@datagrok/bio 1.7.5 → 1.7.8

package/src/tests/detectors-test.ts

@@ -113,6 +113,8 @@ MWRSWY-CKHP
     testIdCsv = 'testIdCsv',
     testSmilesCsv = 'testSmilesCsv',
     testSmiles2Csv = 'testSmiles2Csv',
+    testCerealCsv = 'testCerealCsv',
+    testActivityCliffsCsv = 'testActivityCliffsCsv',
   }
 
   const samples: { [key: string]: string } = {
@@ -128,6 +130,8 @@ MWRSWY-CKHP
     'testIdCsv': 'System:AppData/Bio/tests/testId.csv',
     'testSmilesCsv': 'System:AppData/Bio/tests/testSmiles.csv',
     'testSmiles2Csv': 'System:AppData/Bio/tests/testSmiles2.csv',
+    'testActivityCliffsCsv': 'System:AppData/Bio/tests/testActivityCliffs.csv', // smiles
+    'testCerealCsv': 'System:AppData/Bio/tests/testCereal.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -303,8 +307,16 @@ MWRSWY-CKHP
     await _testNeg(readSamples(Samples.testSmiles2Csv), 'SMILES');
   });
 
+  test('samplesTestActivityCliffsNegativeSmiles', async () => {
+    await _testNeg(readSamples(Samples.testActivityCliffsCsv), 'smiles');
+  });
+
   test('samplesFastaPtPosSequence', async () => {
-    await (_testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT'));
+    await _testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT');
+  });
+
+  test('samplesTestCerealNegativeCerealName', async () => {
+    await _testNeg(readSamples(Samples.testCerealCsv), 'cereal_name');
   });
 });
 

package/src/tests/splitters-test.ts

@@ -21,10 +21,36 @@ category('splitters', () => {
       ['meI', 'hHis', 'Aca', 'N', 'T', 'dK', 'Thr_PO3H2', 'Aca',
         'D-Tyr_Et', 'D-Dap', 'dV', 'E', 'N', 'pnG', 'Phe_4Me']
     ],
+    // HELM editor dialog returns HELM string with multichar monomer names in square brackets
+    helm3: [
+      'PEPTIDE1{[meI].[hHis].[Aca].N.T.[dK].[Thr_PO3H2].[Aca].[D-Tyr_Et].[D-Dap].[dV].E.N.[pnG].[Phe_4Me]}$$$',
+      ['meI', 'hHis', 'Aca', 'N', 'T', 'dK', 'Thr_PO3H2', 'Aca',
+        'D-Tyr_Et', 'D-Dap', 'dV', 'E', 'N', 'pnG', 'Phe_4Me']
+    ],
+
+    testHelm1: [
+      'RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$',
+      ['R(U)P', 'R(T)P', 'R(G)P', 'R(C)P', 'R(A)']
+    ],
+
+    testHelm2: [
+      'RNA1{P.R(U)P.R(T)}$$$$',
+      ['P', 'R(U)P', 'R(T)']
+    ],
+    testHelm3: [
+      'RNA1{P.R(U).P.R(T)}$$$$',
+      ['P', 'R(U)', 'P', 'R(T)']
+    ],
   };
 
   test('helm1', async () => { await _testHelmSplitter(data.helm1[0], data.helm1[1]); });
   test('helm2', async () => { await _testHelmSplitter(data.helm2[0], data.helm2[1]); });
+  test('helm3-multichar', async () => { await _testHelmSplitter(data.helm3[0], data.helm3[1]); });
+
+  // examples from Helm/tests/test.csv file
+  test('testHelm1', async () => { await _testHelmSplitter(data.testHelm1[0], data.testHelm1[1]); });
+  test('testHelm2', async () => { await _testHelmSplitter(data.testHelm2[0], data.testHelm2[1]); });
+  test('testHelm3', async () => { await _testHelmSplitter(data.testHelm3[0], data.testHelm3[1]); });
 });
 
 export async function _testHelmSplitter(src: string, tgt: string[]) {

package/src/utils/cell-renderer.ts

@@ -219,7 +219,6 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
       g.restore();
       return;
-
     }
   }
 }

package/src/utils/convert.ts

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
+import $ from 'cash-dom';
 
 import {Subscription} from 'rxjs';
 import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
@@ -27,14 +28,26 @@ export function convert(col: DG.Column): void {
   const filteredNotations = notations.filter((e) => e !== current);
   const targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations);
 
-  const separatorInput = ui.choiceInput('Choose separator', separatorArray[0], separatorArray);
+  const separatorInput = ui.choiceInput('Separator', separatorArray[0], separatorArray);
+
+  // hide the separator input for non-SEPARATOR target notations
+  if (targetNotationInput.value !== NOTATION.SEPARATOR)
+    $(separatorInput.root).hide();
+  else
+    $(separatorInput.root).show();
+
+  targetNotationInput.onChanged(async () => {
+    if (targetNotationInput.value !== NOTATION.SEPARATOR)
+      $(separatorInput.root).hide();
+    else
+      $(separatorInput.root).show();
+  });
 
   if (convertDialog == null) {
     convertDialog = ui.dialog('Convert sequence notation')
       .add(ui.div([
         ui.h1('Current notation: ' + current),
         targetNotationInput.root,
-        // TODO: conditional separator input
         separatorInput.root
       ]))
       .onOK(async () => {
@@ -46,18 +59,19 @@ export function convert(col: DG.Column): void {
       .show();
 
     convertDialogSubs.push(convertDialog.onClose.subscribe((value) => {
-      convertDialogSubs.forEach((s) => {s.unsubscribe(); });
+      convertDialogSubs.forEach((s) => { s.unsubscribe(); });
       convertDialogSubs = [];
       convertDialog = null;
     }));
   }
 }
 
-export async function convertDo(srcCol: DG.Column, targetNotation: NOTATION, separator: string | null): Promise<DG.Column> {
+export async function convertDo(
+  srcCol: DG.Column, targetNotation: NOTATION, separator: string | null
+): Promise<DG.Column> {
   const converter = new NotationConverter(srcCol);
   const newColumn = converter.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);
   await grok.data.detectSemanticTypes(srcCol.dataFrame);
   return newColumn;
 }
-

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

@@ -30,9 +30,10 @@ function _fastaToStrings(fasta: string): string[] {
  *
  * @param {DG.Column} srcCol Column with sequences.
  * @param {boolean} isAligned Whether the column is aligned.
+ * @param {string} unUsedName
  * @return {Promise<DG.Column>} Aligned sequences.
  */
-export async function runKalign(srcCol: DG.Column, isAligned = false): Promise<DG.Column> {
+export async function runKalign(srcCol: DG.Column, isAligned = false, unUsedName: string = ''): Promise<DG.Column> {
   let sequences = srcCol.toList();
 
   if (isAligned)
@@ -56,7 +57,7 @@ export async function runKalign(srcCol: DG.Column, isAligned = false): Promise<D
     throw new Error(`kalign output no result`);
 
   const aligned = _fastaToStrings(buf).slice(0, sequences.length);
-  const tgtCol = DG.Column.fromStrings(`msa(${srcCol.name})`, aligned);
+  const tgtCol = DG.Column.fromStrings(unUsedName, aligned);
 
   // units
   const srcUnits = srcCol.getTag(DG.TAGS.UNITS);

package/src/utils/utils.ts

@@ -1,7 +1,10 @@
 import * as DG from 'datagrok-api/dg';
 import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import * as grok from 'datagrok-api/grok';
-import { CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL, RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME } from '../const';
+import {
+  CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL,
+  RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME
+} from '../const';
 
 export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
 export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
@@ -50,7 +53,7 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
   const resultLib = [];
   for (let i = 0; i < table.rowCount; i++) {
     const monomer: { [key: string]: string | any } = {};
-    Object.keys(jsonSdfMonomerLibDict).forEach(key => {
+    Object.keys(jsonSdfMonomerLibDict).forEach((key) => {
       if (key === MONOMER_SYMBOL) {
         const monomerSymbol = table.get(jsonSdfMonomerLibDict[key], i);
         monomer[key] = monomerSymbol === '.' ? table.get(SDF_MONOMER_NAME, i) : monomerSymbol;
@@ -59,21 +62,20 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
         const jsonRgroups: any[] = [];
         rgroups.forEach((g: string) => {
           const rgroup: { [key: string]: string | any } = {};
-          const altAtom = g.substring(g.lastIndexOf("]") + 1);
-          let radicalNum = g.match(/\[R(\d+)\]/)![1];
+          const altAtom = g.substring(g.lastIndexOf(']') + 1);
+          const radicalNum = g.match(/\[R(\d+)\]/)![1];
           rgroup[CAP_GROUP_SMILES] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
           rgroup[RGROUP_ALTER_ID] = altAtom === 'H' ? `R${radicalNum}-H` : `R${radicalNum}-OH`;
           rgroup[CAP_GROUP_NAME] = altAtom === 'H' ? `H` : `OH`;
           rgroup[RGROUP_LABEL] = `R${radicalNum}`;
           jsonRgroups.push(rgroup);
-        })
+        });
         monomer[key] = jsonRgroups;
       } else {
-        if((jsonSdfMonomerLibDict as { [key: string]: string | any })[key]) {
+        if ((jsonSdfMonomerLibDict as { [key: string]: string | any })[key])
           monomer[key] = table.get((jsonSdfMonomerLibDict as { [key: string]: string | any })[key], i);
-        }
       }
-    })
+    });
     resultLib.push(monomer);
   }
   return resultLib;

package/test-Bio-34f75e5127b8-cdc230d8.html

@@ -0,0 +1,339 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit cdc230d8.</title><style type="text/css">html,
+body {
+  font-family: Arial, Helvetica, sans-serif;
+  font-size: 1rem;
+  margin: 0;
+  padding: 0;
+  color: #333;
+}
+body {
+  padding: 2rem 1rem;
+  font-size: 0.85rem;
+}
+#jesthtml-content {
+  margin: 0 auto;
+  max-width: 70rem;
+}
+header {
+  display: flex;
+  align-items: center;
+}
+#title {
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+  flex-grow: 1;
+}
+#logo {
+  height: 4rem;
+}
+#timestamp {
+  color: #777;
+  margin-top: 0.5rem;
+}
+
+/** SUMMARY */
+#summary {
+  color: #333;
+  margin: 2rem 0;
+  display: flex;
+  font-family: monospace;
+  font-size: 1rem;
+}
+#summary > div {
+  margin-right: 2rem;
+  background: #eee;
+  padding: 1rem;
+  min-width: 15rem;
+}
+#summary > div:last-child {
+  margin-right: 0;
+}
+@media only screen and (max-width: 720px) {
+  #summary {
+    flex-direction: column;
+  }
+  #summary > div {
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+    margin-top: 2rem;
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+  #summary > div:first-child {
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+  }
+}
+
+.summary-total {
+  font-weight: bold;
+  margin-bottom: 0.5rem;
+}
+.summary-passed {
+  color: #4f8a10;
+  border-left: 0.4rem solid #4f8a10;
+  padding-left: 0.5rem;
+}
+.summary-failed,
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+  color: #d8000c;
+  border-left: 0.4rem solid #d8000c;
+  padding-left: 0.5rem;
+}
+.summary-pending {
+  color: #9f6000;
+  border-left: 0.4rem solid #9f6000;
+  padding-left: 0.5rem;
+}
+.summary-empty {
+  color: #999;
+  border-left: 0.4rem solid #999;
+}
+
+.test-result {
+  padding: 1rem;
+  margin-bottom: 0.25rem;
+}
+.test-result:last-child {
+  border: 0;
+}
+.test-result.passed {
+  background-color: #dff2bf;
+  color: #4f8a10;
+}
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+  background-color: #ffbaba;
+  color: #d8000c;
+}
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+  background-color: #ffdf61;
+  color: #9f6000;
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+.test-info {
+  display: flex;
+  justify-content: space-between;
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+.test-suitename {
+  width: 20%;
+  text-align: left;
+  font-weight: bold;
+  word-break: break-word;
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+  font-style: italic;
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+  text-align: right;
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+  width: 10%;
+  text-align: right;
+  font-size: 0.75rem;
+}
+
+.failureMessages {
+  padding: 0 1rem;
+  margin-top: 1rem;
+  border-top: 1px dashed #d8000c;
+}
+.failureMessages.suiteFailure {
+  border-top: none;
+}
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+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+
+.suite-container {
+  margin-bottom: 2rem;
+}
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+  padding: 1rem;
+  background-color: #eee;
+  color: #777;
+  display: flex;
+  align-items: center;
+  margin-bottom: 0.25rem;
+}
+.suite-info .suite-path {
+  word-break: break-all;
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+  font-family: monospace;
+  font-size: 1rem;
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+  margin-left: 0.5rem;
+  padding: 0.2rem 0.3rem;
+  font-size: 0.75rem;
+}
+.suite-info .suite-time.warn {
+  background-color: #d8000c;
+  color: #fff;
+}
+
+/* CONSOLE LOGS */
+.suite-consolelog {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #efefef;
+}
+.suite-consolelog-header {
+  font-weight: bold;
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+  margin: 0.5rem 0;
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+  font-weight: bold;
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+.suite-consolelog-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+
+/* OBSOLETE SNAPSHOTS */
+.suite-obsolete-snapshots {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #ffbaba;
+  color: #d8000c;
+}
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+  font-weight: bold;
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+}
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+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit cdc230d8.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-19 10:23:49</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">179.806s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">168.85s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
+Test result : Bio.splitters.testHelm1 : Error: Expected R(U)P at position 0, got U
+Test result : Bio.splitters.testHelm2 : Error: Expected R(U)P at position 1, got U
+Test result : Bio.splitters.testHelm3 : Error: Expected R(U) at position 1, got U)
+Test result : Bio.converters.testFastaGapsToSeparator : Error: Units are not specified in column
+Test result : Bio.converters.testFastaGapsToHelm : Error: Units are not specified in column
+Test result : Bio.converters.HelmDnaToFasta : Error: Units are not specified in column
+Test result : Bio.converters.HelmDnaToSeparator : Error: Units are not specified in column
+
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:67:20
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
+    at runMicrotasks (&lt;anonymous&gt;)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:40:11
+    at Generator.next (&lt;anonymous&gt;)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
+    at new Promise (&lt;anonymous&gt;)
+    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
+    at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:65:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
+    at runMicrotasks (&lt;anonymous&gt;)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Bio.WebLogo.testGetStats : OK
+Test result : Bio.WebLogo.testGetAlphabetSimilarity : OK
+Test result : Bio.WebLogo.testPickupPaletteN1 : OK
+Test result : Bio.WebLogo.testPickupPaletteN1e : OK
+Test result : Bio.WebLogo.testPickupPaletteAA1 : OK
+Test result : Bio.WebLogo.testPickupPaletteX : OK
+Test result : Bio.WebLogo.monomerToText.longMonomerSingle : OK
+Test result : Bio.WebLogo.monomerToText.longMonomerShort : OK
+Test result : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
+Test result : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
+Test result : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
+Test result : Bio.Palettes.testPaletteN : OK
+Test result : Bio.Palettes.testPaletteAA : OK
+Test result : Bio.detectors.Negative1 : OK
+Test result : Bio.detectors.Negative2 : OK
+Test result : Bio.detectors.Negative3 : OK
+Test result : Bio.detectors.NegativeSmiles : OK
+Test result : Bio.detectors.Dna1 : OK
+Test result : Bio.detectors.Rna1 : OK
+Test result : Bio.detectors.AA1 : OK
+Test result : Bio.detectors.MsaDna1 : OK
+Test result : Bio.detectors.MsaAA1 : OK
+Test result : Bio.detectors.SepDna : OK
+Test result : Bio.detectors.SepRna : OK
+Test result : Bio.detectors.SepPt : OK
+Test result : Bio.detectors.SepUn1 : OK
+Test result : Bio.detectors.SepUn2 : OK
+Test result : Bio.detectors.SepMsaN1 : OK
+Test result : Bio.detectors.SamplesFastaCsvPt : OK
+Test result : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
+Test result : Bio.detectors.SamplesFastaCsvNegativeLength : OK
+Test result : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
+Test result : Bio.detectors.SamplesFastaFastaPt : OK
+Test result : Bio.detectors.samplesPeptidesComplexNegativeID : OK
+Test result : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
+Test result : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
+Test result : Bio.detectors.samplesMsaComplexUn : OK
+Test result : Bio.detectors.samplesMsaComplexNegativeActivity : OK
+Test result : Bio.detectors.samplesIdCsvNegativeID : OK
+Test result : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
+Test result : Bio.detectors.samplesHelmCsvHELM : OK
+Test result : Bio.detectors.samplesHelmCsvNegativeActivity : OK
+Test result : Bio.detectors.samplesTestHelmNegativeID : OK
+Test result : Bio.detectors.samplesTestHelmNegativeTestType : OK
+Test result : Bio.detectors.samplesTestHelmPositiveHelmString : OK
+Test result : Bio.detectors.samplesTestHelmNegativeValid : OK
+Test result : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
+Test result : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
+Test result : Bio.detectors.samplesTestHelmNegativeSmiles : OK
+Test result : Bio.detectors.samplesTestDemogNegativeAll : OK
+Test result : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
+Test result : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
+Test result : Bio.detectors.samplesFastaPtPosSequence : OK
+Test result : Bio.detectors.samplesTestCerealNegativeCerealName : OK
+Test result : Bio.MSA.test_table.is_not_empty : OK
+Test result : Bio.sequenceSpace.sequenceSpaceOpens : OK
+Test result : Bio.activityCliffs.activityCliffsOpen : OK
+Test result : Bio.splitters.helm1 : OK
+Test result : Bio.splitters.helm2 : OK
+Test result : Bio.splitters.helm3-multichar : OK
+Test result : Bio.renderers.afterMsa : OK
+Test result : Bio.renderers.afterConvert : OK
+Test result : Bio.converters.testFastaPtToSeparator : OK
+Test result : Bio.converters.testFastaDnaToSeparator : OK
+Test result : Bio.converters.testFastaRnaToSeparator : OK
+Test result : Bio.converters.testFastaPtToHelm : OK
+Test result : Bio.converters.testFastaDnaToHelm : OK
+Test result : Bio.converters.testFastaRnaToHelm : OK
+Test result : Bio.converters.testSeparatorPtToFasta : OK
+Test result : Bio.converters.testSeparatorDnaToFasta : OK
+Test result : Bio.converters.testSeparatorRnaToFasta : OK
+Test result : Bio.converters.testSeparatorGapsToFasta : OK
+Test result : Bio.converters.testSeparatorPtToHelm : OK
+Test result : Bio.converters.testSeparatorDnaToHelm : OK
+Test result : Bio.converters.testSeparatorRnaToHelm : OK
+Test result : Bio.converters.testSeparatorGapsToHelm : OK
+Test result : Bio.converters.HelmRnaToFasta : OK
+Test result : Bio.converters.HelmPtToFasta : OK
+Test result : Bio.converters.HelmRnaToSeparator : OK
+Test result : Bio.converters.HelmPtToSeparator : OK
+</pre></div></div></div></div></body></html>