@datagrok/peptides 1.3.8 → 1.3.9

package/src/utils/algorithms.ts

@@ -0,0 +1,91 @@
+import * as DG from 'datagrok-api/dg';
+
+import * as C from './constants';
+import * as type from './types';
+import {getTypedArrayConstructor} from './misc';
+
+//TODO: move out
+export function findMutations(activityCol: DG.Column<number>, monomerColumns: DG.Column<string>[],
+  settings: type.PeptidesSettings = {}): type.SubstitutionsInfo {
+  const nCols = monomerColumns.length;
+  if (nCols == 0)
+    throw new Error(`PepAlgorithmError: Couldn't find any column of semType '${C.SEM_TYPES.MONOMER}'`);
+
+  const substitutionsInfo: type.SubstitutionsInfo = new Map();
+  const nRows = activityCol.length;
+  for (let seq1Idx = 0; seq1Idx < nRows - 1; seq1Idx++) {
+    for (let seq2Idx = seq1Idx + 1; seq2Idx < nRows; seq2Idx++) {
+      let substCounter = 0;
+      const activityValSeq1 = activityCol.get(seq1Idx)!;
+      const activityValSeq2 = activityCol.get(seq2Idx)!;
+      const delta = activityValSeq1 - activityValSeq2;
+      if (Math.abs(delta) < (settings.minActivityDelta ?? 0))
+        continue;
+
+      let substCounterFlag = false;
+      const tempData: { pos: string, seq1monomer: string, seq2monomer: string, seq1Idx: number, seq2Idx: number }[] =
+        [];
+      for (const currentPosCol of monomerColumns) {
+        const seq1monomer = currentPosCol.get(seq1Idx)!;
+        const seq2monomer = currentPosCol.get(seq2Idx)!;
+        if (seq1monomer == seq2monomer)
+          continue;
+
+        substCounter++;
+        substCounterFlag = substCounter > (settings.maxMutations ?? 1);
+        if (substCounterFlag)
+          break;
+
+        tempData.push({
+          pos: currentPosCol.name,
+          seq1monomer: seq1monomer,
+          seq2monomer: seq2monomer,
+          seq1Idx: seq1Idx,
+          seq2Idx: seq2Idx,
+        });
+      }
+
+      if (substCounterFlag || substCounter == 0)
+        continue;
+
+      for (const tempDataElement of tempData) {
+        const position = tempDataElement.pos;
+
+        //Working with seq1monomer
+        const seq1monomer = tempDataElement.seq1monomer;
+        if (!substitutionsInfo.has(seq1monomer))
+          substitutionsInfo.set(seq1monomer, new Map());
+
+        let positionsMap = substitutionsInfo.get(seq1monomer)!;
+        if (!positionsMap.has(position))
+          positionsMap.set(position, new Map());
+
+        let indexes = positionsMap.get(position)!;
+
+        !indexes.has(seq1Idx) ? indexes.set(seq1Idx, [seq2Idx]) : (indexes.get(seq1Idx)! as number[]).push(seq2Idx);
+
+        //Working with seq2monomer
+        const seq2monomer = tempDataElement.seq2monomer;
+        if (!substitutionsInfo.has(seq2monomer))
+          substitutionsInfo.set(seq2monomer, new Map());
+
+        positionsMap = substitutionsInfo.get(seq2monomer)!;
+        if (!positionsMap.has(position))
+          positionsMap.set(position, new Map());
+
+        indexes = positionsMap.get(position)!;
+        !indexes.has(seq2Idx) ? indexes.set(seq2Idx, [seq1Idx]) : (indexes.get(seq2Idx)! as number[]).push(seq1Idx);
+      }
+    }
+  }
+
+  const TypedArray = getTypedArrayConstructor(nRows);
+  for (const positionMap of substitutionsInfo.values()) {
+    for (const indexMap of positionMap.values()) {
+      for (const [index, indexArray] of indexMap.entries())
+        indexMap.set(index, new TypedArray(indexArray));
+    }
+  }
+
+  return substitutionsInfo;
+}

package/src/utils/cell-renderer.ts

@@ -1,8 +1,8 @@
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
 import * as C from './constants';
 import * as types from './types';
+import * as bio from '@datagrok-libraries/bio';
 
 function renderCellSelection(canvasContext: CanvasRenderingContext2D, bound: DG.Rect): void {
   canvasContext.strokeStyle = '#000';
@@ -100,86 +100,40 @@ export function renderLogoSummaryCell(canvasContext: CanvasRenderingContext2D, c
     renderCellSelection(canvasContext, bound);
 }
 
-export function renderBarchart(ctx: CanvasRenderingContext2D, col: DG.Column, monomerColStats: types.MonomerColStats,
-  bounds: DG.Rect, max: number): types.BarCoordinates {
-  let sum = col.length - (monomerColStats['-']?.count ?? 0);
-  const colorPalette = bio.getPaletteByType(col.tags[C.TAGS.ALPHABET]);
-  const name = col.name;
-  const colNameSize = ctx.measureText(name);
-  const margin = 0.2;
-  const innerMargin = 0.02;
-  const selectLineRatio = 0.1;
-  const fontSize = 11;
-
-  const xMargin = bounds.x + bounds.width * margin;
-  const yMargin = bounds.y + bounds.height * margin / 4;
-  const wMargin = bounds.width - bounds.width * margin * 2;
-  const hMargin = bounds.height - bounds.height * margin;
-  const barWidth = 10;
-  ctx.fillStyle = 'black';
-  ctx.textBaseline = 'top';
-  ctx.font = `${hMargin * margin / 2}px`;
-  ctx.fillText(name, xMargin + (wMargin - colNameSize.width) / 2, yMargin + hMargin + hMargin * margin / 4);
-
-
-  const barCoordinates: types.BarCoordinates = {};
-
-  const xStart = xMargin + (wMargin - barWidth) / 2;
-  for (const [monomer, monomerStats] of Object.entries(monomerColStats)) {
-    if (monomer == '-')
-      continue;
-
-    const count = monomerStats.count;
-    const sBarHeight = hMargin * count / max;
-    const gapSize = sBarHeight * innerMargin;
-    const verticalShift = (max - sum) / max;
-    const textSize = ctx.measureText(monomer);
-    const subBarHeight = sBarHeight - gapSize;
-    const yStart = yMargin + hMargin * verticalShift + gapSize / 2;
-    barCoordinates[monomer] = new DG.Rect(xStart, yStart, barWidth, subBarHeight);
-
-    const color = colorPalette.get(monomer);
-    ctx.strokeStyle = color;
-    ctx.fillStyle = color;
-
-    if (textSize.width <= subBarHeight) {
-      if (color != bio.SeqPaletteBase.undefinedColor)
-        ctx.fillRect(xStart, yStart, barWidth, subBarHeight);
-      else {
-        ctx.strokeRect(xStart + 0.5, yStart, barWidth - 1, subBarHeight);
-        barCoordinates[monomer].x -= 0.5;
-        barCoordinates[monomer].width -= 1;
-      }
-
-      const leftMargin = (wMargin - (monomer.length > 1 ? fontSize : textSize.width - 8)) / 2;
-      const absX = xMargin + leftMargin;
-      const absY = yStart + subBarHeight / 2 + (monomer.length == 1 ? 4 : 0);
-      const origTransform = ctx.getTransform();
-
-      if (monomer.length > 1) {
-        ctx.translate(absX, absY);
-        ctx.rotate(Math.PI / 2);
-        ctx.translate(-absX, -absY);
-      }
-
-      ctx.fillStyle = 'black';
-      ctx.font = `${fontSize}px monospace`;
-      ctx.textAlign = 'center';
-      ctx.textBaseline = 'bottom';
-      ctx.fillText(monomer, absX, absY);
-      ctx.setTransform(origTransform);
-    } else
-      ctx.fillRect(xStart, yStart, barWidth, subBarHeight);
-
-    const selectedCount = monomerStats.selected;
-    if (selectedCount) {
-      ctx.fillStyle = 'rgb(255,165,0)';
-      ctx.fillRect(xStart - wMargin * selectLineRatio * 2, yStart,
-        barWidth * selectLineRatio, hMargin * selectedCount / max - gapSize);
-    }
 
-    sum -= count;
+export function drawLogoInBounds(ctx: CanvasRenderingContext2D, bounds: DG.Rect, statsInfo: types.StatsInfo,
+  rowCount: number, cp: bio.SeqPalette, drawOptions: types.DrawOptions = {}): void {
+  drawOptions.fontStyle ??= '16px Roboto, Roboto Local, sans-serif';
+  drawOptions.upperLetterHeight ??= 12.2;
+  drawOptions.upperLetterAscent ??= 0.25;
+  drawOptions.marginVertical ??= 5;
+  drawOptions.marginHorizontal ??= 5;
+
+  const totalSpaceBetweenLetters = (statsInfo.orderedIndexes.length - 1) * drawOptions.upperLetterAscent;
+  const barHeight = bounds.height - 2 * drawOptions.marginVertical - totalSpaceBetweenLetters;
+  const leftShift = drawOptions.marginHorizontal * 2;
+  const barWidth = bounds.width - leftShift - drawOptions.marginHorizontal;
+  const xStart = bounds.x + leftShift;
+  let currentY = bounds.y + drawOptions.marginVertical;
+
+
+  for (const index of statsInfo.orderedIndexes) {
+    const monomer = statsInfo.monomerCol.get(index)!;
+    const monomerHeight = barHeight * (statsInfo.countCol.get(index)! / rowCount);
+
+    ctx.resetTransform();
+    if (monomer !== '-') {
+      const monomerTxt = bio.monomerToShort(monomer, 5);
+      const mTm: TextMetrics = ctx.measureText(monomerTxt);
+
+      ctx.fillStyle = cp.get(monomer) ?? cp.get('other');
+      ctx.textAlign = 'left';
+      ctx.textBaseline = 'top';
+      ctx.font = drawOptions.fontStyle;
+      // Hacks to scale uppercase characters to target rectangle
+      ctx.setTransform(barWidth / mTm.width, 0, 0, monomerHeight / drawOptions.upperLetterHeight, xStart, currentY);
+      ctx.fillText(monomerTxt, 0, 0);
+    }
+    currentY += monomerHeight + drawOptions.upperLetterAscent;
   }
-
-  return barCoordinates;
 }

package/src/utils/types.ts

@@ -1,5 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
 export type DataFrameDict = {[key: string]: DG.DataFrame};
 
@@ -8,13 +7,31 @@ export type UTypedArray = Uint8Array | Uint16Array | Uint32Array;
 export type SubstitutionsInfo = Map<string, Map<string, Map<number, number[] | UTypedArray>>>;
 export type PositionToAARList = {[postiton: string]: string[]};
 
-export type HELMMonomer = bio.Monomer;
-
 export type MonomerColStats = {[monomer: string]: {count: number, selected: number}};
 export type MonomerDfStats = {[position: string]: MonomerColStats};
 
-export type BarCoordinates = {[monomer: string]: DG.Rect};
-
 export type ScalingMethods = 'none' | 'lg' | '-lg';
-export type PeptidesSettings =
-  {scaling?: ScalingMethods, isBidirectional?: boolean, maxMutations?: number, minActivityDelta?: number};
+export type PeptidesSettings = {
+  scaling?: ScalingMethods,
+  isBidirectional?: boolean,
+  maxMutations?: number,
+  minActivityDelta?: number,
+  columns?: {[col: string]: string},
+};
+
+export type DrawOptions = {
+  fontStyle?: string,
+  upperLetterHeight?: number,
+  upperLetterAscent?: number,
+  bounds?: DG.Rect,
+  textAlign?: CanvasTextAlign,
+  textBaseline?: CanvasTextBaseline,
+  marginVertical?: number,
+  marginHorizontal?: number,
+};
+
+export type StatsInfo = {
+  monomerCol: DG.Column<string>,
+  countCol: DG.Column<number>,
+  orderedIndexes: Int32Array,
+}

package/src/widgets/manual-alignment.ts

@@ -1,11 +1,11 @@
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
 import $ from 'cash-dom';
 import '../styles.css';
 import {PeptidesModel} from '../model';
+import {splitAlignedSequences} from '@datagrok-libraries/bio';
 
 /** Manual sequence alignment widget.
  *
@@ -19,7 +19,7 @@ export function manualAlignmentWidget(alignedSequenceCol: DG.Column<string>, cur
   const applyChangesBtn = ui.button('Apply', async () => {
     const newSequence = sequenceInput.value;
     const affectedRowIndex = currentDf.currentRowIdx;
-    const splitSequence = bio.splitAlignedSequences(DG.Column.fromStrings('splitSequence', [newSequence]));
+    const splitSequence = splitAlignedSequences(DG.Column.fromStrings('splitSequence', [newSequence]));
 
     alignedSequenceCol.set(affectedRowIndex, newSequence);
     for (const part of splitSequence.columns) {

package/src/widgets/peptides.ts

@@ -1,13 +1,13 @@
 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 '../styles.css';
 import * as C from '../utils/constants';
 import {PeptidesModel} from '../model';
 import $ from 'cash-dom';
 import {scaleActivity} from '../utils/misc';
+import {WebLogoViewer} from '@datagrok-libraries/bio';
 
 /** Peptide analysis widget.
  *
@@ -97,7 +97,7 @@ Promise<{host: HTMLElement, callback: () => Promise<void>}> {
     inputElements.push(startBtn);
   }
 
-  const viewer = await df.plot.fromType('WebLogo') as bio.WebLogoViewer;
+  const viewer = await df.plot.fromType('WebLogo') as WebLogoViewer;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
@@ -149,6 +149,7 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
     }
 
     newDf.setTag('monomerType', monomerType);
+    newDf.setTag('newAnalysis', '1');
     model = await PeptidesModel.getInstance(newDf);
   } else
     grok.shell.error('The activity column must be of numeric type!');

package/src/widgets/settings.ts

@@ -5,27 +5,59 @@ import * as DG from 'datagrok-api/dg';
 import * as type from '../utils/types';
 import {PeptidesModel} from '../model';
 
+import $ from 'cash-dom';
+import wu from 'wu';
+
 //TODO: show sliderInput values
 export function getSettingsDialog(model: PeptidesModel): DG.Dialog {
+  const accordion = ui.accordion();
   const settings = model.settings;
-  const result: type.PeptidesSettings = {};
+  const result: type.PeptidesSettings = {columns: {}};
   const activityScaling = ui.choiceInput('Activity scaling', settings.scaling ?? 'none', ['none', 'lg', '-lg'],
     () => result.scaling = activityScaling.value! as type.ScalingMethods);
   const bidirectionalAnalysis = ui.boolInput('Bidirectional analysis', settings.isBidirectional ?? false,
     () => result.isBidirectional = bidirectionalAnalysis.value!);
+  accordion.addPane('General', () => ui.inputs([activityScaling, bidirectionalAnalysis]), true);
+
   const maxMutations = ui.sliderInput('Max mutations', settings.maxMutations ?? 1, 0, 50, () => {
     const val = Math.round(maxMutations.value!);
+    $(maxMutations.root).find('label.ui-input-description').remove();
     result.maxMutations = val;
+    maxMutations.addPostfix(val.toString());
   });
+  maxMutations.addPostfix((settings.maxMutations ?? 1).toString());
   const minActivityDelta = ui.sliderInput('Min activity delta', settings.minActivityDelta ?? 0, 0, 100, () => {
     const val = Math.round(minActivityDelta.value!);
     result.minActivityDelta = val;
+    $(minActivityDelta.root).find('label.ui-input-description').remove();
+    minActivityDelta.addPostfix(val.toString());
   });
-
-  const accordion = ui.accordion();
-  accordion.addPane('General', () => ui.inputs([activityScaling, bidirectionalAnalysis]), true);
+  minActivityDelta.addPostfix((settings.minActivityDelta ?? 0).toString());
   accordion.addPane('Mutation Cliffs', () => ui.inputs([maxMutations, minActivityDelta]), true);
 
+  const inputsRows: HTMLElement[] = [];
+  for (const col of model.df.columns.numerical) {
+    const isIncluded = ui.boolInput('', typeof (settings.columns ?? {})[col.name] !== 'undefined',
+      () => {
+        if (isIncluded)
+          result.columns![col.name] = aggregation.stringValue;
+        else
+          delete result.columns![col.name];
+      }) as DG.InputBase<boolean>;
+    const aggregation = ui.choiceInput('Aggregation', (settings.columns ?? {})[col.name] ?? 'avg', Object.values(DG.STATS),
+      () => {
+        if (isIncluded)
+          result.columns![col.name] = aggregation.stringValue;
+        else
+          delete result.columns![col.name];
+      }) as DG.InputBase<string>;
+    $(aggregation.root).find('label').css('width', 'auto');
+    const inputsRow = ui.inputsRow(col.name, [isIncluded, aggregation]);
+    $(inputsRow).find('div.ui-div').css('display', 'inline-flex');
+    inputsRows.push(inputsRow);
+  }
+  accordion.addPane('Columns to include', () => ui.divV(inputsRows), false);
+
   const dialog = ui.dialog('Peptides settings').add(accordion);
   dialog.root.style.width = '400px';
   dialog.onOK(() => model.settings = result);
@@ -33,5 +65,3 @@ export function getSettingsDialog(model: PeptidesModel): DG.Dialog {
 
   return dialog.show();
 }
-
-

package/test-Peptides-62cc009524f3-0949dc07.html

@@ -0,0 +1,276 @@
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 0949dc07.</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">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 0949dc07.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-11 14:09:20</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/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">96.038s</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">82.695s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 329 : Peptides.Core.Start analysis: сomplex : Error: For column 'macromolecule' of alphabet 'UN' tag '.alphabetSize' is mandatory.
+
+    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:68:20
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
+    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/Peptides/src/__jest__/test-node.ts:62:11)
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/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/Peptides/src/__jest__/remote.test.ts:40:11
+    at Generator.next (&lt;anonymous&gt;)
+    at /home/runner/work/public/public/packages/Peptides/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/Peptides/src/__jest__/remote.test.ts:30:12)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:23)
+    at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/utils.js:391:28)
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:66:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 4295 : Peptides.Core.Start analysis: simple : OK
+Test result : Success : 7421 : Peptides.Core.Save and load project : OK
+Test result : Success : 0 : Peptides.Peptide space.test_table.is_not_empty : OK
+Test result : Success : 2686 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
+Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
+Test result : Success : 0 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
+Test result : Success : 2238 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
+Test result : Success : 2625 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
+Test result : Success : 3350 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
+Test result : Success : 3819 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 208 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
+Test result : Success : 594 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 171 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
+Test result : Success : 556 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 8614 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
+Test result : Success : 9838 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 2113 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
+Test result : Success : 2618 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
+Test result : Success : 3392 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
+Test result : Success : 3850 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
+Test result : Success : 232 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
+Test result : Success : 818 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 193 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
+Test result : Success : 587 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 8223 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
+Test result : Success : 9416 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
+</pre></div></div></div></div></body></html>