@datagrok/bio 2.4.30 → 2.4.39

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

@@ -39,7 +39,7 @@ export function substructureSearchDialog(col: DG.Column<string>): void {
   });
 
   const df = DG.DataFrame.create(1);
-  df.columns.addNewString(SUBSTR_HELM_COL_NAME).init((i) => '');
+  df.columns.addNewString(SUBSTR_HELM_COL_NAME).init((_i) => '');
   df.col(SUBSTR_HELM_COL_NAME)!.semType = col.semType;
   df.col(SUBSTR_HELM_COL_NAME)!.setTag(DG.TAGS.UNITS, NOTATION.HELM);
   const grid = df.plot.grid();
@@ -56,7 +56,7 @@ export function substructureSearchDialog(col: DG.Column<string>): void {
   ui.dialog('Substructure Search')
     .add(ui.divV([
       ui.divText(`Notation: ${units}`),
-      inputsDiv
+      inputsDiv,
     ]))
     .onOK(async () => {
       let substructure = units === NOTATION.HELM ? df.get(SUBSTR_HELM_COL_NAME, 0) : substructureInput.value;
@@ -104,7 +104,7 @@ function prepareSubstructureRegex(substructure: string, separator: string) {
 export async function helmSubstructureSearch(substructure: string, col: DG.Column<string>): Promise<DG.BitSet> {
   if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
     await invalidateMols(col, true);
-  const substructureCol: DG.Column<string> = DG.Column.string('helm', 1).init((i) => substructure);
+  const substructureCol: DG.Column<string> = DG.Column.string('helm', 1).init((_i) => substructure);
   substructureCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
   const substructureMolsCol =
     await getMonomericMols(substructureCol, true, col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT]);

package/src/tests/Palettes-test.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect} from '@datagrok-libraries/utils/src/test';
 
 import {_testPaletteN, _testPaletteAA} from '@datagrok-libraries/bio/src/tests/palettes-tests';
 import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';

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

@@ -7,14 +7,11 @@ import {
   countForMonomerAtPosition,
   PositionInfo as PI,
   PositionMonomerInfo as PMI,
-  WebLogoViewer
+  WebLogoViewer,
 } from '../viewers/web-logo-viewer';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 category('WebLogo-positions', () => {
-  let tvList: DG.TableView[];
-  let dfList: DG.DataFrame[];
-  let currentView: DG.ViewBase;
-
   const csvDf1 = `seq
 ATC-G-TTGC--
 ATC-G-TTGC--
@@ -24,16 +21,10 @@ ATC-G-TTGC--
 
 
   before(async () => {
-    tvList = [];
-    dfList = [];
-    // currentView = grok.shell.v;
   });
 
   after(async () => {
     // Closing opened views causes the error 'Cannot read properties of null (reading 'f')'
-    // dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
-    // tvList.forEach((tv: DG.TableView) => tv.close());
-    // grok.shell.v = currentView;
   });
 
   test('allPositions', async () => {
@@ -49,9 +40,6 @@ ATC-G-TTGC--
     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: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -73,11 +61,10 @@ ATC-G-TTGC--
 
     for (let i = 0; i < positions.length; i++) {
       expect(positions[i].name, resAllDf1[i].name);
-      for (const key in positions[i].freq) {
+      for (const key in positions[i].freq)
         expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
-      }
     }
-  });
+  }, {skipReason: 'GROK-13300'});
 
   test('positions with shrinkEmptyTail option true (filtered)', async () => {
     const csvDf2 = `seq
@@ -104,9 +91,6 @@ ATC-G-TTGC--
       {'shrinkEmptyTail': true})) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
-    tvList.push(tv);
-    dfList.push(df);
-
     const positions: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -125,11 +109,10 @@ ATC-G-TTGC--
 
     for (let i = 0; i < positions.length; i++) {
       expect(positions[i].name, resAllDf1[i].name);
-      for (const key in positions[i].freq) {
+      for (const key in positions[i].freq)
         expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
-      }
     }
-  });
+  }, {skipReason: 'GROK-13300'});
 
   test('positions with skipEmptyPositions option', async () => {
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
@@ -145,9 +128,6 @@ ATC-G-TTGC--
       {'skipEmptyPositions': true})) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
-    tvList.push(tv);
-    dfList.push(df);
-
     const resPosList: PI[] = wlViewer['positions'];
 
     const tgtPosList: PI[] = [
@@ -159,7 +139,7 @@ ATC-G-TTGC--
       new PI(6, '7', {'T': new PMI(5)}),
       new PI(7, '8', {'T': new PMI(5)}),
       new PI(8, '9', {'G': new PMI(5)}),
-      new PI(9, '10', {'C': new PMI(5)})
+      new PI(9, '10', {'C': new PMI(5)}),
     ];
 
     expect(resPosList.length, tgtPosList.length);
@@ -168,7 +148,7 @@ ATC-G-TTGC--
       const tgtPos = tgtPosList[posI];
       expectPositionInfo(resPos, tgtPos);
     }
-  });
+  }, {skipReason: 'GROK-13300'});
 
   test('count sequences for monomer at position', async () => {
     const df: DG.DataFrame = buildDfWithSeqCol(csvDf1, NOTATION.FASTA, ALPHABET.DNA, 'SEQ.MSA');
@@ -179,13 +159,10 @@ ATC-G-TTGC--
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo', {
       startPositionName: '3',
       endPositionName: '7',
-      skipEmptyPositions: true
+      skipEmptyPositions: true,
     })) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
-    tvList.push(tv);
-    dfList.push(df);
-
     const resPosList: PI[] = wlViewer['positions'];
     const tgtPosList: PI[] = [
       new PI(2, '3', {'C': new PMI(5)}),
@@ -201,11 +178,11 @@ ATC-G-TTGC--
       expectPositionInfo(resPos, tgtPos);
     }
 
-    const splitter: SplitterFunc = wlViewer['splitter']!;
     const atPI1: PI = resPosList[1];
-    const countAt1 = countForMonomerAtPosition(df, seqCol, df.filter, splitter, 'G', atPI1);
+    const uh = UnitsHandler.getOrCreate(seqCol);
+    const countAt1 = countForMonomerAtPosition(df, uh, df.filter, 'G', atPI1);
     expect(countAt1, 5);
-  });
+  }, {skipReason: 'GROK-13300'});
 });
 
 function expectPositionInfo(actualPos: PI, expectedPos: PI): void {

package/src/tests/_first-tests.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {category, test} from '@datagrok-libraries/utils/src/test';
 
 category('_first', () => {
   /** The first test of the package to evaluate problems with imports. */

package/src/tests/activity-cliffs-tests.ts

@@ -6,6 +6,7 @@ import {after, before, category, test} from '@datagrok-libraries/utils/src/test'
 
 import {readDataframe} from './utils';
 import {_testActivityCliffsOpen} from './activity-cliffs-utils';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 
 
 category('activityCliffs', async () => {
@@ -28,20 +29,23 @@ category('activityCliffs', async () => {
   });
 
   test('activityCliffsOpens', async () => {
-    actCliffsDf = await readDataframe('tests/sample_MSA_data.csv');
+    actCliffsDf = await readDataframe(
+      DG.Test.isInBenchmark ? 'test/peptides_motif-with-random_10000.csv' : 'tests/100_3_clustests.csv',
+    );
     dfList.push(actCliffsDf);
     actCliffsTableView = grok.shell.addTableView(actCliffsDf);
     viewList.push(actCliffsTableView);
+    const cliffsNum = DG.Test.isInBenchmark ? 6 : 3;
 
-    await _testActivityCliffsOpen(actCliffsDf, 57, 'UMAP', 'MSA');
-  }, {skipReason: 'GROK-12774'});
+    await _testActivityCliffsOpen(actCliffsDf, cliffsNum, DimReductionMethods.UMAP, 'sequence');
+  });
 
   test('activityCliffsWithEmptyRows', async () => {
-    actCliffsDfWithEmptyRows = await readDataframe('tests/sample_MSA_data_empty_vals.csv');
+    actCliffsDfWithEmptyRows = await readDataframe('tests/100_3_clustests_empty_vals.csv');
     dfList.push(actCliffsDfWithEmptyRows);
     actCliffsTableViewWithEmptyRows = grok.shell.addTableView(actCliffsDfWithEmptyRows);
     viewList.push(actCliffsTableViewWithEmptyRows);
 
-    await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 57, 'UMAP', 'MSA');
-  }, {skipReason: 'GROK-12774'});
+    await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 3, DimReductionMethods.UMAP, 'sequence');
+  });
 });

package/src/tests/activity-cliffs-utils.ts

@@ -1,14 +1,16 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {delay, expect} from '@datagrok-libraries/utils/src/test';
+import {expect} from '@datagrok-libraries/utils/src/test';
 import {activityCliffs} from '../package';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 
-export async function _testActivityCliffsOpen(df: DG.DataFrame, numberCliffs: number, method: string, colName: string) {
+export async function _testActivityCliffsOpen(df: DG.DataFrame, numberCliffs: number, method: DimReductionMethods,
+  colName: string) {
   await grok.data.detectSemanticTypes(df);
   const scatterPlot = await activityCliffs(
-    df, df.getCol(colName), df.getCol('Activity'),
-    50, method);
+    df, df.getCol(colName), df.getCol('activity'),
+    90, method);
   // const scatterPlot = (await grok.functions.call('Bio:activityCliffs', {
   //   table: df, molecules: df.getCol(colName), activities: df.getCol('Activity'),
   //   similarity: 50, methodName: method

package/src/tests/bio-tests.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 {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
 import {
   getAlphabetSimilarity,
-  getStats,
   monomerToShort,
   pickUpPalette,
   splitterAsFasta,
@@ -14,13 +13,14 @@ import {
 import {Nucleotides, NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
 import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
 import {UnknownSeqPalette} from '@datagrok-libraries/bio/src/unknown';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {getStatsForCol} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 
 category('bio', () => {
   const csvDfN1: string = `seq
 ACGTCT
 CAGTGT
-TTCAAC
-`;
+TTCAAC`;
 
   /** 2 - is an error monomer
    * This sequence set should be classified as nucleotides sequences.
@@ -29,44 +29,39 @@ TTCAAC
   const csvDfN1e: string = `seq
 ACGTAT
 CAGTTG
-TTCG2C
-`;
+TTCG2C`;
 
   /** Pure amino acids sequence */
   const csvDfAA1: string = `seq
 FWPHEYV
 YNRQWYV
-MKPSEYV
-`;
+MKPSEYV`;
 
   /** A - alanine, G - glycine, T -= threonine, C - cysteine, W - tryptophan
    * This sequence set should be detected as amino acids more than nucleotides.
    */
-  const csvDfAA2: string = `seq
+  const _csvDfAA2: string = `seq
 AGTCAT
 AGTCGC
-AGTCATW
-`;
+AGTCATW`;
 
   /** This sequence set should be recognized as unknown. */
   const csvDfX: string = `seq
 XZJ{}2
 5Z4733
 3Z6></
-675687
-`;
+675687`;
 
   // anonymous functions specified in test() registering must return Promise<any>
   test('testGetStatsHelm1', async () => {
     const csv = `seq
-PEPTIDE1{meI}$$$$
-`;
+PEPTIDE1{meI}$$$$`;
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
     const seqCol: DG.Column = df.getCol('seq')!;
-    const stats = getStats(seqCol, 1, splitterAsHelm);
+    const stats = getStatsForCol(seqCol, 1, splitterAsHelm);
 
     expectObject(stats.freq, {
-      'meI': 1
+      'meI': 1,
     });
     expect(stats.sameLength, true);
   });
@@ -82,19 +77,19 @@ PEPTIDE1{meI}$$$$
 
 category('WebLogo.monomerToShort', () => {
   test('longMonomerSingle', async () => {
-    await expect(monomerToShort('S', 5), 'S');
+    expect(monomerToShort('S', 5), 'S');
   });
   test('longMonomerShort', async () => {
-    await expect(monomerToShort('Short', 5), 'Short');
+    expect(monomerToShort('Short', 5), 'Short');
   });
   test('longMonomerLong56', async () => {
-    await expect(monomerToShort('Long56', 5), 'Long5…');
+    expect(monomerToShort('Long56', 5), 'Long5…');
   });
   test('longMonomerComplexFirstPartShort', async () => {
-    await expect(monomerToShort('Long-long', 5), 'Long…');
+    expect(monomerToShort('Long-long', 5), 'Long…');
   });
   test('longMonomerComplexFirstPartLong56', async () => {
-    await expect(monomerToShort('Long56-long', 5), 'Long5…');
+    expect(monomerToShort('Long56-long', 5), 'Long5…');
   });
 });
 
@@ -102,13 +97,13 @@ 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 = getStats(seqCol, 5, splitterAsFasta);
+  const stats = getStatsForCol(seqCol, 5, splitterAsFasta);
 
   expectObject(stats.freq, {
     'A': 4,
     'C': 5,
     'G': 3,
-    'T': 6
+    'T': 6,
   });
   expect(stats.sameLength, true);
 }
@@ -119,7 +114,7 @@ export async function _testGetAlphabetSimilarity() {
     'C': 3015,
     'G': 3015,
     'T': 2048,
-    '-': 1000
+    '-': 1000,
   };
   const alphabet: Set<string> = new Set(Object.keys(Nucleotides.Names));
   const res = getAlphabetSimilarity(freq, alphabet);

package/src/tests/checkInputColumn-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, test, expect, expectArray} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect} from '@datagrok-libraries/utils/src/test';
 
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {checkInputColumn} from '../utils/check-input-column';
@@ -15,11 +15,6 @@ seq3,
 seq4`;
 
   test('testMsaPos', async () => {
-    const func: DG.Func = DG.Func.find({package: 'Bio', name: 'multipleSequenceAlignmentDialog'})[0];
-    const funcInputColumnProperty: DG.Property = func.inputs.find((i) => i.name == 'sequence')!;
-
-    const k = 11;
-
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
     const col: DG.Column = df.getCol('seq');
     col.semType = DG.SEMTYPE.MACROMOLECULE;
@@ -27,7 +22,7 @@ seq4`;
     col.setTag(bioTAGS.alphabet, ALPHABET.DNA);
     col.setTag(bioTAGS.aligned, 'SEQ');
 
-    const [res, msg]: [boolean, string] = checkInputColumn(
+    const [res, _msg]: [boolean, string] = checkInputColumn(
       col, 'Test', [NOTATION.FASTA],
       [ALPHABET.DNA, ALPHABET.RNA, ALPHABET.PT]);
 
@@ -42,7 +37,7 @@ seq4`;
     // col.setTag(bio.TAGS.alphabetSize, '11');
     col.setTag(bioTAGS.alphabetIsMultichar, 'true');
 
-    const [res, msg]: [boolean, string] = checkInputColumn(
+    const [res, _msg]: [boolean, string] = checkInputColumn(
       col, 'Test', [NOTATION.FASTA],
       [ALPHABET.DNA, ALPHABET.RNA, ALPHABET.PT]);
 
@@ -59,7 +54,7 @@ seq4`;
     col.setTag(bioTAGS.alphabetIsMultichar, 'true');
     col.setTag(bioTAGS.aligned, 'SEQ');
 
-    const [res, msg]: [boolean, string] = checkInputColumn(
+    const [res, _msg]: [boolean, string] = checkInputColumn(
       col, 'Test', [NOTATION.FASTA],
       [ALPHABET.DNA, ALPHABET.RNA, ALPHABET.PT]);
 
@@ -68,7 +63,6 @@ seq4`;
 
   test('testGetActionFunctionMeta', async () => {
     const func: DG.Func = DG.Func.find({package: 'Bio', name: 'multipleSequenceAlignmentDialog'})[0];
-    const sequenceInput: DG.Property = func.inputs.find((i) => i.name == 'sequence')!;
-    const k = 11;
+    const _sequenceInput: DG.Property = func.inputs.find((i) => i.name == 'sequence')!;
   });
 });

package/src/tests/converters-test.ts

@@ -45,94 +45,76 @@ category('converters', () => {
     fastaPt: `seq
 FWPHEY
 YNRQWYV
-MKPSEYV
-`,
+MKPSEYV`,
     separatorPt: `seq
 F-W-P-H-E-Y
 Y-N-R-Q-W-Y-V
-M-K-P-S-E-Y-V
-`,
+M-K-P-S-E-Y-V`,
     helmPt: `seq
 PEPTIDE1{F.W.P.H.E.Y}$$$$
 PEPTIDE1{Y.N.R.Q.W.Y.V}$$$$
-PEPTIDE1{M.K.P.S.E.Y.V}$$$$
-`,
+PEPTIDE1{M.K.P.S.E.Y.V}$$$$`,
     fastaDna: `seq
 ACGTC
 CAGTGT
-TTCAAC
-`,
+TTCAAC`,
     separatorDna: `seq
 A/C/G/T/C
 C/A/G/T/G/T
-T/T/C/A/A/C
-`,
+T/T/C/A/A/C`,
     helmDna: `seq
 DNA1{D(A)P.D(C)P.D(G)P.D(T)P.D(C)P}$$$$
 DNA1{D(C)P.D(A)P.D(G)P.D(T)P.D(G)P.D(T)P}$$$$
-DNA1{D(T)P.D(T)P.D(C)P.D(A)P.D(A)P.D(C)P}$$$$
-`,
+DNA1{D(T)P.D(T)P.D(C)P.D(A)P.D(A)P.D(C)P}$$$$`,
     fastaRna: `seq
 ACGUC
 CAGUGU
-UUCAAC
-`,
+UUCAAC`,
     separatorRna: `seq
 A*C*G*U*C
 C*A*G*U*G*U
-U*U*C*A*A*C
-`,
+U*U*C*A*A*C`,
     helmRna: `seq
 RNA1{R(A)P.R(C)P.R(G)P.R(U)P.R(C)P}$$$$
 RNA1{R(C)P.R(A)P.R(G)P.R(U)P.R(G)P.R(U)P}$$$$
-RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$$
-`,
+RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$$`,
     fastaGaps: `seq
 FW-PH-EYY
 FYNRQWYV-
-FKP-Q-SEYV
-`,
+FKP-Q-SEYV`,
     separatorGaps: `seq
 F/W//P/H//E/Y/Y
 F/Y/N/R/Q/W/Y/V/
-F/K/P//Q//S/E/Y/V
-`,
+F/K/P//Q//S/E/Y/V`,
     helmGaps: `seq
 PEPTIDE1{F.W.*.P.H.*.E.Y.Y}$$$$
 PEPTIDE1{F.Y.N.R.Q.W.Y.V.*}$$$$
-PEPTIDE1{F.K.P.*.Q.*.S.E.Y.V}$$$$
-`,
+PEPTIDE1{F.K.P.*.Q.*.S.E.Y.V}$$$$`,
 
     fastaUn: `seq
 [meI][hHis][Aca]NT[dE][Thr_PO3H2][Aca]D
 [meI][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]
-[Lys_Boc][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]
-`,
+[Lys_Boc][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]`,
     separatorUn: `seq
 meI-hHis-Aca-N-T-dE-Thr_PO3H2-Aca-D
 meI-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2
-Lys_Boc-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2
-`,
+Lys_Boc-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2`,
     helmUn: `seq
 PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D}$$$$
 PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$
-PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$
-`,
+PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$`,
     helmLoneDeoxyribose: `seq
 DNA1{D(A).D(C).D(G).D(T).D(C)}$$$$
 DNA1{D(C).D(A).D(G).D(T).D(G).D(T)P}$$$$
-DNA1{D(T).D(T).D(C).D(A).D(A).D(C)P}$$$$
-`,
+DNA1{D(T).D(T).D(C).D(A).D(A).D(C)P}$$$$`,
     helmLoneRibose: `seq
 RNA1{R(A).R(C).R(G).R(U).R(C)}$$$$
 RNA1{R(C).R(A).R(G).R(U).R(G).R(U)P}$$$$
-RNA1{R(U).R(U).R(C).R(A).R(A).R(C)P}$$$$
-`,
+RNA1{R(U).R(U).R(C).R(A).R(A).R(C)P}$$$$`,
     helmLonePhosphorus: `seq
 RNA1{P.P.R(A)P.R(C)P.R(G)P.R(U)P.R(C)P}$$$$
 RNA1{P.P.R(C)P.R(A)P.P.R(G)P.R(U)P.R(G)P.R(U)P}$$$$
-RNA1{P.R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P.P.P}$$$$
-`,
+RNA1{P.R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P.P.P}$$$$`,
   };
 
   /** Also detects semantic types
@@ -171,7 +153,7 @@ RNA1{P.R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P.P.P}$$$$
     const tgtCol: DG.Column = tgtDf.getCol('seq');
 
     expectArray(resCol.toList(), tgtCol.toList());
-    const uh: UnitsHandler = new UnitsHandler(resCol);
+    const _uh: UnitsHandler = UnitsHandler.getOrCreate(resCol);
   }
 
   // FASTA tests