@datagrok/bio - npm Package Compare versions

Comparing version 2.0.19 to 2.0.20

package.json

@@ -8,3 +8,3 @@ {
   },
-  "version": "2.0.19",
+  "version": "2.0.20",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
@@ -18,3 +18,3 @@ "repository": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.0.0",
+    "@datagrok-libraries/bio": "^5.1.0",
     "@datagrok-libraries/chem-meta": "1.0.1",
@@ -21,0 +21,0 @@ "@datagrok-libraries/ml": "^6.2.0",

src/package.ts

@@ -453,3 +453,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
 export function splitToMonomers(col: DG.Column<string>): void {
-  if (!col.getTag(bio.UnitsHandler.TAGS.aligned).includes(C.MSA))
+  if (!col.getTag(bio.TAGS.aligned).includes(C.MSA))
     return grok.shell.error('Splitting is applicable only for aligned sequences');
@@ -523,2 +523,3 @@
 }
+
 //name: BioSubstructureFilter
@@ -525,0 +526,0 @@ //description: Substructure filter for linear macromolecules

src/substructure-search/substructure-search.ts

 import * as grok from 'datagrok-api/grok';
 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 bio from '@datagrok-libraries/bio';
+
 import * as C from '../utils/constants';
@@ -33,3 +34,3 @@ import {getMonomericMols} from '../calculations/monomerLevelMols';
   df.col('substr_helm')!.semType = col.semType;
-  df.col('substr_helm')!.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+  df.col('substr_helm')!.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
   const grid = df.plot.grid();
@@ -40,4 +41,4 @@ const separatorInput = ui.textInput('Separator', separator);
 
-  const inputs = units === NOTATION.HELM ? ui.divV([editHelmLink]) :
-    units === NOTATION.SEPARATOR ? ui.inputs([substructureInput, separatorInput]) :
+  const inputs = units === bio.NOTATION.HELM ? ui.divV([editHelmLink]) :
+    units === bio.NOTATION.SEPARATOR ? ui.inputs([substructureInput, separatorInput]) :
       ui.inputs([substructureInput]);
@@ -53,4 +54,4 @@
     .onOK(async () => {
-      let substructure = units === NOTATION.HELM ? df.get('substr_helm', 0) : substructureInput.value;
-      if (units === NOTATION.SEPARATOR && separatorInput.value !== separator && separatorInput.value !== '')
+      let substructure = units === bio.NOTATION.HELM ? df.get('substr_helm', 0) : substructureInput.value;
+      if (units === bio.NOTATION.SEPARATOR && separatorInput.value !== separator && separatorInput.value !== '')
         substructure = substructure.replaceAll(separatorInput.value, separator);
@@ -62,3 +63,3 @@ const matchesColName = `Matches: ${substructure}`;
         let matches: BitSet;
-        if (units === NOTATION.HELM)
+        if (units === bio.NOTATION.HELM)
           matches = await helmSubstructureSearch(substructure, col);
@@ -87,3 +88,3 @@ else
     .init((i) => i === col.length ? substructure : col.get(i));
-  helmColWithSubstructure.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+  helmColWithSubstructure.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
   const monomericMolsCol = await getMonomericMols(helmColWithSubstructure, true);
@@ -90,0 +91,0 @@ const molSubstructure = monomericMolsCol.get(col.length);

src/tests/checkInputColumn-tests.ts

@@ -1,10 +0,11 @@
-import {after, before, category, test, expect, expectArray} 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, expectArray} from '@datagrok-libraries/utils/src/test';
+
 import {checkInputColumn, multipleSequenceAlignmentAny} from '../package';
 import {UNITS} from 'datagrok-api/dg';
-import {ALPHABET, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
@@ -30,3 +31,3 @@
     col.setTag(DG.TAGS.UNITS, 'fasta');
-    col.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
+    col.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
 
@@ -44,4 +45,4 @@ const [res, msg]: [boolean, string] = checkInputColumn(
     col.setTag(DG.TAGS.UNITS, 'helm');
-    col.setTag(UnitsHandler.TAGS.alphabetSize, '11');
-    col.setTag(UnitsHandler.TAGS.alphabetIsMultichar, 'true');
+    col.setTag(bio.TAGS.alphabetSize, '11');
+    col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
 
@@ -59,5 +60,5 @@ const [res, msg]: [boolean, string] = checkInputColumn(
     col.setTag(DG.TAGS.UNITS, 'fasta');
-    col.setTag(UnitsHandler.TAGS.alphabet, 'UN');
-    col.setTag(UnitsHandler.TAGS.alphabetSize, '11');
-    col.setTag(UnitsHandler.TAGS.alphabetIsMultichar, 'true');
+    col.setTag(bio.TAGS.alphabet, 'UN');
+    col.setTag(bio.TAGS.alphabetSize, '11');
+    col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
 
@@ -64,0 +65,0 @@ const [res, msg]: [boolean, string] = checkInputColumn(

src/tests/convert-test.ts

 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';
 
@@ -8,4 +9,2 @@ import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
 import {ConverterFunc} from './types';
-import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
-import {NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
@@ -137,8 +136,8 @@ // import {mmSemType} from '../const';
 
-  function converter(tgtNotation: NOTATION, tgtSeparator: string | null = null): ConverterFunc {
-    if (tgtNotation === NOTATION.SEPARATOR && !tgtSeparator)
+  function converter(tgtNotation: bio.NOTATION, tgtSeparator: string | null = null): ConverterFunc {
+    if (tgtNotation === bio.NOTATION.SEPARATOR && !tgtSeparator)
       throw new Error(`Argument 'separator' is missed for notation '${tgtNotation.toString()}'.`);
 
     return function(srcCol: DG.Column): DG.Column {
-      const converter = new NotationConverter(srcCol);
+      const converter = new bio.NotationConverter(srcCol);
       const resCol = converter.convert(tgtNotation, tgtSeparator);
@@ -162,3 +161,3 @@ expect(resCol.getTag('units'), tgtNotation);
     expectArray(resCol.toList(), tgtCol.toList());
-    const uh: UnitsHandler = new UnitsHandler(resCol);
+    const uh: bio.UnitsHandler = new bio.UnitsHandler(resCol);
   }
@@ -169,12 +168,12 @@
   test('testFastaPtToSeparator', async () => {
-    await _testConvert(Samples.fastaPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
+    await _testConvert(Samples.fastaPt, converter(bio.NOTATION.SEPARATOR, '-'), Samples.separatorPt);
   });
   test('testFastaDnaToSeparator', async () => {
-    await _testConvert(Samples.fastaDna, converter(NOTATION.SEPARATOR, '/'), Samples.separatorDna);
+    await _testConvert(Samples.fastaDna, converter(bio.NOTATION.SEPARATOR, '/'), Samples.separatorDna);
   });
   test('testFastaRnaToSeparator', async () => {
-    await _testConvert(Samples.fastaRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
+    await _testConvert(Samples.fastaRna, converter(bio.NOTATION.SEPARATOR, '*'), Samples.separatorRna);
   });
   test('testFastaGapsToSeparator', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
+    await _testConvert(Samples.fastaGaps, converter(bio.NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
   });
@@ -184,12 +183,12 @@
   test('testFastaPtToHelm', async () => {
-    await _testConvert(Samples.fastaPt, converter(NOTATION.HELM), Samples.helmPt);
+    await _testConvert(Samples.fastaPt, converter(bio.NOTATION.HELM), Samples.helmPt);
   });
   test('testFastaDnaToHelm', async () => {
-    await _testConvert(Samples.fastaDna, converter(NOTATION.HELM), Samples.helmDna);
+    await _testConvert(Samples.fastaDna, converter(bio.NOTATION.HELM), Samples.helmDna);
   });
   test('testFastaRnaToHelm', async () => {
-    await _testConvert(Samples.fastaRna, converter(NOTATION.HELM), Samples.helmRna);
+    await _testConvert(Samples.fastaRna, converter(bio.NOTATION.HELM), Samples.helmRna);
   });
   test('testFastaGapsToHelm', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.HELM), Samples.helmGaps);
+    await _testConvert(Samples.fastaGaps, converter(bio.NOTATION.HELM), Samples.helmGaps);
   });
@@ -201,12 +200,12 @@
   test('testSeparatorPtToFasta', async () => {
-    await _testConvert(Samples.separatorPt, converter(NOTATION.FASTA), Samples.fastaPt);
+    await _testConvert(Samples.separatorPt, converter(bio.NOTATION.FASTA), Samples.fastaPt);
   });
   test('testSeparatorDnaToFasta', async () => {
-    await _testConvert(Samples.separatorDna, converter(NOTATION.FASTA), Samples.fastaDna);
+    await _testConvert(Samples.separatorDna, converter(bio.NOTATION.FASTA), Samples.fastaDna);
   });
   test('testSeparatorRnaToFasta', async () => {
-    await _testConvert(Samples.separatorRna, converter(NOTATION.FASTA), Samples.fastaRna);
+    await _testConvert(Samples.separatorRna, converter(bio.NOTATION.FASTA), Samples.fastaRna);
   });
   test('testSeparatorGapsToFasta', async () => {
-    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
+    await _testConvert(Samples.separatorGaps, converter(bio.NOTATION.FASTA), Samples.fastaGaps);
   });
@@ -216,12 +215,12 @@
   test('testSeparatorPtToHelm', async () => {
-    await _testConvert(Samples.separatorPt, converter(NOTATION.HELM), Samples.helmPt);
+    await _testConvert(Samples.separatorPt, converter(bio.NOTATION.HELM), Samples.helmPt);
   });
   test('testSeparatorDnaToHelm', async () => {
-    await _testConvert(Samples.separatorDna, converter(NOTATION.HELM), Samples.helmDna);
+    await _testConvert(Samples.separatorDna, converter(bio.NOTATION.HELM), Samples.helmDna);
   });
   test('testSeparatorRnaToHelm', async () => {
-    await _testConvert(Samples.separatorRna, converter(NOTATION.HELM), Samples.helmRna);
+    await _testConvert(Samples.separatorRna, converter(bio.NOTATION.HELM), Samples.helmRna);
   });
   test('testSeparatorGapsToHelm', async () => {
-    await _testConvert(Samples.separatorGaps, converter(NOTATION.HELM), Samples.helmGaps);
+    await _testConvert(Samples.separatorGaps, converter(bio.NOTATION.HELM), Samples.helmGaps);
   });
@@ -233,9 +232,9 @@
   test('testHelmDnaToFasta', async () => {
-    await _testConvert(Samples.helmDna, converter(NOTATION.FASTA), Samples.fastaDna);
+    await _testConvert(Samples.helmDna, converter(bio.NOTATION.FASTA), Samples.fastaDna);
   });
   test('testHelmRnaToFasta', async () => {
-    await _testConvert(Samples.helmRna, converter(NOTATION.FASTA), Samples.fastaRna);
+    await _testConvert(Samples.helmRna, converter(bio.NOTATION.FASTA), Samples.fastaRna);
   });
   test('testHelmPtToFasta', async () => {
-    await _testConvert(Samples.helmPt, converter(NOTATION.FASTA), Samples.fastaPt);
+    await _testConvert(Samples.helmPt, converter(bio.NOTATION.FASTA), Samples.fastaPt);
   });
@@ -245,9 +244,9 @@
   test('testHelmDnaToSeparator', async () => {
-    await _testConvert(Samples.helmDna, converter(NOTATION.SEPARATOR, '/'), Samples.separatorDna);
+    await _testConvert(Samples.helmDna, converter(bio.NOTATION.SEPARATOR, '/'), Samples.separatorDna);
   });
   test('testHelmRnaToSeparator', async () => {
-    await _testConvert(Samples.helmRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
+    await _testConvert(Samples.helmRna, converter(bio.NOTATION.SEPARATOR, '*'), Samples.separatorRna);
   });
   test('testHelmPtToSeparator', async () => {
-    await _testConvert(Samples.helmPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
+    await _testConvert(Samples.helmPt, converter(bio.NOTATION.SEPARATOR, '-'), Samples.separatorPt);
   });
@@ -257,10 +256,10 @@
   test('testHelmLoneRibose', async () => {
-    await _testConvert(Samples.helmLoneRibose, converter(NOTATION.FASTA), Samples.fastaRna);
+    await _testConvert(Samples.helmLoneRibose, converter(bio.NOTATION.FASTA), Samples.fastaRna);
   });
   test('testHelmLoneDeoxyribose', async () => {
-    await _testConvert(Samples.helmLoneDeoxyribose, converter(NOTATION.SEPARATOR, '/'), Samples.separatorDna);
+    await _testConvert(Samples.helmLoneDeoxyribose, converter(bio.NOTATION.SEPARATOR, '/'), Samples.separatorDna);
   });
   test('testHelmLonePhosphorus', async () => {
-    await _testConvert(Samples.helmLonePhosphorus, converter(NOTATION.FASTA), Samples.fastaRna);
+    await _testConvert(Samples.helmLonePhosphorus, converter(bio.NOTATION.FASTA), Samples.fastaRna);
   });
 });

src/tests/detectors-test.ts

@@ -1,7 +0,8 @@
-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 {importFasta} from '../package';
@@ -403,6 +404,6 @@ import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
   expect(col.getTag(DG.TAGS.UNITS), units);
-  expect(col.getTag(UnitsHandler.TAGS.aligned), aligned);
-  expect(col.getTag(UnitsHandler.TAGS.alphabet), alphabet);
+  expect(col.getTag(bio.TAGS.aligned), aligned);
+  expect(col.getTag(bio.TAGS.alphabet), alphabet);
   if (separator)
-    expect(col.getTag(UnitsHandler.TAGS.separator), separator);
+    expect(col.getTag(bio.TAGS.separator), separator);
 
@@ -409,0 +410,0 @@ const uh = new UnitsHandler(col);

src/tests/Palettes-test.ts

 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';
 
@@ -8,4 +9,2 @@ 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 {ALPHABET, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
 
@@ -17,11 +16,11 @@ category('Palettes', () => {
   test('testPalettePtMe', async () => {
-    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 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 colorL = AminoacidsPalettes.GrokGroups.get('L');
-    const colorA = AminoacidsPalettes.GrokGroups.get('A');
-    const colorG = AminoacidsPalettes.GrokGroups.get('G');
-    const colorF = AminoacidsPalettes.GrokGroups.get('F');
+    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');
 
@@ -28,0 +27,0 @@ expect(colorMeNle, colorL);

src/tests/renderers-test.ts

@@ -0,8 +1,9 @@
+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';
 
-import * as grok from 'datagrok-api/grok';
-import * as DG from 'datagrok-api/dg';
 import {importFasta, multipleSequenceAlignmentAny} from '../package';
 import {convertDo} from '../utils/convert';
-import {ALPHABET, NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {SEM_TYPES, TAGS} from '../utils/constants';
@@ -140,5 +141,5 @@ import {generateLongSequence, generateManySequences, performanceTest} from './test-sequnces-generators';
     expect(srcSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
-    expect(srcSeqCol.getTag(DG.TAGS.UNITS), NOTATION.FASTA);
-    expect(srcSeqCol.getTag(UnitsHandler.TAGS.aligned), 'SEQ');
-    expect(srcSeqCol.getTag(UnitsHandler.TAGS.alphabet), ALPHABET.PT);
+    expect(srcSeqCol.getTag(DG.TAGS.UNITS), bio.NOTATION.FASTA);
+    expect(srcSeqCol.getTag(bio.TAGS.aligned), 'SEQ');
+    expect(srcSeqCol.getTag(bio.TAGS.alphabet), bio.ALPHABET.PT);
     expect(srcSeqCol.getTag(DG.TAGS.CELL_RENDERER), 'sequence');
@@ -150,9 +151,9 @@
     expect(msaSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
-    expect(msaSeqCol.getTag(DG.TAGS.UNITS), NOTATION.FASTA);
-    expect(msaSeqCol.getTag(UnitsHandler.TAGS.aligned), 'SEQ.MSA');
-    expect(msaSeqCol.getTag(UnitsHandler.TAGS.alphabet), ALPHABET.PT);
+    expect(msaSeqCol.getTag(DG.TAGS.UNITS), bio.NOTATION.FASTA);
+    expect(msaSeqCol.getTag(bio.TAGS.aligned), 'SEQ.MSA');
+    expect(msaSeqCol.getTag(bio.TAGS.alphabet), bio.ALPHABET.PT);
     expect(msaSeqCol.getTag(DG.TAGS.CELL_RENDERER), 'sequence');
 
     // check newColumn with UnitsHandler constructor
-    const uh: UnitsHandler = new UnitsHandler(msaSeqCol);
+    const uh: bio.UnitsHandler = new bio.UnitsHandler(msaSeqCol);
 
@@ -179,3 +180,3 @@ dfList.push(df);
 
-    const tgtCol: DG.Column = await convertDo(srcCol, NOTATION.SEPARATOR, '/');
+    const tgtCol: DG.Column = await convertDo(srcCol, bio.NOTATION.SEPARATOR, '/');
 
@@ -186,3 +187,3 @@ const resCellRenderer = tgtCol.getTag(DG.TAGS.CELL_RENDERER);
     // check tgtCol with UnitsHandler constructor
-    const uh: UnitsHandler = new UnitsHandler(tgtCol);
+    const uh: bio.UnitsHandler = new bio.UnitsHandler(tgtCol);
   }
@@ -189,0 +190,0 @@

src/tests/WebLogo-positions-test.ts

@@ -7,4 +7,2 @@ import * as grok from 'datagrok-api/grok';
 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';
 
@@ -42,4 +40,4 @@ category('WebLogo-positions', () => {
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
-    seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
+    seqCol.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
+    seqCol.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
 
@@ -92,4 +90,4 @@ const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo')) as bio.WebLogo;
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
-    seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
+    seqCol.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
+    seqCol.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
 
@@ -137,4 +135,4 @@ df.filter.init((i) => {
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
-    seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
+    seqCol.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
+    seqCol.setTag(bio.TAGS.alphabet, bio.ALPHABET.DNA);
 
@@ -141,0 +139,0 @@ const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo',

src/utils/cell-renderer.ts

@@ -10,19 +10,2 @@ import * as grok from 'datagrok-api/grok';
 
-
-function getPaletteByType(paletteType: string): bio.SeqPalette {
-  switch (paletteType) {
-  case 'PT':
-    return bio.AminoacidsPalettes.GrokGroups;
-  case 'NT':
-    return bio.NucleotidesPalettes.Chromatogram;
-  case 'DNA':
-    return bio.NucleotidesPalettes.Chromatogram;
-  case 'RNA':
-    return bio.NucleotidesPalettes.Chromatogram;
-    // other
-  default:
-    return bio.UnknownSeqPalettes.Color;
-  }
-}
-
 function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number): number {
@@ -65,3 +48,3 @@ return grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
   onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    if (gridCell.cell.column.getTag(bio.UnitsHandler.TAGS.aligned) !== 'SEQ.MSA')
+    if (gridCell.cell.column.getTag(bio.TAGS.aligned) !== 'SEQ.MSA')
       return;
@@ -131,3 +114,3 @@
 
-    const palette = getPaletteByType(paletteType);
+    const palette = bio.getPaletteByType(paletteType);
 
@@ -233,3 +216,3 @@ const separator = gridCell.cell.column.getTag('separator') ?? '';
 
-    const palette = getPaletteByType(gridCell.cell.column.getTag(C.TAGS.ALPHABET));
+    const palette = bio.getPaletteByType(gridCell.cell.column.getTag(C.TAGS.ALPHABET));
     const s: string = gridCell.cell.value;
@@ -321,3 +304,3 @@ if (!s)
   if (units != 'HELM')
-    palette = getPaletteByType(units.substring(units.length - 2));
+    palette = bio.getPaletteByType(units.substring(units.length - 2));
 
@@ -324,0 +307,0 @@ const vShift = 7;

src/utils/multiple-sequence-alignment.ts

@@ -5,2 +5,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
@@ -62,10 +63,10 @@ import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
   //aligned
-  const srcAligned = srcCol.getTag(UnitsHandler.TAGS.aligned);
+  const srcAligned = srcCol.getTag(bio.TAGS.aligned);
   const tgtAligned = srcAligned + '.MSA';
   //alphabet
-  const srcAlphabet = srcCol.getTag(UnitsHandler.TAGS.alphabet);
+  const srcAlphabet = srcCol.getTag(bio.TAGS.alphabet);
 
   tgtCol.setTag(DG.TAGS.UNITS, srcUnits);
-  tgtCol.setTag(UnitsHandler.TAGS.aligned, tgtAligned);
-  tgtCol.setTag(UnitsHandler.TAGS.alphabet, srcAlphabet);
+  tgtCol.setTag(bio.TAGS.aligned, tgtAligned);
+  tgtCol.setTag(bio.TAGS.alphabet, srcAlphabet);
   tgtCol.semType = DG.SEMTYPE.MACROMOLECULE;
@@ -72,0 +73,0 @@ return tgtCol;

src/utils/utils.ts

@@ -22,3 +22,3 @@ import * as grok from 'datagrok-api/grok';
   const units = col.tags[DG.TAGS.UNITS];
-  const sep = col.getTag(UnitsHandler.TAGS.separator);
+  const sep = col.getTag(bio.TAGS.separator);
   const splitterFunc: bio.SplitterFunc = bio.getSplitter(units, sep);
@@ -25,0 +25,0 @@ const encodedStringArray = [];

src/viewers/vd-regions-viewer.ts

@@ -113,6 +113,4 @@ import * as ui from 'datagrok-api/ui';
 
-  public override onTableAttached() {
-    window.setTimeout(async () => {
-      await this.init();
-    }, 0 /* next event cycle */);
+  public override async onTableAttached() {
+    await this.init();
   }
@@ -119,0 +117,0 @@

src/widgets/bio-substructure-filter.ts

@@ -9,6 +9,7 @@ /**
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
 import wu from 'wu';
 import {linearSubstructureSearch} from '../substructure-search/substructure-search';
 import {Subject, Subscription} from 'rxjs';
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/units-handler';
 import * as C from '../utils/constants';
@@ -23,2 +24,3 @@
   get calculating(): boolean { return this.loader.style.display == 'initial'; }
+
   set calculating(value: boolean) { this.loader.style.display = value ? 'initial' : 'none'; }
@@ -49,3 +51,3 @@
     const notation = this.column?.getTag(DG.TAGS.UNITS);
-    this.bioFilter = notation === NOTATION.FASTA ?
+    this.bioFilter = notation === bio.NOTATION.FASTA ?
       new FastaFilter() : new SeparatorFilter(this.column!.getTag(C.TAGS.SEPARATOR));
@@ -88,6 +90,6 @@ this.root.appendChild(this.bioFilter!.filterPanel);
   /**
-    * Performs the actual filtering
-    * When the results are ready, triggers `rows.requestFilter`, which in turn triggers `applyFilter`
-    * that would simply apply the bitset synchronously.
-    */
+   * Performs the actual filtering
+   * When the results are ready, triggers `rows.requestFilter`, which in turn triggers `applyFilter`
+   * that would simply apply the bitset synchronously.
+   */
   async _onInputChanged(): Promise<void> {
@@ -152,5 +154,5 @@ if (!this.isFiltering) {
     return this.separatorInput.value && this.separatorInput.value !== this.colSeparator ?
-      this.substructureInput.value.replaceAll(this.separatorInput.value, this.colSeparator):
+      this.substructureInput.value.replaceAll(this.separatorInput.value, this.colSeparator) :
       this.substructureInput.value;
   }
 }

No alert changes

Worsened metrics

Total package byte prevSize

11312474

-0.09%

Lines of code

56329

-0.06%

Dependency changes

• Updated

  @datagrok-libraries/bio@^5.1.0