@datagrok/bio 2.1.11 → 2.1.12

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.1.11",
+  "version": "2.1.12",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -14,19 +14,18 @@
   },
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.10.0",
+    "@datagrok-libraries/bio": "^5.16.0",
     "@datagrok-libraries/chem-meta": "^1.0.1",
-    "@datagrok-libraries/ml": "^6.2.2",
-    "@datagrok-libraries/utils": "^1.15.5",
+    "@datagrok-libraries/ml": "^6.3.3",
+    "@datagrok-libraries/utils": "^1.19.4",
     "cash-dom": "^8.0.0",
-    "datagrok-api": "^1.8.2",
+    "datagrok-api": "^1.11.1",
     "dayjs": "^1.11.4",
     "openchemlib": "6.0.1",
     "rxjs": "^6.5.5",
     "wu": "latest"
   },
   "devDependencies": {
-    "@types/jest": "^27.5.1",
     "@types/js-yaml": "^4.0.5",
     "@types/node": "^17.0.24",
     "@types/node-fetch": "^2.6.2",
@@ -35,15 +34,13 @@
     "@typescript-eslint/parser": "^4.20.0",
     "eslint": "^7.23.0",
     "eslint-config-google": "latest",
-    "jest": "^27.5.1",
-    "jest-html-reporter": "^3.6.0",
     "js-yaml": "^4.1.0",
     "node-fetch": "^2.6.7",
     "puppeteer": "^13.7.0",
-    "ts-jest": "^27.0.0",
     "ts-loader": "^9.2.5",
     "typescript": "^4.2.3",
     "webpack": "^5.64.1",
+    "webpack-bundle-analyzer": "latest",
     "webpack-cli": "^4.6.0"
   },
   "grokDependencies": {
@@ -68,9 +65,10 @@
     "release-sequences1-local": "grok publish local --release",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix",
-    "test": "jest",
-    "test-local": "set HOST=localhost && jest",
-    "build-bio-local": "npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build && npm --prefix ./../../libraries/bio run build && npm run build"
+    "test": "grok test",
+    "test-local": "grok test --host localhost",
+    "build-bio-local": "npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build && npm --prefix ./../../libraries/bio run build && npm run build",
+    "analyze": "webpack --profile --json > ./stats.json && npx webpack-bundle-analyzer ./stats.json"
   },
   "canEdit": [
     "Developers"

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

@@ -1,16 +1,16 @@
 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 {getSimilarityFromDistance} from '@datagrok-libraries/ml/src/distance-metrics-methods';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {TAGS} from '../utils/constants';
 import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
 import * as C from '../utils/constants';
-import { GridColumn } from 'datagrok-api/dg';
-import { invalidateMols, MONOMERIC_COL_TAGS } from '../substructure-search/substructure-search';
+import {GridColumn} from 'datagrok-api/dg';
+import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
+import {getSplitter} from '@datagrok-libraries/bio';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
   const stringArray = col.toList();
@@ -105,7 +105,7 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
   const molDifferences: { [key: number]: HTMLCanvasElement } = {};
   const units = params.seqCol.getTag(DG.TAGS.UNITS);
   const separator = params.seqCol.getTag(TAGS.SEPARATOR);
-  const splitter = bio.getSplitter(units, separator);
+  const splitter = getSplitter(units, separator);
   const subParts1 = splitter(sequencesArray[0]);
   const subParts2 = splitter(sequencesArray[1]);
   const canvas = createDifferenceCanvas(subParts1, subParts2, units, molDifferences);

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

@@ -1,14 +1,15 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+
 import BitArray from '@datagrok-libraries/utils/src/bit-array';
-import {similarityMetric, getDiverseSubset} from '@datagrok-libraries/utils/src/similarity-metrics';
+import {getDiverseSubset} from '@datagrok-libraries/utils/src/similarity-metrics';
 import $ from 'cash-dom';
 import {ArrayUtils} from '@datagrok-libraries/utils/src/array-utils';
 import {SequenceSearchBaseViewer} from './sequence-search-base-viewer';
 import {getMonomericMols} from '../calculations/monomerLevelMols';
 import {updateDivInnerHTML} from '../utils/ui-utils';
-import { Subject } from 'rxjs';
+import {Subject} from 'rxjs';
 
 export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   renderMolIds: number[] | null = null;

package/src/analysis/sequence-search-base-viewer.ts

@@ -1,7 +1,8 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
-import {CHEM_SIMILARITY_METRICS} from '@datagrok-libraries/utils/src/similarity-metrics';
+
+import {CHEM_SIMILARITY_METRICS} from '@datagrok-libraries/ml/src/distance-metrics-methods';
 import * as C from '../utils/constants';
 
 export class SequenceSearchBaseViewer extends DG.JsViewer {

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

@@ -1,7 +1,6 @@
 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';
@@ -9,6 +8,7 @@ import * as C from '../utils/constants';
 import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
+import {getSplitter} from '@datagrok-libraries/bio';
 
 export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   hotSearch: boolean;
@@ -84,7 +84,7 @@ 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 = bio.getSplitter(units, separator);
+    const splitter = 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

@@ -1,10 +1,10 @@
 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 {getSplitter, getStats} from '@datagrok-libraries/bio';
 
 const V2000_ATOM_NAME_POS = 31;
 
@@ -12,11 +12,11 @@ export async function getMonomericMols(mcol: DG.Column,
   pattern: boolean = false, monomersDict?: Map<string, string>): Promise<DG.Column> {
   const separator: string = mcol.tags[C.TAGS.SEPARATOR];
   const units: string = mcol.tags[DG.TAGS.UNITS];
-  const splitter = bio.getSplitter(units, separator);
+  const splitter = getSplitter(units, separator);
   let molV3000Array;
   monomersDict ??= new Map();
   const monomers = units === 'helm' ?
-    getHelmMonomers(mcol) : Object.keys(bio.getStats(mcol, 0, splitter).freq).filter((it) => it !== '');
+    getHelmMonomers(mcol) : Object.keys(getStats(mcol, 0, splitter).freq).filter((it) => it !== '');
 
   for (let i = 0; i < monomers.length; i++) {
     if (!monomersDict.has(monomers[i]))

package/src/package.ts

@@ -43,7 +43,7 @@ import {getMonomericMols} from './calculations/monomerLevelMols';
 import {delay} from '@datagrok-libraries/utils/src/test';
 import {from, Observable, Subject} from 'rxjs';
 import {
-  TAGS as bio_TAGS,
+  TAGS as bioTAGS,
   Monomer, IMonomerLib, MonomerWorks, MonomerLib, readLibrary,
   SeqPalette, UnitsHandler, WebLogoViewer, getStats, splitterAsHelm
 } from '@datagrok-libraries/bio';
@@ -70,13 +70,13 @@ export class SeqPaletteCustom implements SeqPalette {
 //tags: init
 export async function initBio() {
   await loadLibraries();
-  let monomers: string[] = [];
-  let logPs: number[] = [];
+  const monomers: string[] = [];
+  const logPs: number[] = [];
   const module = await grok.functions.call('Chem:getRdKitModule');
 
 
   const series = monomerLib!.getMonomerMolsByType('PEPTIDE')!;
-  Object.keys(series).forEach(symbol => {
+  Object.keys(series).forEach((symbol) => {
     monomers.push(symbol);
     const block = series[symbol].replaceAll('#R', 'O ');
     const mol = module.get_mol(block);
@@ -88,10 +88,9 @@ export async function initBio() {
   const sum = logPs.reduce((a, b) => a + b, 0);
   const avg = (sum / logPs.length) || 0;
 
-  let palette: { [monomer: string]: string } = {};
-  for (let i = 0; i < monomers.length; i++) {
+  const palette: { [monomer: string]: string } = {};
+  for (let i = 0; i < monomers.length; i++)
     palette[monomers[i]] = logPs[i] < avg ? '#4682B4' : '#DC143C';
-  }
 
   hydrophobPalette = new SeqPaletteCustom(palette);
 }
@@ -99,7 +98,7 @@ export async function initBio() {
 async function loadLibraries() {
   //TODO handle if files are in place
 
-  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
+  const uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
   if (uploadedLibraries.length == 0 && monomerLib == null)
     monomerLib = new MonomerLib({});
   for (let i = 0; i < uploadedLibraries.length; ++i)
@@ -111,9 +110,8 @@ async function loadLibraries() {
 export async function monomerManager(value: string) {
   if (monomerLib == null)
     monomerLib = await readLibrary(LIB_PATH, value);
-  else {
+  else
     monomerLib!.update(await readLibrary(LIB_PATH, value));
-  }
 }
 
 //name: getBioLib
@@ -137,20 +135,21 @@ export async function manageFiles() {
 //output: widget result
 export async function libraryPanel(seqColumn: DG.Column): Promise<DG.Widget> {
   //@ts-ignore
-  let filesButton: HTMLButtonElement = ui.button('Manage', manageFiles);
-  let divInputs: HTMLDivElement = ui.div();
-  let librariesList: string[] = (await _package.files.list(`${LIBS_PATH}`, false, '')).map(it => it.fileName);
-  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
+  const filesButton: HTMLButtonElement = ui.button('Manage', manageFiles);
+  const divInputs: HTMLDivElement = ui.div();
+  const librariesList: string[] = (await _package.files.list(`${LIBS_PATH}`, false, ''))
+    .map((it) => it.fileName);
+  const uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
   for (let i = 0; i < uploadedLibraries.length; ++i) {
-    let libraryName: string = uploadedLibraries[i];
+    const libraryName: string = uploadedLibraries[i];
     divInputs.append(ui.boolInput(libraryName, true, async () => {
       grok.dapi.userDataStorage.remove(STORAGE_NAME, libraryName, true);
       await loadLibraries();
     }).root);
   }
-  let unusedLibraries: string[] = librariesList.filter(x => !uploadedLibraries.includes(x));
+  const unusedLibraries: string[] = librariesList.filter((x) => !uploadedLibraries.includes(x));
   for (let i = 0; i < unusedLibraries.length; ++i) {
-    let libraryName: string = unusedLibraries[i];
+    const libraryName: string = unusedLibraries[i];
     divInputs.append(ui.boolInput(libraryName, false, () => {
       monomerManager(libraryName);
       grok.dapi.userDataStorage.postValue(STORAGE_NAME, libraryName, libraryName, true);
@@ -292,9 +291,9 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
   };
   const tags = {
     'units': macroMolecule.getTag(DG.TAGS.UNITS),
-    'aligned': macroMolecule.getTag(bio_TAGS.aligned),
-    'separator': macroMolecule.getTag(bio_TAGS.separator),
-    'alphabet': macroMolecule.getTag(bio_TAGS.alphabet),
+    'aligned': macroMolecule.getTag(bioTAGS.aligned),
+    'separator': macroMolecule.getTag(bioTAGS.separator),
+    'alphabet': macroMolecule.getTag(bioTAGS.alphabet),
   };
   const sp = await getActivityCliffs(
     df,
@@ -326,7 +325,8 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
 //input: bool plotEmbeddings = true
 export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: DG.Column, methodName: string,
   similarityMetric: string = 'Tanimoto', plotEmbeddings: boolean): Promise<DG.Viewer | undefined> {
-  //delay is required for initial function dialog to close before starting invalidating of molfiles. Otherwise dialog is freezing
+  // Delay is required for initial function dialog to close before starting invalidating of molfiles.
+  // Otherwise, dialog is freezing
   await delay(10);
   if (!checkInputColumnUi(macroMolecule, 'Sequence space'))
     return;
@@ -346,14 +346,13 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: D
   for (const col of embeddings) {
     const listValues = col.toList();
     emptyValsIdxs.forEach((ind: number) => listValues.splice(ind, 0, null));
-    table.columns.add(DG.Column.fromList('double', col.name, listValues));
+    table.columns.add(DG.Column.float(col.name, table.rowCount).init((i) => listValues[i]));
   }
   if (plotEmbeddings) {
     return grok.shell
       .tableView(table.name)
       .scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
   }
-  ;
 
   /*   const encodedCol = encodeMonomers(macroMolecule);
   if (!encodedCol)
@@ -406,7 +405,9 @@ export async function toAtomicLevel(df: DG.DataFrame, macroMolecule: DG.Column):
 //input: dataframe table
 //input: column sequence { semType: Macromolecule, units: ['fasta'], alphabet: ['DNA', 'RNA', 'PT'] }
 //output: column result
-export async function multipleSequenceAlignmentAny(table: DG.DataFrame, sequence: DG.Column): Promise<DG.Column | null> {
+export async function multipleSequenceAlignmentAny(
+  table: DG.DataFrame, sequence: DG.Column
+): Promise<DG.Column | null> {
   const func: DG.Func = DG.Func.find({package: 'Bio', name: 'multipleSequenceAlignmentAny'})[0];
 
   if (!checkInputColumnUi(sequence, 'MSA', ['fasta'], ['DNA', 'RNA', 'PT']))

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

@@ -1,12 +1,12 @@
 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 {getMonomericMols} from '../calculations/monomerLevelMols';
 import {updateDivInnerHTML} from '../utils/ui-utils';
-import { delay } from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/utils/src/test';
+import {NOTATION} from '@datagrok-libraries/bio';
 
 export const MONOMER_MOLS_COL = 'monomeric-mols';
 
@@ -39,14 +39,14 @@ export function substructureSearchDialog(col: DG.Column): void {
   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, bio.NOTATION.HELM);
+  df.col('substr_helm')!.setTag(DG.TAGS.UNITS, NOTATION.HELM);
   const grid = df.plot.grid();
   const separatorInput = ui.textInput('Separator', separator);
 
   const inputsDiv = ui.div();
 
-  const inputs = units === bio.NOTATION.HELM ? ui.divV([editHelmLink]) :
-    units === bio.NOTATION.SEPARATOR ? ui.inputs([substructureInput, separatorInput]) :
+  const inputs = units === NOTATION.HELM ? ui.divV([editHelmLink]) :
+    units === NOTATION.SEPARATOR ? ui.inputs([substructureInput, separatorInput]) :
       ui.inputs([substructureInput]);
 
   updateDivInnerHTML(inputsDiv, inputs);
@@ -57,15 +57,15 @@ export function substructureSearchDialog(col: DG.Column): void {
       inputsDiv
     ]))
     .onOK(async () => {
-      let substructure = units === bio.NOTATION.HELM ? df.get('substr_helm', 0) : substructureInput.value;
-      if (units === bio.NOTATION.SEPARATOR && separatorInput.value !== separator && separatorInput.value !== '')
+      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) {
         let matches: DG.BitSet;
-        if (units === bio.NOTATION.HELM)
+        if (units === NOTATION.HELM)
           matches = await helmSubstructureSearch(substructure, col);
         else
           matches = linearSubstructureSearch(substructure, col);
@@ -102,7 +102,7 @@ export async function helmSubstructureSearch(substructure: string, col: DG.Colum
   if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
     await invalidateMols(col, true);
   const substructureCol = DG.Column.string('helm', 1).init((i) => substructure);
-  substructureCol.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
+  substructureCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
   const substructureMolsCol =
     await getMonomericMols(substructureCol, true, col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT]);
   const matchesCol = await grok.functions.call('Chem:searchSubstructure', {

package/src/tests/Palettes-test.ts

@@ -1,26 +1,26 @@
 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 {_testPaletteN, _testPaletteAA} from '@datagrok-libraries/bio/src/tests/palettes-tests';
+import { AminoacidsPalettes } from '@datagrok-libraries/bio';
 
 category('Palettes', () => {
   test('testPaletteN', async () => { await _testPaletteN(); });
   test('testPaletteAA', async () => { await _testPaletteAA(); });
 
   test('testPalettePtMe', async () => {
-    const colorMeNle = bio.AminoacidsPalettes.GrokGroups.get('MeNle');
-    const colorMeA = bio.AminoacidsPalettes.GrokGroups.get('MeA');
-    const colorMeG = bio.AminoacidsPalettes.GrokGroups.get('MeG');
-    const colorMeF = bio.AminoacidsPalettes.GrokGroups.get('MeF');
+    const colorMeNle = AminoacidsPalettes.GrokGroups.get('MeNle');
+    const colorMeA = AminoacidsPalettes.GrokGroups.get('MeA');
+    const colorMeG = AminoacidsPalettes.GrokGroups.get('MeG');
+    const colorMeF = AminoacidsPalettes.GrokGroups.get('MeF');
 
-    const colorL = bio.AminoacidsPalettes.GrokGroups.get('L');
-    const colorA = bio.AminoacidsPalettes.GrokGroups.get('A');
-    const colorG = bio.AminoacidsPalettes.GrokGroups.get('G');
-    const colorF = bio.AminoacidsPalettes.GrokGroups.get('F');
+    const colorL = AminoacidsPalettes.GrokGroups.get('L');
+    const colorA = AminoacidsPalettes.GrokGroups.get('A');
+    const colorG = AminoacidsPalettes.GrokGroups.get('G');
+    const colorF = AminoacidsPalettes.GrokGroups.get('F');
 
     expect(colorMeNle, colorL);
     expect(colorMeA, colorA);

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

@@ -1,9 +1,16 @@
 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, delay} from '@datagrok-libraries/utils/src/test';
+import {
+  ALPHABET,
+  NOTATION,
+  PositionInfo,
+  PositionMonomerInfo,
+  TAGS as bioTAGS,
+  WebLogoViewer
+} from '@datagrok-libraries/bio';
 
 category('WebLogo-positions', () => {
   let tvList: DG.TableView[];
@@ -25,7 +32,7 @@ ATC-G-TTGC--
   });
 
   after(async () => {
-    dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df);});
+    dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
     tvList.forEach((tv: DG.TableView) => tv.close());
     grok.shell.v = currentView;
   });
@@ -36,31 +43,31 @@ ATC-G-TTGC--
 
     const seqCol: DG.Column = df.getCol('seq');
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
-    seqCol.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
-    seqCol.setTag(bio.TAGS.aligned, 'SEQ.MSA');
+    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+    seqCol.setTag(bioTAGS.alphabet, ALPHABET.DNA);
+    seqCol.setTag(bioTAGS.aligned, 'SEQ.MSA');
 
-    const wlViewer: bio.WebLogoViewer = (await df.plot.fromType('WebLogo')) as bio.WebLogoViewer;
+    const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo')) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    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)}),
+    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)}),
     ];
 
     expect(positions.length, resAllDf1.length);
@@ -73,8 +80,8 @@ ATC-G-TTGC--
     }
   });
 
-  test('positions with shrinkEmptyTail option true (filterd)', async () => {
-    let csvDf2 = `seq 
+  test('positions with shrinkEmptyTail option true (filtered)', async () => {
+    const csvDf2 = `seq 
 -TC-G-TTGC--
 -TC-GCTTGC--
 -T--C-GT-
@@ -86,33 +93,33 @@ ATC-G-TTGC--
 
     const seqCol: DG.Column = df.getCol('seq');
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
-    seqCol.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
-    seqCol.setTag(bio.TAGS.aligned, 'SEQ');
+    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+    seqCol.setTag(bioTAGS.alphabet, ALPHABET.DNA);
+    seqCol.setTag(bioTAGS.aligned, 'SEQ');
 
     df.filter.init((i) => {
       return i > 2;
     });
     df.filter.fireChanged();
-    const wlViewer: bio.WebLogoViewer = (await df.plot.fromType('WebLogo',
-      {'shrinkEmptyTail': true})) as bio.WebLogoViewer;
+    const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo',
+      {'shrinkEmptyTail': true})) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    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)}),
+    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)}),
     ];
 
     expect(positions.length, resAllDf1.length);
@@ -131,29 +138,29 @@ ATC-G-TTGC--
 
     const seqCol: DG.Column = df.getCol('seq');
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
-    seqCol.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
-    seqCol.setTag(bio.TAGS.aligned, 'SEQ.MSA');
+    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+    seqCol.setTag(bioTAGS.alphabet, ALPHABET.DNA);
+    seqCol.setTag(bioTAGS.aligned, 'SEQ.MSA');
 
-    const wlViewer: bio.WebLogoViewer = (await df.plot.fromType('WebLogo',
-      {'skipEmptyPositions': true})) as bio.WebLogoViewer;
+    const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo',
+      {'skipEmptyPositions': true})) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    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)})
+    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)})
     ];
 
     expect(positions.length, resAllDf1.length);