE.LEFT, sarNode, 'Peptide Space Viewer', 0.3);
+
+        nodeList.push(sarNode);
+        nodeList.push(sarVNode);
+        nodeList.push(psNode);
+
+        $(switchViewers).removeClass('fa-toggle-off');
+        $(switchViewers).addClass('fa-toggle-on');
+      } else {
+        const substViewer = view.addViewer(
+          'substitution-analysis-viewer', {'activityColumnName': options['activityColumnName']},
+        );
+        nodeList.push(view.dockManager.dock(substViewer, DG.DOCK_TYPE.RIGHT, null, 'Substitution Analysis'));
+        $(switchViewers).removeClass('fa-toggle-on');
+        $(switchViewers).addClass('fa-toggle-off');
+      }
+      isSA = !isSA;
+    });
+
     const ribbonPanels = view.getRibbonPanels();
-    view.setRibbonPanels([[hideIcon]]);
+    view.setRibbonPanels([[hideIcon, switchViewers]]);
+    // view.setRibbonPanels([[hideIcon]]);
   }
 }

package/src/semantics.ts

@@ -0,0 +1,5 @@
+export const SEMTYPE = {
+  ALIGNED: 'alignedSequence',
+};
+
+

package/src/styles.css

@@ -0,0 +1,46 @@
+.pep-textarea-box {
+  position: relative;
+}
+
+.pep-textarea-box:hover .pep-snippet-editor-icon {
+  visibility: visible;
+}
+
+.pep-snippet-editor-icon {
+  position: absolute;
+  top: 5px;
+  visibility: hidden;
+  margin: 5px;
+  z-index: 1;
+}
+
+.pep-reset-icon {
+  right: 10px;
+}
+
+.pep-snippet-editor-icon i {
+  font-size: 13px;
+}
+
+.pep-snippet-editor-icon:hover {
+  background-color: var(--steel-1);
+  border-radius: 2px;
+}
+
+.pep-snippet-inline-icon i {
+  font-size: 13px;
+}
+
+.pep-textinput {
+  height: 50px;
+  overflow: hidden;
+}
+
+#pep-hist-host #center {
+  height: 131px;
+}
+
+#pep-hist-host > #root {
+  height: unset;
+  width: 100%;
+}

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

@@ -0,0 +1,40 @@
+import {category, test} from '@datagrok-libraries/utils/src/test';
+import {
+  _testViewerIsDrawing,
+  _testDimensionalityReducer,
+  _testPeptideSimilaritySpaceViewer,
+} from './utils';
+import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimensionality';
+import {cleanAlignedSequencesColumn} from '../utils/peptide-similarity-space';
+
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
+
+category('peptides', async () => {
+  const table = await grok.data.files.openTable('Demo:TestJobs:Files:DemoFiles/bio/peptides.csv');
+  const view = grok.shell.v as DG.TableView;
+
+  test('PeptideSimilaritySpaceWidget.is_drawing', async () => {
+    await _testViewerIsDrawing(table, view);
+  });
+
+  const alignedSequencesColumn = table.getCol('AlignedSequence');
+  const columnData = cleanAlignedSequencesColumn(alignedSequencesColumn);
+
+  for (const method of DimensionalityReducer.availableMethods) {
+    for (const measure of DimensionalityReducer.availableMetrics) {
+      test(`DimensinalityReducer.${method}.${measure}.is_numeric`, async () => {
+        await _testDimensionalityReducer(columnData, method, measure);
+      });
+    }
+  }
+
+  for (const method of DimensionalityReducer.availableMethods) {
+    for (const measure of DimensionalityReducer.availableMetrics) {
+      test(`peptides.PeptideSimilaritySpaceViewer.${method}.${measure}.is_proper`, async () => {
+        await _testPeptideSimilaritySpaceViewer(table, alignedSequencesColumn, method, measure, 100);//, view);
+      });
+    }
+  }
+});

package/src/tests/peptides-tests.ts

@@ -0,0 +1,84 @@
+import {after, before, category, expect, test} from "@datagrok-libraries/utils/src/test";
+import {splitAlignedPeptides} from "../utils/split-aligned";
+import * as DG from "datagrok-api/dg";
+import * as grok from "datagrok-api/grok";
+import * as ui from "datagrok-api/ui";
+import { Peptides } from "../peptides";
+import { describe } from "../describe";
+import { analyzePeptidesWidget } from "../widgets/analyze-peptides";
+import { manualAlignmentWidget } from "../widgets/manual-alignment";
+import { peptideMoleculeWidget } from "../widgets/peptide-molecule";
+
+export let _package = new DG.Package();
+
+category('peptides', async () => {
+  let peptidesDf: DG.DataFrame;
+  let options: {[key: string]: string};
+  let peptidesGrid: DG.Grid;
+  let asCol: DG.Column;
+  let pepView: DG.TableView;
+
+  before(async () => {
+    // peptidesDf = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
+    const csv = `ID,AlignedSequence,IC50
+    1,NH2--A-Q-T-T-Y-K-N-Y-R-R-N-L-L--COOH,4.6411368455908086e-4
+    2,NH2-M-A-N-T-T-Y-K-N-Y-R-N-N-L-L--COOH,0.003327324930165897
+    3,NH2--A-N-T-T-Y-K-C-Y-R-R-N-L-L--COOH,3.0748148478921324e-4
+    4,NH2--A-N-T-T-Y-K-F-Y-R-R-N-L-L--COOH,0.0015532837750281958
+    5,NH2--A-V-T-T-Y-K-N-Y-R-R-N-L-L--COOH,6.549885174778741e-4
+    6,NH2--A-N-T-T-Y-K-N-Y-R-R-N-L-L--COOH,0.00213298315038382
+    7,NH2--A-N-T-T-Y-K-N-Y-R-F-N-L-L--COOH,0.002171297321903189
+    8,NH2--A-N-T-T-Y-K-N-Y-R-R-N-H-L--COOH,0.002060711496394637
+    9,NH2-M-A-N-T-T-Y-K-N-Y-R-R-N-L-L--COOH,0.0016058870359321516
+    10,NH2--A-N-T-T-Y-K-N-Y-R-N-N-L-L--COOH,0.00212911675087592
+    11,NH2--A-N-T-T-Y-K-N-Y-R-R-N-L-L--COOH,0.002736311013579287
+    12,NH2--A-N-T-T-Y-K-N-Y-R-R-N-L-L--COOH,5.673074652436946e-5
+    13,NH2-C-A-N-T-T-Y-K-N-Y-R-R-N-L-L--COOH,0.0032881139376902814
+    14,NH2--A-N-T-T-Y-K-N-Y-R-H-N-L-L--COOH,0.0012828163841736553
+    15,NH2-Y-A-N-T-T-Y-K-N-Y-R-D-N-L-L--COOH,7.186983807098166e-4
+    16,NH2-M-A-N-T-T-Y-K-N-Y-R-N-N-L-L--COOH,0.00659708587488309
+    17,NH2-P-A-N-T-T-Y-K-N-Y-R-G-N-L-L--COOH,3.7620528849324097e-4
+    18,NH2-Y-A-N-T--Y-K-N-Y-R-S-N-L-L--COOH,6.812868474160967e-4
+    19,NH2--A-N-T-T-Y-K-N-Y-R-S-N-L-L--COOH,0.0010148578953195436`;
+    peptidesDf = DG.DataFrame.fromCsv(csv);
+    options = {
+      'activityColumnName': 'IC50',
+      'scaling': '-lg',
+    };
+    peptidesGrid = peptidesDf.plot.grid();
+    asCol = peptidesDf.getCol('AlignedSequence');
+    pepView = grok.shell.addTableView(peptidesDf);
+  });
+
+  test('utils.split-sequence', async () => {
+    splitAlignedPeptides(peptidesDf.getCol('AlignedSequence'));
+  });
+
+  test('describe', async () => {
+    await describe(
+      peptidesDf, options['activityColumnName'], options['scaling'],  peptidesGrid, true,
+      DG.BitSet.create(peptidesDf.rowCount, (i) => i % 2 === 0), true);
+  });
+
+  test('Peptides-class', async () => {
+    const peptides = new Peptides();
+    peptides.init(peptidesGrid, pepView, peptidesDf, options, asCol);
+  });
+
+  test('widgets.analyze-peptides', async () => {
+    await analyzePeptidesWidget(asCol, pepView, peptidesGrid, peptidesDf);
+  });
+
+  test('widgets.manual-alignment', async () => {
+    manualAlignmentWidget(asCol, peptidesDf);
+  });
+
+  test('widgets.peptide-molecule', async () => {
+    await peptideMoleculeWidget('NH2--A-N-T-T-Y-K-N-Y-R-S-N-L-L--COOH');
+  });
+
+  after(async () => {
+    pepView.close();
+    grok.shell.closeTable(peptidesDf);
+  })
+});

package/src/tests/utils.ts

@@ -0,0 +1,87 @@
+import * as DG from 'datagrok-api/dg';
+
+import {expect} from '@datagrok-libraries/utils/src/test';
+import {PeptideSimilaritySpaceWidget, createPeptideSimilaritySpaceViewer} from '../utils/peptide-similarity-space';
+import {
+  createDimensinalityReducingWorker,
+} from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
+
+/**
+ * Tests if peptide space viewer is drawing without exceptions.
+ *
+ * @param {DG.DataFrame} table Demo table.
+ * @param {DG.TableView} view Demo view.
+ */
+export async function _testViewerIsDrawing(table: DG.DataFrame, view: DG.TableView) {
+  let noException = true;
+
+  try {
+    const widget = new PeptideSimilaritySpaceWidget(table.getCol('AlignedSequence'), view);
+    await widget.draw();
+  } catch (error) {
+    noException = false;
+  }
+  expect(noException, true);
+}
+
+/**
+ * Tests if dimensionality reducer works for both the method and the measure chosen.
+ *
+ * @param {Array<string>} columnData Strings to process.
+ * @param {string} method Embedding method.
+ * @param {string} measure Measure to apply to a pair of strings.
+ */
+export async function _testDimensionalityReducer(columnData: Array<string>, method: string, measure: string) {
+  const cyclesCount = 100;
+  const embcols = await createDimensinalityReducingWorker(columnData, method, measure, cyclesCount);
+  const [X, Y] = embcols as Array<Float32Array>;
+
+  expect(X.every((v) => v !== null && v !== NaN), true);
+  expect(Y.every((v) => v !== null && v !== NaN), true);
+}
+
+/**
+ * Tests if PeptideSimilaritySpaceViewer works for both the method and the measure chosen.
+ *
+ * @export
+ * @param {DG.DataFrame} table Table.
+ * @param {DG.Column} alignedSequencesColumn Aligned sequences column.
+ * @param {string} method Embedding method.
+ * @param {string} measure Strings similarity measure.
+ * @param {number} cyclesCount Number of embedding iterations.
+ * @param {(DG.TableView | null)} view Viewer to show graphics on.
+ * @param {(string | null)} [activityColumnName] Name of column with activity.
+ */
+export async function _testPeptideSimilaritySpaceViewer(
+  table: DG.DataFrame,
+  alignedSequencesColumn: DG.Column,
+  method: string,
+  measure: string,
+  cyclesCount: number,
+  //view: DG.TableView | null,
+  //activityColumnName?: string | null,
+) {
+  const viewer = await createPeptideSimilaritySpaceViewer(
+    table,
+    alignedSequencesColumn,
+    method,
+    measure,
+    cyclesCount,
+    null, //    view,
+    //    activityColumnName,
+  );
+  const df = viewer.dataFrame;
+  let noException = true;
+
+  try {
+    const axesNames = ['~X', '~Y', '~MW'];
+    const axes = axesNames.map((v) => df?.getCol(v).getRawData() as Float32Array);
+
+    for (const ax of axes) {
+      expect(ax.every((v) => v !== null && v !== NaN), true);
+    }
+  } catch (error) {
+    noException = false;
+  }
+  expect(noException, true);
+}

package/src/utils/chem-palette.ts

@@ -56,7 +56,7 @@ export class ChemPalette {
   /**
    * Get color for the provided amino acid residue.
    * @param {string} c Amino acid residue string.
-   * @returns {string} Color.
+   * @return {string} Color.
    */
   getColor(c: string): string {
     const [color] = this.getColorPivot(c);
@@ -66,7 +66,7 @@ export class ChemPalette {
   /**
    * Get color for the provided amino acid residue pivot
    * @param {string} [c=''] Amino acid residue string.
-   * @returns {[string, string, number]}
+   * @return {[string, string, number]}
    */
   getColorAAPivot(c: string = ''): [string, string, number] {
     if (c.length == 1 || c[1] == '(') {

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

@@ -0,0 +1,89 @@
+import * as DG from 'datagrok-api/dg';
+
+//@ts-ignore
+import Aioli from '@biowasm/aioli';
+
+import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
+//@ts-ignore
+import {SEMTYPE} from '../semantics';
+
+/**
+ * Converts array of sequences into simple fasta string.
+ *
+ * @param {string[]} sequences Input list of sequences.
+ * @return {string} Fasta-formatted string.
+ */
+function _stringsToFasta(sequences: string[]): string {
+  return sequences.reduce((a, v, i) => a + `>sample${i + 1}\n${v}\n`, '');
+}
+
+/**
+ * Extracts array of sequences from simple fasta string.
+ *
+ * @param {string} fasta Fasta-formatted string.
+ * @return {string[]} Output list of sequences.
+ */
+function _fastaToStrings(fasta: string): string[] {
+  return fasta.replace(/>sample\d+(\r\n|\r|\n)/g, '').split('\n');
+}
+
+/**
+ * Converts aligned sequence to semantic type format.
+ *
+ * @param {string} seq Source sequence.
+ * @return {string} Formatted sequence.
+ */
+function _castAligned(seq: string): string {
+  let delimited = '';
+
+  for (let i = 0; i < seq.length; ++i) {
+    const char = seq[i];
+    delimited += char == '-' ? char : `-${char}`;
+  }
+  return `NH2${delimited}-COOH`;
+}
+
+/**
+ * Formats a batch of sequences to correspond the semantic type.
+ *
+ * @param {string[]} alignment List of aligned sequences.
+ * @return {string[]} Formatted sequences.
+ */
+function _stringsToAligned(alignment: string[]): string[] {
+  const nItems = alignment.length;
+  const aligned = new Array<string>(nItems);
+
+  for (let i = 0; i < nItems; ++i) {
+    aligned[i] = _castAligned(alignment[i]);
+  }
+  return aligned;
+}
+
+/**
+ * Runs Aioli environment with kalign tool.
+ *
+ * @param {DG.Column} col Column with sequences.
+ * @param {boolean} isAligned Whether the column is aligned.
+ * @return {Promise<DG.Column>} Aligned sequences.
+ */
+export async function runKalign(col: DG.Column, isAligned = false) : Promise<DG.Column> {
+  let sequences = col.toList();
+
+  if (isAligned) {
+    sequences = sequences.map((v: string, _) => AlignedSequenceEncoder.clean(v).replace(/\-/g, ''));
+  }
+
+  const fasta = _stringsToFasta(sequences);
+
+  const CLI = await new Aioli('kalign/3.3.1');
+  await CLI.fs.writeFile('input.fa', fasta);
+  const output = await CLI.exec(`kalign input.fa -f fasta -o result.fasta`);
+  const buf = await CLI.cat('result.fasta');
+
+  console.warn(output);
+
+  const aligned = _fastaToStrings(buf).slice(0, sequences.length);
+  const alignedCol = DG.Column.fromStrings(`(${col.name})msa`, _stringsToAligned(aligned));
+  alignedCol.semType = SEMTYPE.ALIGNED;
+  return alignedCol;
+}

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.
  *
@@ -53,6 +27,17 @@ function inferActivityColumnsName(table: DG.DataFrame): string | null {
   return null;
 }
 
+/**
+ * Cast an aligned sequences column to clean sequences.
+ *
+ * @export
+ * @param {DG.Column} col Column to process.
+ * @return {Array<string>} Clean sequences array.
+ */
+export function cleanAlignedSequencesColumn(col: DG.Column): Array<string> {
+  return col.toList().map((v, _) => AlignedSequenceEncoder.clean(v));
+}
+
 /**
  * Creates scatter plot with sequences embeded.
  *
@@ -75,7 +60,6 @@ export async function createPeptideSimilaritySpaceViewer(
   cyclesCount: number,
   view: DG.TableView | null,
   activityColumnName?: string | null,
-  zoom: boolean = false,
 ): Promise<DG.ScatterPlotViewer> {
   const pi = DG.TaskBarProgressIndicator.create('Creating embedding.');
 
@@ -157,7 +141,7 @@ 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;
@@ -181,7 +165,6 @@ export class PeptideSimilaritySpaceWidget {
       this.cycles,
       null,
       null,
-      true,
     );
     viewer.root.style.width = 'auto';
     return viewer;