@datagrok/bio 2.1.10 → 2.1.12

package/src/tests/renderers-test.ts

@@ -1,6 +1,5 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
 import {after, before, category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
 
@@ -9,6 +8,7 @@ import {convertDo} from '../utils/convert';
 import {SEM_TYPES, TAGS} from '../utils/constants';
 import {generateLongSequence, generateManySequences, performanceTest} from './utils/sequences-generators';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
+import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS, UnitsHandler} from '@datagrok-libraries/bio';
 
 category('renderers', () => {
   let tvList: DG.TableView[];
@@ -103,7 +103,7 @@ category('renderers', () => {
   async function _rendererMacromoleculeDifference() {
     const seqDiffCol: DG.Column = DG.Column.fromStrings('SequencesDiff',
       ['meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca#D-Tyr_Et/Tyr_ab-dehydroMe/meN/E/N/dV']);
-    seqDiffCol.tags[DG.TAGS.UNITS] = bio.NOTATION.SEPARATOR;
+    seqDiffCol.tags[DG.TAGS.UNITS] = NOTATION.SEPARATOR;
     seqDiffCol.tags[TAGS.SEPARATOR] = '/';
     seqDiffCol.semType = SEM_TYPES.MACROMOLECULE_DIFFERENCE;
     const df = DG.DataFrame.fromColumns([seqDiffCol]);
@@ -138,22 +138,22 @@ category('renderers', () => {
       `semType="${srcSeqCol!.semType}", units="${srcSeqCol!.getTag(DG.TAGS.UNITS)}", ` +
       `cell.renderer="${srcSeqCol!.getTag(DG.TAGS.CELL_RENDERER)}"`);
     expect(srcSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
-    expect(srcSeqCol.getTag(DG.TAGS.UNITS), bio.NOTATION.FASTA);
-    expect(srcSeqCol.getTag(bio.TAGS.aligned), bio.ALIGNMENT.SEQ);
-    expect(srcSeqCol.getTag(bio.TAGS.alphabet), bio.ALPHABET.PT);
+    expect(srcSeqCol.getTag(DG.TAGS.UNITS), NOTATION.FASTA);
+    expect(srcSeqCol.getTag(bioTAGS.aligned), ALIGNMENT.SEQ);
+    expect(srcSeqCol.getTag(bioTAGS.alphabet), ALPHABET.PT);
     expect(srcSeqCol.getTag(DG.TAGS.CELL_RENDERER), 'sequence');
 
     const msaSeqCol: DG.Column = (await multipleSequenceAlignmentAny(df, srcSeqCol!))!;
     tv.grid.invalidate();
 
     expect(msaSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
-    expect(msaSeqCol.getTag(DG.TAGS.UNITS), bio.NOTATION.FASTA);
-    expect(msaSeqCol.getTag(bio.TAGS.aligned), bio.ALIGNMENT.SEQ_MSA);
-    expect(msaSeqCol.getTag(bio.TAGS.alphabet), bio.ALPHABET.PT);
+    expect(msaSeqCol.getTag(DG.TAGS.UNITS), NOTATION.FASTA);
+    expect(msaSeqCol.getTag(bioTAGS.aligned), ALIGNMENT.SEQ_MSA);
+    expect(msaSeqCol.getTag(bioTAGS.alphabet), ALPHABET.PT);
     expect(msaSeqCol.getTag(DG.TAGS.CELL_RENDERER), 'sequence');
 
     // check newColumn with UnitsHandler constructor
-    const uh: bio.UnitsHandler = new bio.UnitsHandler(msaSeqCol);
+    const uh: UnitsHandler = new UnitsHandler(msaSeqCol);
 
     dfList.push(df);
     tvList.push(tv);
@@ -175,13 +175,13 @@ category('renderers', () => {
     tvList.push(tv);
     dfList.push(df);
 
-    const tgtCol: DG.Column = await convertDo(srcCol, bio.NOTATION.SEPARATOR, '/');
+    const tgtCol: DG.Column = await convertDo(srcCol, NOTATION.SEPARATOR, '/');
 
     const resCellRenderer = tgtCol.getTag(DG.TAGS.CELL_RENDERER);
     expect(resCellRenderer, 'sequence');
 
     // check tgtCol with UnitsHandler constructor
-    const uh: bio.UnitsHandler = new bio.UnitsHandler(tgtCol);
+    const uh: UnitsHandler = new UnitsHandler(tgtCol);
   }
 
   async function _selectRendererBySemType() {
@@ -190,7 +190,7 @@ category('renderers', () => {
     /**/
     const seqDiffCol: DG.Column = DG.Column.fromStrings('SequencesDiff',
       ['meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca#D-Tyr_Et/Tyr_ab-dehydroMe/meN/E/N/dV']);
-    seqDiffCol.tags[DG.TAGS.UNITS] = bio.NOTATION.SEPARATOR;
+    seqDiffCol.tags[DG.TAGS.UNITS] = NOTATION.SEPARATOR;
     seqDiffCol.tags[TAGS.SEPARATOR] = '/';
     seqDiffCol.semType = SEM_TYPES.MACROMOLECULE_DIFFERENCE;
     const df = DG.DataFrame.fromColumns([seqDiffCol]);
@@ -200,10 +200,11 @@ category('renderers', () => {
 
     await delay(100);
     const renderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
-    if (renderer !== 'MacromoleculeDifference') // this is value of MacromoleculeDifferenceCR.cellType
+    if (renderer !== 'MacromoleculeDifference') { // this is value of MacromoleculeDifferenceCR.cellType
       throw new Error(`Units 'separator', separator '/' and semType 'MacromoleculeDifference' ` +
         `have been manually set on column but after df was added as table, ` +
         `view renderer has set to '${renderer}' instead of correct 'MacromoleculeDifference'.`);
+    }
   }
 
   /** GROK-11212 Do not overwrite / recalculate 'cell.renderer' tag that has been set programmatically
@@ -211,7 +212,7 @@ category('renderers', () => {
   async function _setRendererManually() {
     const seqDiffCol: DG.Column = DG.Column.fromStrings('SequencesDiff',
       ['meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca#D-Tyr_Et/Tyr_ab-dehydroMe/meN/E/N/dV']);
-    seqDiffCol.tags[DG.TAGS.UNITS] = bio.NOTATION.SEPARATOR;
+    seqDiffCol.tags[DG.TAGS.UNITS] = NOTATION.SEPARATOR;
     seqDiffCol.tags[TAGS.SEPARATOR] = '/';
     seqDiffCol.semType = SEM_TYPES.MACROMOLECULE;
     const tgtCellRenderer = 'MacromoleculeDifference';
@@ -224,9 +225,10 @@ category('renderers', () => {
 
     await delay(100);
     const resCellRenderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
-    if (resCellRenderer !== tgtCellRenderer) // this is value of MacromoleculeDifferenceCR.cellType
+    if (resCellRenderer !== tgtCellRenderer) { // this is value of MacromoleculeDifferenceCR.cellType
       throw new Error(`Tag 'cell.renderer' has been manually set to '${tgtCellRenderer}' for column ` +
         `but after df was added as table, tag 'cell.renderer' has reset to '${resCellRenderer}' ` +
         `instead of manual '${tgtCellRenderer}'.`);
+    }
   }
 });

package/src/tests/splitters-test.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 {after, before, category, test, expect, expectArray, expectObject} from '@datagrok-libraries/utils/src/test';
 import * as C from '../utils/constants';
 import {splitToMonomers, _package, getHelmMonomers} from '../package';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
+import {splitterAsFasta, splitterAsHelm} from '@datagrok-libraries/bio';
 
 
 category('splitters', () => {
@@ -122,13 +122,13 @@ PEPTIDE1{hHis.Aca.Cys_SEt}$$$,5.72388
 });
 
 export async function _testFastaSplitter(src: string, tgt: string[]) {
-  const res: string[] = bio.splitterAsFasta(src);
+  const res: string[] = splitterAsFasta(src);
   console.debug(`Bio: tests: splitters: src=${JSON.stringify(src)}, res=${JSON.stringify(res)} .`);
   expectArray(res, tgt);
 }
 
 export async function _testHelmSplitter(src: string, tgt: string[]) {
-  const res: string[] = bio.splitterAsHelm(src);
+  const res: string[] = splitterAsHelm(src);
   console.debug(`Bio: tests: splitters: src=${JSON.stringify(src)}, res=${JSON.stringify(res)} .`);
   expectArray(res, tgt);
 }

package/src/tests/utils/sequences-generators.ts

@@ -1,18 +1,18 @@
 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 {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio';
 
 
 export function generateManySequences(): DG.Column[] {
-  let columns: DG.Column[] = [];
+  const columns: DG.Column[] = [];
   columns.push(DG.Column.fromList('string', 'MSA', new Array(10 ** 6).fill('meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me')));
   columns.push(DG.Column.fromList('string', 'Activity', new Array(10 ** 6).fill('5.30751')));
   return columns;
 }
 
 export function generateLongSequence(): DG.Column[] {
-  let columns: DG.Column[] = [];
+  const columns: DG.Column[] = [];
   const longSequence = `meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr`.repeat(10 ** 5);
   columns.push(DG.Column.fromList('string', 'MSA', new Array(10 ** 2).fill(longSequence)));
   columns.push(DG.Column.fromList('string', 'Activity', new Array(10 ** 2).fill('7.30751')));
@@ -21,10 +21,10 @@ export function generateLongSequence(): DG.Column[] {
 
 export function setTagsMacromolecule(col: DG.Column) {
   col.semType = DG.SEMTYPE.MACROMOLECULE;
-  col.setTag(DG.TAGS.UNITS, bio.NOTATION.SEPARATOR);
-  col.setTag(bio.TAGS.aligned, bio.ALIGNMENT.SEQ_MSA);
-  col.setTag(bio.TAGS.alphabet, bio.ALPHABET.UN);
-  col.setTag(bio.TAGS.separator, '/');
+  col.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+  col.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
+  col.setTag(bioTAGS.alphabet, ALPHABET.UN);
+  col.setTag(bioTAGS.separator, '/');
   return col;
 }
 

package/src/utils/cell-renderer.ts

@@ -3,11 +3,20 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {printLeftOrCentered, DrawStyle} from '@datagrok-libraries/bio/src/utils/cell-renderer';
-import * as bio from '@datagrok-libraries/bio';
 import * as C from './constants';
+import {
+  ALIGNMENT,
+  getPaletteByType,
+  getSplitter,
+  monomerToShort,
+  SeqPalette,
+  SplitterFunc,
+  TAGS as bioTAGS,
+  UnknownSeqPalettes
+} from '@datagrok-libraries/bio';
 
 const undefinedColor = 'rgb(100,100,100)';
-const monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = bio.monomerToShort;
+const monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = monomerToShort;
 
 function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number): number {
   return grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
@@ -46,7 +55,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   }
 
   onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    if (gridCell.cell.column.getTag(bio.TAGS.aligned) !== bio.ALIGNMENT.SEQ_MSA)
+    if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
       return;
 
     const maxLengthWordsSum = gridCell.cell.column.temp['bio-sum-maxLengthWords'];
@@ -74,7 +83,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     }
     left = (argsX >= maxLengthWordsSum[left]) ? left + 1 : left;
     const separator = gridCell.cell.column.getTag('separator') ?? '';
-    const splitterFunc: bio.SplitterFunc = bio.getSplitter('separator', separator);
+    const splitterFunc: SplitterFunc = getSplitter('separator', separator);
     const subParts: string[] = splitterFunc(gridCell.cell.value);
     (((subParts[left]?.length ?? 0) > 0)) ?
       ui.tooltip.show(ui.div(subParts[left]), e.x + 16, e.y + 16) : ui.tooltip.hide();
@@ -95,7 +104,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
     cellStyle: DG.GridCellStyle
-  ): void {
+  ) {
     const grid = gridCell.gridRow !== -1 ? gridCell.grid : null;
     const cell = gridCell.cell;
     const paletteType = gridCell.cell.column.getTag(C.TAGS.ALPHABET);
@@ -111,11 +120,11 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     //TODO: can this be replaced/merged with splitSequence?
     const units = gridCell.cell.column.getTag(DG.TAGS.UNITS);
 
-    const palette = bio.getPaletteByType(paletteType);
+    const palette = getPaletteByType(paletteType);
 
     const separator = gridCell.cell.column.getTag('separator') ?? '';
     const splitLimit = gridCell.bounds.width / 5;
-    const splitterFunc: bio.SplitterFunc = bio.getSplitter(units, separator, splitLimit);
+    const splitterFunc: SplitterFunc = getSplitter(units, separator, splitLimit);
     const referenceSequence: string[] = splitterFunc(((gridCell.cell.column?.temp['reference-sequence'] != null) && (gridCell.cell.column?.temp['reference-sequence'] != ''))
       ? gridCell.cell.column.temp['reference-sequence'] : gridCell.cell.column.temp['current-word'] ?? '');
     const monomerWidth = (gridCell.cell.column?.temp['monomer-width'] != null) ? gridCell.cell.column.temp['monomer-width'] : 'short';
@@ -146,7 +155,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         });
         samples += 1;
       }
-      let minLength = 3 * 7;
+      const minLength = 3 * 7;
       for (let i = 0; i <= maxIndex; i++) {
         if (maxLengthWords[i] < minLength) {
           maxLengthWords[i] = minLength;
@@ -168,15 +177,15 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const subParts: string[] = splitterFunc(cell.value);
     let x1 = x;
     let color = undefinedColor;
-    let drawStyle = bio.DrawStyle.classic;
+    let drawStyle = DrawStyle.classic;
     if (gridCell.cell.column.getTag('aligned').includes('MSA') && gridCell.cell.column.getTag('units') === 'separator')
-      drawStyle = bio.DrawStyle.MSA;
+      drawStyle = DrawStyle.MSA;
 
     subParts.every((amino, index) => {
       color = palette.get(amino);
       g.fillStyle = undefinedColor;
-      let last = index === subParts.length - 1;
-      x1 = bio.printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell, referenceSequence, maxLengthOfMonomer);
+      const last = index === subParts.length - 1;
+      x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell, referenceSequence, maxLengthOfMonomer);
       return x1 - minDistanceRenderer - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x) <= gridCell.bounds.width;
     });
 
@@ -212,14 +221,14 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
     g.textBaseline = 'middle';
     g.textAlign = 'center';
 
-    const palette = bio.getPaletteByType(gridCell.cell.column.getTag(C.TAGS.ALPHABET));
+    const palette = getPaletteByType(gridCell.cell.column.getTag(C.TAGS.ALPHABET));
     const s: string = gridCell.cell.value;
     if (!s)
       return;
     const color = palette.get(s);
 
     g.fillStyle = color;
-    g.fillText(s, x + (w / 2), y + (h / 2), w);
+    g.fillText(monomerToShort(s, 3), x + (w / 2), y + (h / 2), w);
   }
 }
 
@@ -255,7 +264,7 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
     w = getUpdatedWidth(grid, g, x, w);
     //TODO: can this be replaced/merged with splitSequence?
     const [s1, s2] = s.split('#');
-    const splitter = bio.getSplitter(units, separator);
+    const splitter = getSplitter(units, separator);
     const subParts1 = splitter(s1);
     const subParts2 = splitter(s2);
     drawMoleculeDifferenceOnCanvas(g, x, y, w, h, subParts1, subParts2, units);
@@ -272,8 +281,8 @@ export function drawMoleculeDifferenceOnCanvas(
   subParts2: string [],
   units: string,
   fullStringLength?: boolean,
-  molDifferences?: { [key: number]: HTMLCanvasElement }) {
-
+  molDifferences?: { [key: number]: HTMLCanvasElement }
+): void {
   if (subParts1.length !== subParts2.length) {
     const emptyMonomersArray = new Array<string>(Math.abs(subParts1.length - subParts2.length)).fill('');
     subParts1.length > subParts2.length ?
@@ -297,9 +306,9 @@ export function drawMoleculeDifferenceOnCanvas(
   g.font = '12px monospace';
   g.textBaseline = 'top';
 
-  let palette: bio.SeqPalette = bio.UnknownSeqPalettes.Color;
+  let palette: SeqPalette = UnknownSeqPalettes.Color;
   if (units != 'HELM')
-    palette = bio.getPaletteByType(units.substring(units.length - 2));
+    palette = getPaletteByType(units.substring(units.length - 2));
 
   const vShift = 7;
   for (let i = 0; i < subParts1.length; i++) {
@@ -309,12 +318,12 @@ export function drawMoleculeDifferenceOnCanvas(
 
     if (amino1 != amino2) {
       const color2 = palette.get(amino2);
-      const subX0 = bio.printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
-      const subX1 = bio.printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
+      const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
+      const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
       updatedX = Math.max(subX1, subX0);
       if (molDifferences)
         molDifferences[i] = createDifferenceCanvas(amino1, amino2, color1, color2, updatedY, vShift, h);
-    } else { updatedX = bio.printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5); }
+    } else { updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5); }
     updatedX += 4;
   }
   g.restore();
@@ -338,7 +347,7 @@ function createDifferenceCanvas(
   canvas.width = width + 4;
   context.font = '12px monospace';
   context.textBaseline = 'top';
-  bio.printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
-  bio.printLeftOrCentered(0, y + shift, width, h, context, amino2, color2, 0, true);
+  printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
+  printLeftOrCentered(0, y + shift, width, h, context, amino2, color2, 0, true);
   return canvas;
 }

package/src/utils/convert.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 $ from 'cash-dom';
 import {Subscription} from 'rxjs';
+import {NOTATION, NotationConverter} from '@datagrok-libraries/bio';
 
 
 let convertDialog: DG.Dialog | null = null;
@@ -16,13 +16,13 @@ let convertDialogSubs: Subscription[] = [];
  * @param {DG.column} col Column with 'Macromolecule' semantic type
  */
 export function convert(col: DG.Column): void {
-  const converter = new bio.NotationConverter(col);
-  const currentNotation: bio.NOTATION = converter.notation;
+  const converter = new NotationConverter(col);
+  const currentNotation: NOTATION = converter.notation;
   //TODO: read all notations
   const notations = [
-    bio.NOTATION.FASTA,
-    bio.NOTATION.SEPARATOR,
-    bio.NOTATION.HELM
+    NOTATION.FASTA,
+    NOTATION.SEPARATOR,
+    NOTATION.HELM
   ];
   const separatorArray = ['-', '.', '/'];
   const filteredNotations = notations.filter((e) => e !== currentNotation);
@@ -32,7 +32,7 @@ export function convert(col: DG.Column): void {
 
   // hide the separator input for non-SEPARATOR target notations
   const toggleSeparator = () => {
-    if (targetNotationInput.value !== bio.NOTATION.SEPARATOR)
+    if (targetNotationInput.value !== NOTATION.SEPARATOR)
       $(separatorInput.root).hide();
     else
       $(separatorInput.root).show();
@@ -63,7 +63,7 @@ export function convert(col: DG.Column): void {
         separatorInput.root
       ]))
       .onOK(async () => {
-        const targetNotation = targetNotationInput.value as bio.NOTATION;
+        const targetNotation = targetNotationInput.value as NOTATION;
         const separator: string | null = separatorInput.value;
 
         await convertDo(col, targetNotation, separator);
@@ -80,9 +80,9 @@ export function convert(col: DG.Column): void {
 
 /** Creates a new column with converted sequences and detects its semantic type */
 export async function convertDo(
-  srcCol: DG.Column, targetNotation: bio.NOTATION, separator: string | null
+  srcCol: DG.Column, targetNotation: NOTATION, separator: string | null
 ): Promise<DG.Column> {
-  const converter = new bio.NotationConverter(srcCol);
+  const converter = new NotationConverter(srcCol);
   const newColumn = converter.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);
 

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

@@ -2,10 +2,9 @@
 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 {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
-
+import {TAGS as bioTAGS} from '@datagrok-libraries/bio';
 //@ts-ignore
 import Aioli from '@biowasm/aioli';
 
@@ -39,7 +38,7 @@ export async function runKalign(srcCol: DG.Column, isAligned = false, unUsedName
   const fasta = _stringsToFasta(sequences);
   const CLI = await new Aioli([
     'base/1.0.0',
-    {tool: 'kalign', version: '3.3.1', reinit: true,}
+    {tool: 'kalign', version: '3.3.1', reinit: true}
   ]);
 
   console.log(['fasta.length =', fasta.length]);
@@ -59,14 +58,14 @@ export async function runKalign(srcCol: DG.Column, isAligned = false, unUsedName
   // units
   const srcUnits = srcCol.getTag(DG.TAGS.UNITS);
   //aligned
-  const srcAligned = srcCol.getTag(bio.TAGS.aligned);
+  const srcAligned = srcCol.getTag(bioTAGS.aligned);
   const tgtAligned = srcAligned + '.MSA';
   //alphabet
-  const srcAlphabet = srcCol.getTag(bio.TAGS.alphabet);
+  const srcAlphabet = srcCol.getTag(bioTAGS.alphabet);
 
   tgtCol.setTag(DG.TAGS.UNITS, srcUnits);
-  tgtCol.setTag(bio.TAGS.aligned, tgtAligned);
-  tgtCol.setTag(bio.TAGS.alphabet, srcAlphabet);
+  tgtCol.setTag(bioTAGS.aligned, tgtAligned);
+  tgtCol.setTag(bioTAGS.alphabet, srcAlphabet);
   tgtCol.semType = DG.SEMTYPE.MACROMOLECULE;
   return tgtCol;
 }

package/src/utils/save-as-fasta.ts

@@ -1,16 +1,16 @@
 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 wu from 'wu';
+import {splitterAsFasta, SplitterFunc, UnitsHandler} from '@datagrok-libraries/bio';
 
 const FASTA_LINE_WIDTH = 60;
 
 /** Shows dialog to select id columns list and seq column, builds and downloads FASTA content */
 export function saveAsFastaUI() {
   // Use grid for column order adjusted by user
-  let grid: DG.Grid = grok.shell.tv.grid;
+  const grid: DG.Grid = grok.shell.tv.grid;
 
   const idGColList: DG.GridColumn[] = wu.count(0).take(grid.columns.length)
     .map((colI: number) => grid.columns.byIndex(colI)!)
@@ -27,7 +27,7 @@ export function saveAsFastaUI() {
     .filter((gc: DG.GridColumn) => {
       const col: DG.Column | null = gc.column;
       if (col && col.semType === DG.SEMTYPE.MACROMOLECULE) {
-        const uh = new bio.UnitsHandler(col);
+        const uh = new UnitsHandler(col);
         return uh.isFasta();
       }
       return false;
@@ -39,7 +39,7 @@ export function saveAsFastaUI() {
 
   const lineWidthInput = ui.intInput('FASTA line width', FASTA_LINE_WIDTH);
 
-  ui.dialog({title: 'Save as FASTA',})
+  ui.dialog({title: 'Save as FASTA'})
     .add(ui.inputs([
       idGColListInput,
       seqColInput,
@@ -57,7 +57,7 @@ export function saveAsFastaUI() {
 
       const resFastaTxt: string = saveAsFastaDo(valueIdColList, valueSeqCol!, valueLineWidth);
 
-      const aEl: HTMLAnchorElement = document.createElement('a',);
+      const aEl: HTMLAnchorElement = document.createElement('a');
       aEl.setAttribute('href', `data:text/plain;charset=utf-8,${encodeURIComponent(resFastaTxt)}`);
       aEl.setAttribute('download', `${grid.dataFrame.name}.fasta`);
       aEl.click();
@@ -69,7 +69,7 @@ export function saveAsFastaUI() {
 export function saveAsFastaDo(
   idColList: DG.Column[], seqCol: DG.Column, lineWidth: number = FASTA_LINE_WIDTH, lineSeparator: string = '\n'
 ): string {
-  const splitter: bio.SplitterFunc = bio.splitterAsFasta;
+  const splitter: SplitterFunc = splitterAsFasta;
 
   const fastaLines: string[] = [];
 
@@ -91,7 +91,7 @@ export function saveAsFastaDo(
 }
 
 /* split sequence for monomers to prevent wrapping monomer partially */
-export function wrapSequence(seq: string, splitter: bio.SplitterFunc, lineWidth: number = FASTA_LINE_WIDTH): string[] {
+export function wrapSequence(seq: string, splitter: SplitterFunc, lineWidth: number = FASTA_LINE_WIDTH): string[] {
   const seqMonomerList = splitter(seq);
   let seqPos: number = 0;
   const seqLength: number = seqMonomerList.length;
@@ -106,4 +106,4 @@ export function wrapSequence(seq: string, splitter: bio.SplitterFunc, lineWidth:
   }
 
   return seqLineList;
-}
+}

package/src/viewers/vd-regions-viewer.ts

@@ -1,9 +1,10 @@
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
-const vrt = bio.VdRegionType;
+import {IVdRegionsViewer, PositionHeight, VdRegion, VdRegionType, WebLogoViewer} from '@datagrok-libraries/bio';
+
+const vrt = VdRegionType;
 
 // Positions of regions for numbering schemes
 // http://www.bioinf.org.uk/abs/info.html
@@ -34,7 +35,7 @@ const vrt = bio.VdRegionType;
 /** Viewer with tabs based on description of chain regions.
  *  Used to define regions of an immunoglobulin LC.
  */
-export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer {
+export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   // private regionsDf: DG.DataFrame;
   private regionsFg: DG.FilterGroup | null = null;
   // private regionsTV: DG.TableView;
@@ -43,7 +44,7 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
   private isOpened: boolean = false;
   private panelNode: DG.DockNode | null = null;
 
-  public regions: bio.VdRegion[] = [];
+  public regions: VdRegion[] = [];
   public regionTypes: string[];
   public chains: string[];
   public sequenceColumnNamePostfix: string;
@@ -58,7 +59,7 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
   }
 
   // TODO: .onTableAttached is not calling on dataFrame set, onPropertyChanged  also not calling
-  public async setDf(value: DG.DataFrame, regions: bio.VdRegion[]) {
+  public async setDf(value: DG.DataFrame, regions: VdRegion[]) {
     console.debug('VdRegionsViewer.setDf()');
     await this.destroyView();
     this.regions = regions;
@@ -78,8 +79,8 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
 
     this.skipEmptyPositions = this.bool('skipEmptyPositions', false);
     this.positionWidth = this.float('positionWidth', 16);
-    this.positionHeight = this.string('positionHeight', bio.PositionHeight.Entropy,
-      {choices: Object.keys(bio.PositionHeight)});
+    this.positionHeight = this.string('positionHeight', PositionHeight.Entropy,
+      {choices: Object.keys(PositionHeight)});
   }
 
   public async init() {
@@ -180,7 +181,7 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
   //#region -- View --
   private host: HTMLElement | null = null;
   private mainLayout: HTMLTableElement | null = null;
-  private logos: { [chain: string]: bio.WebLogoViewer }[] = [];
+  private logos: { [chain: string]: WebLogoViewer }[] = [];
 
   private async destroyView(): Promise<void> {
     // TODO: Unsubscribe from and remove all view elements
@@ -200,16 +201,16 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
     const colNames: { [chain: string]: string } = Object.assign({},
       ...this.chains.map((chain) => ({[chain]: `${chain} ${this.sequenceColumnNamePostfix}`})));
 
-    const regionsFiltered: bio.VdRegion[] = this.regions.filter((r: bio.VdRegion) => this.regionTypes.includes(r.type));
+    const regionsFiltered: VdRegion[] = this.regions.filter((r: VdRegion) => this.regionTypes.includes(r.type));
 
     const orderList: number[] = Array.from(new Set(regionsFiltered.map((r) => r.order))).sort();
 
     this.logos = [];
 
     for (let orderI = 0; orderI < orderList.length; orderI++) {
-      const regionChains: { [chain: string]: bio.WebLogoViewer } = {};
+      const regionChains: { [chain: string]: WebLogoViewer } = {};
       for (const chain of this.chains) {
-        const region: bio.VdRegion | undefined = regionsFiltered
+        const region: VdRegion | undefined = regionsFiltered
           .find((r) => r.order == orderList[orderI] && r.chain == chain);
         regionChains[chain] = (await this.dataFrame.plot.fromType('WebLogo', {
           sequenceColumnName: colNames[chain],
@@ -219,7 +220,7 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
           skipEmptyPositions: this.skipEmptyPositions,
           positionWidth: this.positionWidth,
           positionHeight: this.positionHeight,
-        })) as unknown as bio.WebLogoViewer;
+        })) as unknown as WebLogoViewer;
       }
       // WebLogo creation fires onRootSizeChanged event even before control being added to this.logos
       this.logos[orderI] = regionChains;
@@ -244,7 +245,7 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
           })] : []),
           // List with controls for regions
           ...[...Array(orderList.length).keys()].map((orderI) => {
-            const wl: bio.WebLogoViewer = this.logos[orderI][chain];
+            const wl: WebLogoViewer = this.logos[orderI][chain];
             wl.root.style.height = '100%';
 
             const resDiv = ui.div([wl.root]/*`${chain} ${regionsFiltered[rI]}`*/, {
@@ -261,7 +262,7 @@ export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer
       },
       ['', ...[...Array(orderList.length).keys()].map(
         (orderI: number) => regionsFiltered.find(
-          (r: bio.VdRegion) => r.order == orderList[orderI] && r.chain == this.chains[0]
+          (r: VdRegion) => r.order == orderList[orderI] && r.chain == this.chains[0]
         )!.name || 'Name')]
     );
     this.mainLayout.className = 'mlb-vd-regions-viewer-table2';

package/tsconfig.json

@@ -6,7 +6,7 @@
       // "incremental": true,                         /* Enable incremental compilation */
       "target": "es6",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
       "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
-      "lib": ["es2020", "dom", "ES2021.String"],                       /* Specify library files to be included in the compilation. */
+      "lib": ["es2020", "dom", "ES2021.String"],      /* Specify library files to be included in the compilation. */
       // "allowJs": true,                             /* Allow javascript files to be compiled. */
       // "checkJs": true,                             /* Report errors in .js files. */
       // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */

package/jest.config.js

@@ -1,33 +0,0 @@
-module.exports = {
-  'roots': [
-    '<rootDir>/src',
-  ],
-  'testMatch': [
-    '**/__jest__/**/*.test.+(ts|tsx)',
-  ],
-  moduleFileExtensions: [
-    'ts',
-    'js',
-  ],
-  'transform': {
-    '^.+\\.(ts|tsx)$': 'ts-jest',
-  },
-  transformIgnorePatterns: ['^.+\\.js$'],
-  globals: {
-    'ts-jest': {
-      'tsconfig': {
-        'target': 'es6',
-        'module': 'es2020',
-      },
-    },
-  },
-  reporters: [
-    'default',
-    [
-      './node_modules/jest-html-reporter',
-      {
-        'includeConsoleLog': true,
-      },
-    ],
-  ],
-};