@datagrok/bio 2.0.17 → 2.0.19

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.0.17",
+  "version": "2.0.19",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^4.4.7",
+    "@datagrok-libraries/bio": "^5.0.0",
     "@datagrok-libraries/chem-meta": "1.0.1",
     "@datagrok-libraries/ml": "^6.2.0",
     "@datagrok-libraries/utils": "^1.10.1",
@@ -23,7 +23,7 @@
     "@luma.gl/constants": "^8.5.10",
     "@luma.gl/core": "^8.5.10",
     "@phylocanvas/phylocanvas.gl": "^1.44.0",
-    "cash-dom": "latest",
+    "cash-dom": "^8.0.0",
     "datagrok-api": "^1.7.0",
     "dayjs": "^1.11.4",
     "openchemlib": "6.0.1",
@@ -36,9 +36,9 @@
     "@types/node": "^17.0.24",
     "@types/node-fetch": "^2.6.2",
     "@types/wu": "latest",
-    "@typescript-eslint/eslint-plugin": "latest",
-    "@typescript-eslint/parser": "latest",
-    "eslint": "latest",
+    "@typescript-eslint/eslint-plugin": "^4.20.0",
+    "@typescript-eslint/parser": "^4.20.0",
+    "eslint": "^7.23.0",
     "eslint-config-google": "latest",
     "jest": "^27.5.1",
     "jest-html-reporter": "^3.6.0",
@@ -47,9 +47,9 @@
     "puppeteer": "^13.7.0",
     "ts-jest": "^27.0.0",
     "ts-loader": "^9.2.5",
-    "typescript": "^4.5.4",
-    "webpack": "latest",
-    "webpack-cli": "^4.10.0"
+    "typescript": "^4.2.3",
+    "webpack": "^5.64.1",
+    "webpack-cli": "^4.6.0"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",

package/src/analysis/sequence-activity-cliffs.ts

@@ -1,12 +1,12 @@
-import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
-import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
+import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import * as grok from 'datagrok-api/grok';
-import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {SEM_TYPES, TAGS} from '../utils/constants';
+import {TAGS} from '../utils/constants';
 import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
@@ -14,7 +14,7 @@ export async function getDistances(col: DG.Column, seq: string): Promise<Array<n
   const distances = new Array(stringArray.length).fill(0);
   for (let i = 0; i < stringArray.length; ++i) {
     const distance = stringArray[i] ? AvailableMetrics['String']['Levenshtein'](stringArray[i], seq) : null;
-    distances[i] = distance ? distance/Math.max((stringArray[i] as string).length, seq.length) : null;
+    distances[i] = distance ? distance / Math.max((stringArray[i] as string).length, seq.length) : null;
   }
   return distances;
 }
@@ -61,7 +61,7 @@ export function createTooltipElement(params: ITooltipAndPanelParams): HTMLDivEle
 }
 
 function moleculeInfo(df: DG.DataFrame, idx: number, seqColName: string): HTMLElement {
-  const dict: {[key: string]: string} = {};
+  const dict: { [key: string]: string } = {};
   for (const col of df.columns) {
     if (col.name !== seqColName)
       dict[col.name] = df.get(col.name, idx);
@@ -82,10 +82,10 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
     activitiesArray[idx] = params.activityCol.get(molIdx);
   });
 
-  const molDifferences: {[key: number]: HTMLCanvasElement} = {};
+  const molDifferences: { [key: number]: HTMLCanvasElement } = {};
   const units = params.seqCol.getTag(DG.TAGS.UNITS);
   const separator = params.seqCol.getTag(TAGS.SEPARATOR);
-  const splitter = WebLogo.getSplitter(units, separator);
+  const splitter = bio.getSplitter(units, separator);
   const subParts1 = splitter(sequencesArray[0]);
   const subParts2 = splitter(sequencesArray[1]);
   const canvas = createDifferenceCanvas(subParts1, subParts2, units, molDifferences);

package/src/analysis/sequence-similarity-viewer.ts

@@ -1,14 +1,15 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
 import {SequenceSearchBaseViewer} from './sequence-search-base-viewer';
 import {getMonomericMols} from '../calculations/monomerLevelMols';
 import * as C from '../utils/constants';
 import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
 import {updateDivInnerHTML} from '../utils/ui-utils';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {TableView} from 'datagrok-api/dg';
-import { Subject } from 'rxjs';
+import {Subject} from 'rxjs';
 
 export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   hotSearch: boolean;
@@ -84,7 +85,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     const molDifferences: { [key: number]: HTMLCanvasElement } = {};
     const units = resDf.col('sequence')!.getTag(DG.TAGS.UNITS);
     const separator = resDf.col('sequence')!.getTag(C.TAGS.SEPARATOR);
-    const splitter = WebLogo.getSplitter(units, separator);
+    const splitter = bio.getSplitter(units, separator);
     const subParts1 = splitter(this.moleculeColumn!.get(this.targetMoleculeIdx));
     const subParts2 = splitter(resDf.get('sequence', resDf.currentRowIdx));
     const canvas = createDifferenceCanvas(subParts1, subParts2, units, molDifferences);

package/src/calculations/monomerLevelMols.ts

@@ -1,19 +1,21 @@
 import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
 import * as C from '../utils/constants';
 import {getHelmMonomers} from '../package';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 
 const V2000_ATOM_NAME_POS = 31;
 
 export async function getMonomericMols(mcol: DG.Column, pattern: boolean = false): Promise<DG.Column> {
   const separator: string = mcol.tags[C.TAGS.SEPARATOR];
   const units: string = mcol.tags[DG.TAGS.UNITS];
-  const splitter = WebLogo.getSplitter(units, separator);
+  const splitter = bio.getSplitter(units, separator);
   let molV3000Array;
   const monomersDict = new Map();
   const monomers = units === 'helm' ?
-    getHelmMonomers(mcol) : Object.keys(WebLogo.getStats(mcol, 0, splitter).freq).filter((it) => it !== '');
+    getHelmMonomers(mcol) : Object.keys(bio.getStats(mcol, 0, splitter).freq).filter((it) => it !== '');
 
   for (let i = 0; i < monomers.length; i++)
     monomersDict.set(monomers[i], `${i + 1}`);

package/src/package.ts

@@ -2,18 +2,15 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
 export const _package = new DG.Package();
 
 import {MacromoleculeDifferenceCellRenderer, MonomerCellRenderer} from './utils/cell-renderer';
-import {WebLogo, SeqColStats} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {VdRegionsViewer} from './viewers/vd-regions-viewer';
 import {runKalign, testMSAEnoughMemory} from './utils/multiple-sequence-alignment';
 import {SequenceAlignment, Aligned} from './seq_align';
-import {Nucleotides} from '@datagrok-libraries/bio/src/nucleotides';
-import {Aminoacids} from '@datagrok-libraries/bio/src/aminoacids';
 import {getEmbeddingColsNames, sequenceSpace} from './analysis/sequence-space';
-import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {createPropPanelElement, createTooltipElement, getSimilaritiesMarix} from './analysis/sequence-activity-cliffs';
 import {createJsonMonomerLibFromSdf, encodeMonomers, getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
@@ -21,8 +18,6 @@ import {getMacroMol} from './utils/atomic-works';
 import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
 import {convert} from './utils/convert';
 import {getMacroMolColumnPropertyPanel, representationsWidget} from './widgets/representations';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
 import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-utils';
 import {
   generateManySequences,
@@ -36,6 +31,7 @@ import {SequenceSimilarityViewer} from './analysis/sequence-similarity-viewer';
 import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
 import {substructureSearchDialog} from './substructure-search/substructure-search';
 import {saveAsFastaUI} from './utils/save-as-fasta';
+import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
 
 //tags: init
 export async function initBio() {
@@ -92,7 +88,7 @@ export function checkInputColumn(
   let res: boolean = true;
   let msg: string = '';
 
-  const uh = new UnitsHandler(col);
+  const uh = new bio.UnitsHandler(col);
   if (col.semType !== DG.SEMTYPE.MACROMOLECULE) {
     grok.shell.warning(name + ' analysis is allowed for Macromolecules semantic type');
     res = false;
@@ -142,7 +138,7 @@ export function sequenceAlignment(alignType: string, alignTable: string, gap: nu
 //tags: viewer, panel
 //output: viewer result
 export function webLogoViewer() {
-  return new WebLogo();
+  return new bio.WebLogo();
 }
 
 //name: VdRegions
@@ -308,7 +304,7 @@ export async function compositionAnalysis(): Promise<void> {
     if (col.semType != DG.SEMTYPE.MACROMOLECULE)
       return false;
 
-    const colUH = new UnitsHandler(col);
+    const colUH = new bio.UnitsHandler(col);
     // TODO: prevent for cyclic, branched or multiple chains in Helm
     return true;
   });
@@ -327,7 +323,7 @@ export async function compositionAnalysis(): Promise<void> {
     return;
   } else if (colList.length > 1) {
     const colListNames: string [] = colList.map((col) => col.name);
-    const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
+    const selectedCol = colList.find((c) => { return (new bio.UnitsHandler(c)).isMsa(); });
     const colInput: DG.InputBase = ui.choiceInput(
       'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
     ui.dialog({
@@ -379,7 +375,7 @@ export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget
 //input: string fileContent
 //output: list tables
 export function importFasta(fileContent: string): DG.DataFrame [] {
-  const ffh = new FastaFileHandler(fileContent);
+  const ffh = new bio.FastaFileHandler(fileContent);
   return ffh.importFasta();
 }
 
@@ -454,7 +450,7 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
 //tags: panel, bio
 //input: column col {semType: Macromolecule}
 export function splitToMonomers(col: DG.Column<string>): void {
-  if (!col.getTag(UnitsHandler.TAGS.aligned).includes(C.MSA))
+  if (!col.getTag(bio.UnitsHandler.TAGS.aligned).includes(C.MSA))
     return grok.shell.error('Splitting is applicable only for aligned sequences');
 
   const tempDf = splitAlignedSequences(col);
@@ -471,7 +467,7 @@ export function splitToMonomers(col: DG.Column<string>): void {
 //name: Bio: getHelmMonomers
 //input: column col {semType: Macromolecule}
 export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
-  const stats = WebLogo.getStats(seqCol, 1, WebLogo.splitterAsHelm);
+  const stats = bio.getStats(seqCol, 1, bio.splitterAsHelm);
   return Object.keys(stats.freq);
 }
 
@@ -522,4 +518,14 @@ export function bioSubstructureSearch(col: DG.Column): void {
 //tags: fileExporter
 export function saveAsFasta() {
   saveAsFastaUI();
-}
+}
+//name: BioSubstructureFilter
+//description: Substructure filter for linear macromolecules
+//tags: filter
+//output: filter result
+//meta.semType: Macromolecule
+export function bioSubstructureFilter(): BioSubstructureFilter {
+  return new BioSubstructureFilter();
+}
+
+

package/src/substructure-search/substructure-search.ts

@@ -3,6 +3,9 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/units-handler';
 import * as C from '../utils/constants';
+import {getMonomericMols} from '../calculations/monomerLevelMols';
+import {BitSet} from 'datagrok-api/dg';
+import {updateDivInnerHTML} from '../utils/ui-utils';
 
 /**
  * Searches substructure in each row of Macromolecule column
@@ -12,48 +15,58 @@ import * as C from '../utils/constants';
 export function substructureSearchDialog(col: DG.Column): void {
   const units = col.getTag(DG.TAGS.UNITS);
   const separator = col.getTag(C.TAGS.SEPARATOR);
-  const notations = [NOTATION.FASTA, NOTATION.SEPARATOR];
+  // const notations = [NOTATION.FASTA, NOTATION.SEPARATOR, NOTATION.HELM];
 
   const substructureInput = ui.textInput('Substructure', '');
-  const notationInput = ui.choiceInput('Notation', units, notations);
+
+  const editHelmLink = ui.link('Edit helm', async () => {
+    updateDivInnerHTML(inputsDiv, grid.root);
+    await ui.tools.waitForElementInDom(grid.root);
+    setTimeout(() => {
+      grid.cell('substr_helm', 0).element.children[0].dispatchEvent(new KeyboardEvent('keydown', {key: 'Enter'}));
+    }, 100);
+  });
+
+  const df = DG.DataFrame.create(1);
+  df.columns.addNewString('substr_helm').init((i) => '');
+  df.col('substr_helm')!.semType = col.semType;
+  df.col('substr_helm')!.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+  const grid = df.plot.grid();
   const separatorInput = ui.textInput('Separator', separator);
 
-  // hide the separator input for non-SEPARATOR target notations
-  const toggleSeparator = () => {
-    if (notationInput.value !== NOTATION.SEPARATOR)
-      separatorInput.root.hidden = true;
-    else
-      separatorInput.root.hidden = false;
-  };
+  const inputsDiv = ui.div();
 
-  toggleSeparator();
+  const inputs = units === NOTATION.HELM ? ui.divV([editHelmLink]) :
+    units === NOTATION.SEPARATOR ? ui.inputs([substructureInput, separatorInput]) :
+      ui.inputs([substructureInput]);
 
-  notationInput.onChanged(() => {
-    toggleSeparator();
-  });
+  updateDivInnerHTML(inputsDiv, inputs);
 
   ui.dialog('Substructure search')
-    .add(ui.inputs([
-      substructureInput,
-      notationInput,
-      separatorInput
+    .add(ui.divV([
+      ui.divText(`Notation: ${units}`),
+      inputsDiv
     ]))
-    .onOK(() => {
-      let substructure = substructureInput.value;
-      if (notationInput.value !== NOTATION.FASTA && separatorInput.value !== separator)
+    .onOK(async () => {
+      let substructure = units === NOTATION.HELM ? df.get('substr_helm', 0) : substructureInput.value;
+      if (units === NOTATION.SEPARATOR && separatorInput.value !== separator && separatorInput.value !== '')
         substructure = substructure.replaceAll(separatorInput.value, separator);
       const matchesColName = `Matches: ${substructure}`;
       const colExists = col.dataFrame.columns.names()
         .filter((it) => it.toLocaleLowerCase() === matchesColName.toLocaleLowerCase()).length > 0;
       if (!colExists) {
-        const matches = substructureSearch(substructure, col);
+        let matches: BitSet;
+        if (units === NOTATION.HELM)
+          matches = await helmSubstructureSearch(substructure, col);
+        else
+          matches = linearSubstructureSearch(substructure, col);
         col.dataFrame.columns.add(DG.Column.fromBitSet(matchesColName, matches));
       } else { grok.shell.warning(`Search ${substructure} is already performed`); }
     })
     .show();
 }
 
-export function substructureSearch(substructure: string, col: DG.Column): DG.BitSet {
+export function linearSubstructureSearch(substructure: string, col: DG.Column): DG.BitSet {
   const lowerCaseSubstr = substructure.toLowerCase();
   const resultArray = DG.BitSet.create(col.length);
   for (let i = 0; i < col.length; i++) {
@@ -63,3 +76,19 @@ export function substructureSearch(substructure: string, col: DG.Column): DG.Bit
   }
   return resultArray;
 }
+
+async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<BitSet> {
+  const helmColWithSubstructure = DG.Column.string('helm', col.length + 1)
+    .init((i) => i === col.length ? substructure : col.get(i));
+  helmColWithSubstructure.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+  const monomericMolsCol = await getMonomericMols(helmColWithSubstructure, true);
+  const molSubstructure = monomericMolsCol.get(col.length);
+  const monomericMolsDf = DG.DataFrame.fromColumns([monomericMolsCol]);
+  monomericMolsDf.rows.removeAt(col.length);
+  const matchesCol = await grok.functions.call('Chem:searchSubstructure', {
+    molStringsColumn: monomericMolsDf.columns.byIndex(0),
+    molString: molSubstructure,
+    molBlockFailover: '',
+  });
+  return matchesCol.get(0);
+}

package/src/tests/WebLogo-positions-test.ts

@@ -1,9 +1,9 @@
-import {after, before, category, test, expect, expectObject, delay} from '@datagrok-libraries/utils/src/test';
-
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import {PositionInfo, PositionMonomerInfo, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import * as bio from '@datagrok-libraries/bio';
+
+import {after, before, category, test, expect, expectObject, delay} from '@datagrok-libraries/utils/src/test';
 import {Column} from 'datagrok-api/dg';
 import {ALPHABET, NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
@@ -41,27 +41,27 @@ ATC-G-TTGC--
     seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
     seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
 
-    const wlViewer: WebLogo = (await df.plot.fromType('WebLogo')) as WebLogo;
+    const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo')) as bio.WebLogo;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    const positions: PositionInfo[] = wlViewer['positions'];
-
-    const resAllDf1: PositionInfo[] = [
-      new PositionInfo('1', {'A': new PositionMonomerInfo(2), '-': new PositionMonomerInfo(3)}),
-      new PositionInfo('2', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('3', {'C': new PositionMonomerInfo(5)}),
-      new PositionInfo('4', {'-': new PositionMonomerInfo(5)}),
-      new PositionInfo('5', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('6', {'-': new PositionMonomerInfo(3), 'C': new PositionMonomerInfo(2)}),
-      new PositionInfo('7', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('8', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('9', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('10', {'C': new PositionMonomerInfo(5)}),
-      new PositionInfo('11', {'-': new PositionMonomerInfo(5)}),
-      new PositionInfo('12', {'-': new PositionMonomerInfo(5)})
+    const positions: bio.PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: bio.PositionInfo[] = [
+      new bio.PositionInfo('1', {'A': new bio.PositionMonomerInfo(2), '-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('2', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('3', {'C': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('4', {'-': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('5', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('6', {'-': new bio.PositionMonomerInfo(3), 'C': new bio.PositionMonomerInfo(2)}),
+      new bio.PositionInfo('7', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('8', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('9', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('10', {'C': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('11', {'-': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('12', {'-': new bio.PositionMonomerInfo(5)}),
     ];
 
     expect(positions.length, resAllDf1.length);
@@ -94,25 +94,25 @@ ATC-G-TTGC--
       return i > 2;
     });
     df.filter.fireChanged();
-    const wlViewer: WebLogo = (await df.plot.fromType('WebLogo',
-      {'shrinkEmptyTail': true})) as WebLogo;
+    const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo',
+      {'shrinkEmptyTail': true})) as bio.WebLogo;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    const positions: PositionInfo[] = wlViewer['positions'];
-
-    const resAllDf1: PositionInfo[] = [
-      new PositionInfo('1', {'-': new PositionMonomerInfo(3)}),
-      new PositionInfo('2', {'T': new PositionMonomerInfo(3)}),
-      new PositionInfo('3', {'-': new PositionMonomerInfo(3)}),
-      new PositionInfo('4', {'-': new PositionMonomerInfo(3)}),
-      new PositionInfo('5', {'C': new PositionMonomerInfo(3)}),
-      new PositionInfo('6', {'-': new PositionMonomerInfo(2), 'C': new PositionMonomerInfo(1)}),
-      new PositionInfo('7', {'G': new PositionMonomerInfo(3)}),
-      new PositionInfo('8', {'T': new PositionMonomerInfo(3)}),
-      new PositionInfo('9', {'-': new PositionMonomerInfo(3)}),
+    const positions: bio.PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: bio.PositionInfo[] = [
+      new bio.PositionInfo('1', {'-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('2', {'T': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('3', {'-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('4', {'-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('5', {'C': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('6', {'-': new bio.PositionMonomerInfo(2), 'C': new bio.PositionMonomerInfo(1)}),
+      new bio.PositionInfo('7', {'G': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('8', {'T': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('9', {'-': new bio.PositionMonomerInfo(3)}),
     ];
 
     expect(positions.length, resAllDf1.length);
@@ -134,25 +134,25 @@ ATC-G-TTGC--
     seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
     seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
 
-    const wlViewer: WebLogo = (await df.plot.fromType('WebLogo',
-      {'skipEmptyPositions': true})) as WebLogo;
+    const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo',
+      {'skipEmptyPositions': true})) as bio.WebLogo;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    const positions: PositionInfo[] = wlViewer['positions'];
-
-    const resAllDf1: PositionInfo[] = [
-      new PositionInfo('1', {'A': new PositionMonomerInfo(2), '-': new PositionMonomerInfo(3)}),
-      new PositionInfo('2', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('3', {'C': new PositionMonomerInfo(5)}),
-      new PositionInfo('5', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('6', {'-': new PositionMonomerInfo(3), 'C': new PositionMonomerInfo(2)}),
-      new PositionInfo('7', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('8', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('9', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('10', {'C': new PositionMonomerInfo(5)})
+    const positions: bio.PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: bio.PositionInfo[] = [
+      new bio.PositionInfo('1', {'A': new bio.PositionMonomerInfo(2), '-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('2', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('3', {'C': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('5', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('6', {'-': new bio.PositionMonomerInfo(3), 'C': new bio.PositionMonomerInfo(2)}),
+      new bio.PositionInfo('7', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('8', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('9', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('10', {'C': new bio.PositionMonomerInfo(5)})
     ];
 
     expect(positions.length, resAllDf1.length);

package/src/tests/WebLogo-test.ts

@@ -1,9 +1,9 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
-
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
 import {Nucleotides, NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
 import {Aminoacids, AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
 import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
@@ -63,19 +63,19 @@ XZJ{}2
 
 category('WebLogo.monomerToShort', () => {
   test('longMonomerSingle', async () => {
-    await expect(WebLogo.monomerToShort('S', 5), 'S');
+    await expect(bio.monomerToShort('S', 5), 'S');
   });
   test('longMonomerShort', async () => {
-    await expect(WebLogo.monomerToShort('Short', 5), 'Short');
+    await expect(bio.monomerToShort('Short', 5), 'Short');
   });
   test('longMonomerLong56', async () => {
-    await expect(WebLogo.monomerToShort('Long56', 5), 'Long5…');
+    await expect(bio.monomerToShort('Long56', 5), 'Long5…');
   });
   test('longMonomerComplexFirstPartShort', async () => {
-    await expect(WebLogo.monomerToShort('Long-long', 5), 'Long…');
+    await expect(bio.monomerToShort('Long-long', 5), 'Long…');
   });
   test('longMonomerComplexFirstPartLong56', async () => {
-    await expect(WebLogo.monomerToShort('Long56-long', 5), 'Long5…');
+    await expect(bio.monomerToShort('Long56-long', 5), 'Long5…');
   });
 });
 
@@ -83,7 +83,7 @@ category('WebLogo.monomerToShort', () => {
 export async function _testGetStats(csvDfN1: string) {
   const dfN1: DG.DataFrame = DG.DataFrame.fromCsv(csvDfN1);
   const seqCol: DG.Column = dfN1.col('seq')!;
-  const stats = WebLogo.getStats(seqCol, 5, WebLogo.splitterAsFasta);
+  const stats = bio.getStats(seqCol, 5, bio.splitterAsFasta);
 
   expectObject(stats.freq, {
     'A': 4,
@@ -103,7 +103,7 @@ export async function _testGetAlphabetSimilarity() {
     '-': 1000
   };
   const alphabet: Set<string> = new Set(Object.keys(Nucleotides.Names));
-  const res = WebLogo.getAlphabetSimilarity(freq, alphabet);
+  const res = bio.getAlphabetSimilarity(freq, alphabet);
 
   expect(res > 0.6, true);
 }
@@ -111,7 +111,7 @@ export async function _testGetAlphabetSimilarity() {
 export async function _testPickupPaletteN1(csvDfN1: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfN1);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof NucleotidesPalettes, true);
 }
@@ -119,7 +119,7 @@ export async function _testPickupPaletteN1(csvDfN1: string) {
 export async function _testPickupPaletteN1e(csvDfN1e: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfN1e);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof NucleotidesPalettes, true);
 }
@@ -127,7 +127,7 @@ export async function _testPickupPaletteN1e(csvDfN1e: string) {
 export async function _testPickupPaletteAA1(csvDfAA1: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfAA1);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof AminoacidsPalettes, true);
 }
@@ -135,14 +135,14 @@ export async function _testPickupPaletteAA1(csvDfAA1: string) {
 export async function _testPickupPaletteX(csvDfX: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfX);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof UnknownSeqPalette, true);
 }
 
 export async function _testPickupPaletteAA2(dfAA2: DG.DataFrame) {
   const seqCol: DG.Column = dfAA2.col('seq')!;
-  const cp = WebLogo.pickUpPalette(seqCol);
+  const cp = bio.pickUpPalette(seqCol);
 
   expect(cp instanceof AminoacidsPalettes, true);
 }

package/src/tests/fasta-export-tests.ts

@@ -1,10 +1,10 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
+import * as bio from '@datagrok-libraries/bio';
 
 import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
 import {saveAsFastaDo, wrapSequence} from '../utils/save-as-fasta';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 
 type SaveAsFastaTestArgs = { srcCsv: string, idCols: string [], seqCol: string, lineWidth: number, tgtFasta: string };
 
@@ -88,7 +88,7 @@ MRGGL
   });
 
   function _testWrapSequence(testKey: string, lineWidth: number = 10) {
-    const splitter = WebLogo.splitterAsFasta;
+    const splitter = bio.splitterAsFasta;
 
     const srcSeq: string = wrapData[testKey].src;
     const wrapRes: string[] = wrapSequence(srcSeq, splitter, lineWidth);