@datagrok/bio 2.0.4 → 2.0.6

package/src/utils/cell-renderer.ts

@@ -227,18 +227,18 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
     const color = palette.get(s);
 
     g.fillStyle = color;
-    g.fillText(s, x + (w / 2), y - (h / 2), w);
+    g.fillText(s, x + (w / 2), y + (h / 2), w);
   }
 }
 
 export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
-  get name(): string {return 'MacromoleculeDifferenceCR';}
+  get name(): string { return 'MacromoleculeDifferenceCR'; }
 
-  get cellType(): string {return C.SEM_TYPES.MACROMOLECULE_DIFFERENCE;}
+  get cellType(): string { return C.SEM_TYPES.MACROMOLECULE_DIFFERENCE; }
 
-  get defaultHeight(): number {return 30;}
+  get defaultHeight(): number { return 30; }
 
-  get defaultWidth(): number {return 230;}
+  get defaultWidth(): number { return 230; }
 
   /**
    * Cell renderer function.
@@ -254,51 +254,69 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
    */
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-    cellStyle: DG.GridCellStyle): void {
+    _cellStyle: DG.GridCellStyle): void {
     const grid = gridCell.grid;
     const cell = gridCell.cell;
-
-    w = getUpdatedWidth(grid, g, w, x);
-    g.save();
-    g.beginPath();
-    g.rect(x, y, w, h);
-    g.clip();
-    g.font = '12px monospace';
-    g.textBaseline = 'top';
     const s: string = cell.value ?? '';
-
-    //TODO: can this be replaced/merged with splitSequence?
-    const [s1, s2] = s.split('#');
     const separator = gridCell.tableColumn!.tags[C.TAGS.SEPARATOR];
     const units: string = gridCell.tableColumn!.tags[DG.TAGS.UNITS];
-    const splitter = WebLogo.getSplitter(units, separator);
-    const subParts1 = splitter(s1);
-    const subParts2 = splitter(s2);
-    const [text] = processSequence(subParts1);
-    const textSize = g.measureText(text.join(''));
-    let updatedX = Math.max(x, x + (w - (textSize.width + subParts1.length * 4)) / 2);
-    // 28 is the height of the two substitutions on top of each other + space
-    const updatedY = Math.max(y, y + (h - 28) / 2);
-
-    let palette: SeqPalette = UnknownSeqPalettes.Color;
-    if (units != 'HELM')
-      palette = getPaletteByType(units.substring(units.length - 2));
-
-    const vShift = 7;
-    for (let i = 0; i < subParts1.length; i++) {
-      const amino1 = subParts1[i];
-      const amino2 = subParts2[i];
-      const color1 = palette.get(amino1);
-
-      if (amino1 != amino2) {
-        const color2 = palette.get(amino2);
-        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);
-      } else
-        updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
-      updatedX += 4;
-    }
-    g.restore();
+    w = getUpdatedWidth(grid, g, x, w);
+    drawMoleculeDifferenceOnCanvas(g, x, y, w, h, s, units, separator);
+  }
+}
+
+export function drawMoleculeDifferenceOnCanvas(
+  g: CanvasRenderingContext2D,
+  x: number,
+  y: number,
+  w: number,
+  h: number,
+  s: string,
+  units: string,
+  separator: string,
+  fullStringLength?: boolean) {
+
+  //TODO: can this be replaced/merged with splitSequence?
+  const [s1, s2] = s.split('#');
+  const splitter = WebLogo.getSplitter(units, separator);
+  const subParts1 = splitter(s1);
+  const subParts2 = splitter(s2);
+  const textSize1 = g.measureText(processSequence(subParts1).join(''));
+  const textSize2 = g.measureText(processSequence(subParts2).join(''));
+  const textWidth = Math.max(textSize1.width, textSize2.width);
+  if (fullStringLength) {
+    w = textWidth + subParts1.length * 4;
+    g.canvas.width = textWidth + subParts1.length * 4;
+  }
+  let updatedX = Math.max(x, x + (w - (textWidth + subParts1.length * 4)) / 2);
+  // 28 is the height of the two substitutions on top of each other + space
+  const updatedY = Math.max(y, y + (h - 28) / 2);
+
+  g.save();
+  g.beginPath();
+  g.rect(x, y, fullStringLength ? textWidth + subParts1.length * 4 : w, h);
+  g.clip();
+  g.font = '12px monospace';
+  g.textBaseline = 'top';
+
+  let palette: SeqPalette = UnknownSeqPalettes.Color;
+  if (units != 'HELM')
+    palette = getPaletteByType(units.substring(units.length - 2));
+
+  const vShift = 7;
+  for (let i = 0; i < subParts1.length; i++) {
+    const amino1 = subParts1[i];
+    const amino2 = subParts2[i];
+    const color1 = palette.get(amino1);
+
+    if (amino1 != amino2) {
+      const color2 = palette.get(amino2);
+      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);
+    } else
+      updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
+    updatedX += 4;
   }
+  g.restore();
 }

package/src/utils/convert.ts

@@ -79,6 +79,7 @@ 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: NOTATION, separator: string | null
 ): Promise<DG.Column> {

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

@@ -6,6 +6,8 @@ import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import * as grok from 'datagrok-api/grok';
 import { SplitterFunc, WebLogo } from '@datagrok-libraries/bio/src/viewers/web-logo';
 import { UnitsHandler } from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SEM_TYPES, TAGS} from '../utils/constants';
+import { drawMoleculeDifferenceOnCanvas } from './cell-renderer';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
   const stringArray = col.toList();
@@ -71,47 +73,33 @@ function moleculeInfo(df: DG.DataFrame, idx: number, seqColName: string): HTMLEl
 
 
 export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivElement {
-  const propPanel = ui.divV([]);
-  const columnNames = ui.divH([
-    ui.divText(params.seqCol.name),
-    ui.divText(params.activityCol.name),
-  ]);
-  columnNames.style.fontWeight = 'bold';
-  columnNames.style.justifyContent = 'space-between';
-  propPanel.append(columnNames);
-  const hosts: HTMLDivElement[] = [];
-  params.line.mols.forEach((molIdx: number, hostIdx: number) => {
-    const activity = ui.divText(params.activityCol.get(molIdx).toFixed(2));
-    activity.style.paddingLeft = '15px';
-    activity.style.paddingLeft = '10px';
-    const molHost = ui.divText(params.seqCol.get(molIdx));
-    if (params.df.currentRowIdx === molIdx) {
-      molHost.style.border = 'solid 1px lightgrey';
-    }
-    //@ts-ignore
-    ui.tooltip.bind(molHost, () => moleculeInfo(params.df, molIdx, params.seqCol.name));
-    molHost.onclick = () => {
-      const obj = grok.shell.o;
-      molHost.style.border = 'solid 1px lightgrey';
-      params.df.currentRowIdx = molIdx;
-      hosts.forEach((h, i) => {
-        if (i !== hostIdx) {
-          h.style.border = '';
-        }
-      })
-      setTimeout(() => {
-        grok.shell.o = obj
-      }, 1000);
-    };
-    propPanel.append(ui.divH([
-      molHost,
-      activity,
-    ]));
-    hosts.push(molHost);
+  const propPanel = ui.div();
+
+  propPanel.append(ui.divText(params.seqCol.name, { style: { fontWeight: 'bold' } }));
+
+  const sequencesArray = new Array<string>(2);
+  const activitiesArray = new Array<number>(2);
+  params.line.mols.forEach((molIdx, idx) => {
+    sequencesArray[idx] = params.seqCol.get(molIdx);
+    activitiesArray[idx] = params.activityCol.get(molIdx);
   });
-  propPanel.append(ui.divH([
-    ui.divText(`Cliff: `, {style: {fontWeight: 'bold', paddingRight: '5px'}}),
-    ui.divText(params.sali!.toFixed(2))
-  ]));
+  const canvas = document.createElement('canvas');
+  const context = canvas.getContext('2d');
+  canvas.height = 30;
+  const units = params.seqCol.getTag(DG.TAGS.UNITS);
+  const separator = params.seqCol.getTag(TAGS.SEPARATOR);
+  drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30, sequencesArray.join('#'), units, separator, true);
+  propPanel.append(ui.div(canvas, { style: { width: '300px', overflow: 'scroll' } }));
+
+  function addFiledToPropPanel(name: string, value: number) {
+    propPanel.append(ui.divH([
+      ui.divText(`${name}: `, { style: { fontWeight: 'bold', paddingRight: '5px' } }),
+      ui.divText(value.toFixed(2))
+    ], { style: { paddingTop: '5px' } }));
+  }
+
+  addFiledToPropPanel('Activity delta', Math.abs(activitiesArray[0] - activitiesArray[1]));
+  addFiledToPropPanel('Cliff', params.sali!);
+
   return propPanel;
 }

package/test-Bio-7770371320b2-046cde35.html

@@ -0,0 +1,372 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 046cde35.</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;
+}
+.test-status {
+  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;
+}
+.suite-obsolete-snapshots-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-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=7770371320b2. Commit 046cde35.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-16 12:11:55</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">46.232s</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">28.972s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 197 : Bio.renderers.setRendererManually : Error: Tag 'cell.renderer' has been manually set to 'MacromoleculeDifference' for column but after df was added as table, tag 'cell.renderer' has reset to 'sequence' instead of manual 'MacromoleculeDifference'.
+
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:68:20
+    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:66:11
+    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 : Success : 6 : Bio.WebLogo.testGetStats : OK
+Test result : Success : 0 : Bio.WebLogo.testGetAlphabetSimilarity : OK
+Test result : Success : 3 : Bio.WebLogo.testPickupPaletteN1 : OK
+Test result : Success : 1 : Bio.WebLogo.testPickupPaletteN1e : OK
+Test result : Success : 2 : Bio.WebLogo.testPickupPaletteAA1 : OK
+Test result : Success : 1 : Bio.WebLogo.testPickupPaletteX : OK
+Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerSingle : OK
+Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerShort : OK
+Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
+Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
+Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
+Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
+Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
+Test result : Success : 54 : Bio.detectors.NegativeEmpty : OK
+Test result : Success : 18 : Bio.detectors.Negative1 : OK
+Test result : Success : 31 : Bio.detectors.Negative2 : OK
+Test result : Success : 18 : Bio.detectors.Negative3 : OK
+Test result : Success : 15 : Bio.detectors.NegativeSmiles : OK
+Test result : Success : 10 : Bio.detectors.Dna1 : OK
+Test result : Success : 26 : Bio.detectors.Rna1 : OK
+Test result : Success : 48 : Bio.detectors.AA1 : OK
+Test result : Success : 16 : Bio.detectors.MsaDna1 : OK
+Test result : Success : 9 : Bio.detectors.MsaAA1 : OK
+Test result : Success : 34 : Bio.detectors.SepDna : OK
+Test result : Success : 12 : Bio.detectors.SepRna : OK
+Test result : Success : 14 : Bio.detectors.SepPt : OK
+Test result : Success : 8 : Bio.detectors.SepUn1 : OK
+Test result : Success : 13 : Bio.detectors.SepUn2 : OK
+Test result : Success : 6 : Bio.detectors.SepMsaN1 : OK
+Test result : Success : 383 : Bio.detectors.SamplesFastaCsvPt : OK
+Test result : Success : 7 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
+Test result : Success : 14 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
+Test result : Success : 48 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
+Test result : Success : 117 : Bio.detectors.SamplesFastaFastaPt : OK
+Test result : Success : 707 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
+Test result : Success : 17 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
+Test result : Success : 137 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
+Test result : Success : 162 : Bio.detectors.samplesMsaComplexUn : OK
+Test result : Success : 24 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
+Test result : Success : 83 : Bio.detectors.samplesIdCsvNegativeID : OK
+Test result : Success : 165 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
+Test result : Success : 235 : Bio.detectors.samplesHelmCsvHELM : OK
+Test result : Success : 16 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
+Test result : Success : 139 : Bio.detectors.samplesTestHelmNegativeID : OK
+Test result : Success : 19 : Bio.detectors.samplesTestHelmNegativeTestType : OK
+Test result : Success : 5 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
+Test result : Success : 8 : Bio.detectors.samplesTestHelmNegativeValid : OK
+Test result : Success : 7 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
+Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
+Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
+Test result : Success : 733 : Bio.detectors.samplesTestDemogNegativeAll : OK
+Test result : Success : 380 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
+Test result : Success : 113 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
+Test result : Success : 126 : Bio.detectors.samplesFastaPtPosSequence : OK
+Test result : Success : 158 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
+Test result : Success : 229 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
+Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
+Test result : Success : 14 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
+Test result : Success : 6 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
+Test result : Success : 160 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
+Test result : Success : 8 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
+Test result : Success : 136 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
+Test result : Success : 7 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
+Test result : Success : 184 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
+Test result : Success : 932 : Bio.MSA.isCorrect : OK
+Test result : Success : 293 : Bio.MSA.isCorrectLong : OK
+Test result : Success : 1441 : Bio.sequenceSpace.sequenceSpaceOpens : OK
+Test result : Success : 7627 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
+Test result : Success : 1467 : Bio.activityCliffs.activityCliffsOpen : OK
+Test result : Success : 1356 : Bio.activityCliffs.activityCliffsOpenWithEmptyRows : OK
+Test result : Success : 1 : Bio.splitters.helm1 : OK
+Test result : Success : 1 : Bio.splitters.helm2 : OK
+Test result : Success : 0 : Bio.splitters.helm3-multichar : OK
+Test result : Success : 0 : Bio.splitters.testHelm1 : OK
+Test result : Success : 0 : Bio.splitters.testHelm2 : OK
+Test result : Success : 0 : Bio.splitters.testHelm3 : OK
+Test result : Success : 518 : Bio.splitters.splitToMonomers : OK
+Test result : Success : 157 : Bio.renderers.long sequence performance  : OK
+Test result : Success : 1230 : Bio.renderers.many sequence performance : OK
+Test result : Success : 372 : Bio.renderers.rendererMacromoleculeFasta : OK
+Test result : Success : 289 : Bio.renderers.rendererMacromoleculeSeparator : OK
+Test result : Success : 126 : Bio.renderers.rendererMacromoleculeDifference : OK
+Test result : Success : 812 : Bio.renderers.afterMsa : OK
+Test result : Success : 351 : Bio.renderers.afterConvert : OK
+Test result : Success : 178 : Bio.renderers.selectRendererBySemType : OK
+Test result : Success : 5 : Bio.converters.testFastaPtToSeparator : OK
+Test result : Success : 5 : Bio.converters.testFastaDnaToSeparator : OK
+Test result : Success : 13 : Bio.converters.testFastaRnaToSeparator : OK
+Test result : Success : 5 : Bio.converters.testFastaGapsToSeparator : OK
+Test result : Success : 3 : Bio.converters.testFastaPtToHelm : OK
+Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
+Test result : Success : 11 : Bio.converters.testFastaRnaToHelm : OK
+Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
+Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
+Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
+Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
+Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
+Test result : Success : 1 : Bio.converters.testSeparatorPtToHelm : OK
+Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
+Test result : Success : 1 : Bio.converters.testSeparatorRnaToHelm : OK
+Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
+Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
+Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
+Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
+Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
+Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
+Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
+Test result : Success : 3 : Bio.converters.testHelmLoneRibose : OK
+Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
+Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
+Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
+Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
+Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
+Test result : Success : 116 : Bio.WebLogo-positions.allPositions : OK
+Test result : Success : 126 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
+Test result : Success : 100 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
+Test result : Success : 4 : Bio.checkInputColumn.testMsaPos : OK
+Test result : Success : 1 : Bio.checkInputColumn.testMsaNegHelm : OK
+Test result : Success : 2 : Bio.checkInputColumn.testMsaNegUN : OK
+Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
+</pre></div></div></div></div></body></html>