@datagrok/bio 1.7.4 → 1.7.7

package/src/utils/cell-renderer.ts

@@ -9,6 +9,7 @@ import * as ui from 'datagrok-api/ui';
 
 const lru = new DG.LruCache<any, any>();
 const undefinedColor = 'rgb(100,100,100)';
+const grayColor = '#808080'
 
 function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
@@ -81,7 +82,7 @@ function printLeftOrCentered(
     g.fillStyle = color;
     g.globalAlpha = transparencyRate;
     g.fillText(colorPart, x + dx1, y + dy);
-    g.fillStyle = '#808080';
+    g.fillStyle = grayColor;
     g.fillText(grayPart, x + dx2, y + dy);
   }
 
@@ -96,6 +97,22 @@ function printLeftOrCentered(
   }
 }
 
+function findMonomers(helmString: string) {
+  //@ts-ignore
+  const types = Object.keys(org.helm.webeditor.monomerTypeList());
+  const monomers: any = [];
+  const monomer_names: any = [];
+  for (var i = 0; i < types.length; i++) {
+    //@ts-ignore
+    monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
+    Object.keys(monomers[i]).forEach(k => {
+      monomer_names.push(monomers[i][k].id);
+    });
+  }
+  const split_string = WebLogo.splitterAsHelm(helmString);
+  return new Set(split_string.filter(val => !monomer_names.includes(val)));
+}
+
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   get name(): string { return 'macromoleculeSequence'; }
 
@@ -125,22 +142,47 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const cell = gridCell.cell;
     const tag = gridCell.cell.column.getTag(DG.TAGS.UNITS);
     if (tag === 'HELM') {
-      const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
-      host.setAttribute('dataformat', 'helm');
-      host.setAttribute('data', gridCell.cell.value);
-      gridCell.element = host;
-      //@ts-ignore
-      const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
-      const formula = canvas.getFormula(true);
-      if (!formula) {
-        gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
-      } else {
+      console.log(findMonomers(cell.value));
+      const monomers = findMonomers(cell.value);
+      if (monomers.size == 0) {
+        const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
+        host.setAttribute('dataformat', 'helm');
+        host.setAttribute('data', gridCell.cell.value);
         gridCell.element = host;
-        const molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
-        const coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
-        const molfile = canvas.getMolfile();
-        const result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
-        lru.set(gridCell.cell.value, result);
+        //@ts-ignore
+        const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
+        const formula = canvas.getFormula(true);
+        if (!formula) {
+          gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
+        }
+        return;
+      }
+      if (monomers.size > 0) {
+        w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+        g.save();
+        g.beginPath();
+        g.rect(x, y, w, h);
+        g.clip();
+        g.font = '12px monospace';
+        g.textBaseline = 'top';
+        let x1 = x;
+        const s: string = cell.value ?? '';
+        let subParts: string[] = WebLogo.splitterAsHelm(s);
+        let color = undefinedColor;
+        subParts.forEach((amino, index) => {
+          if (monomers.has(amino)) {
+            color = 'red';
+          } else {
+            color = grayColor;
+          }
+          g.fillStyle = undefinedColor;
+          let last = false;
+          if (index === subParts.length - 1)
+            last = true;
+          x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, '/', last);
+        });
+        g.restore();
+        return;
       }
     } else {
       const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
@@ -176,6 +218,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       });
 
       g.restore();
+      return;
     }
   }
 }

package/src/utils/convert.ts

@@ -1,7 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+
+import {Subscription} from 'rxjs';
 import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
 
+
+let convertDialog: DG.Dialog | null = null;
+let convertDialogSubs: Subscription[] = [];
+
 /**
  * Converts notations of a Macromolecule column
  *
@@ -22,19 +29,37 @@ export function convert(col: DG.Column): void {
 
   const separatorInput = ui.choiceInput('Choose separator', separatorArray[0], separatorArray);
 
-  ui.dialog('Convert sequence notation')
-    .add(ui.div([
-      ui.h1('Current notation: ' + current),
-      targetNotationInput.root,
-      // TODO: conditional separator input
-      separatorInput.root
-    ]))
-    .onOK(() => {
-      //TODO: create new converted column
-      const targetNotation = targetNotationInput.value as NOTATION;
-      const separator = separatorInput.value!;
-      const newColumn = converter.convert(targetNotation, separator);
-      col.dataFrame.columns.add(newColumn);
-    })
-    .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 () => {
+        const targetNotation = targetNotationInput.value as NOTATION;
+        const separator: string | null = separatorInput.value;
+
+        await convertDo(col, targetNotation, separator);
+      })
+      .show();
+
+    convertDialogSubs.push(convertDialog.onClose.subscribe((value) => {
+      convertDialogSubs.forEach((s) => { s.unsubscribe(); });
+      convertDialogSubs = [];
+      convertDialog = null;
+    }));
+  }
+}
+
+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

@@ -32,7 +32,7 @@ function _fastaToStrings(fasta: string): string[] {
  * @param {boolean} isAligned Whether the column is aligned.
  * @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 +56,7 @@ 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

@@ -1,6 +1,7 @@
 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';
 
 export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
 export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
@@ -43,3 +44,37 @@ export function createMomomersMolDict(lib: any[]): { [key: string]: string | any
   });
   return dict;
 }
+
+
+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 => {
+      if (key === MONOMER_SYMBOL) {
+        const monomerSymbol = table.get(jsonSdfMonomerLibDict[key], i);
+        monomer[key] = monomerSymbol === '.' ? table.get(SDF_MONOMER_NAME, i) : monomerSymbol;
+      } else if (key === RGROUP_FIELD) {
+        const rgroups = table.get(jsonSdfMonomerLibDict[key], i).split('\n');
+        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];
+          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]) {
+          monomer[key] = table.get((jsonSdfMonomerLibDict as { [key: string]: string | any })[key], i);
+        }
+      }
+    })
+    resultLib.push(monomer);
+  }
+  return resultLib;
+}

package/test-Bio-34f75e5127b8-7c42ea4b.html

@@ -0,0 +1,335 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 7c42ea4b.</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 {
+  margin: 0;
+  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 {
+    margin-right: 0;
+    margin-top: 2rem;
+  }
+  #summary > div:first-child {
+    margin-top: 0;
+  }
+}
+
+.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,
+.summary-obsolete-snapshots {
+  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;
+}
+.test-result.failed {
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.test-result.pending {
+  background-color: #ffdf61;
+  color: #9f6000;
+}
+
+.test-info {
+  display: flex;
+  justify-content: space-between;
+}
+.test-suitename {
+  width: 20%;
+  text-align: left;
+  font-weight: bold;
+  word-break: break-word;
+}
+.test-title {
+  width: 40%;
+  text-align: left;
+  font-style: italic;
+}
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+  width: 20%;
+  text-align: right;
+}
+.test-duration {
+  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;
+}
+.failureMsg {
+  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;
+}
+.suite-info {
+  padding: 1rem;
+  background-color: #eee;
+  color: #777;
+  display: flex;
+  align-items: center;
+  margin-bottom: 0.25rem;
+}
+.suite-info .suite-path {
+  word-break: break-all;
+  flex-grow: 1;
+  font-family: monospace;
+  font-size: 1rem;
+}
+.suite-info .suite-time {
+  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;
+}
+.suite-consolelog-item {
+  padding: 0.5rem;
+}
+.suite-consolelog-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-consolelog-item-origin {
+  color: #777;
+  font-weight: bold;
+}
+.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;
+}
+.suite-obsolete-snapshots-header {
+  font-weight: bold;
+}
+.suite-obsolete-snapshots-item {
+  padding: 0.5rem;
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+  margin: 0.5rem 0;
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+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-obsolete-snapshots-item-message {
+  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 7c42ea4b.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-15 17:01:22</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">175.127s</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">165.279s</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.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.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>