@datagrok/bio 1.11.2 → 2.0.0

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "1.11.2",
+  "version": "2.0.0",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -16,7 +16,7 @@
     "@biowasm/aioli": ">=2.4.0",
     "@datagrok-libraries/bio": "^4.2.1",
     "@datagrok-libraries/chem-meta": "1.0.0",
-    "@datagrok-libraries/ml": "^6.0.0",
+    "@datagrok-libraries/ml": "^6.1.0",
     "@datagrok-libraries/utils": "^1.6.2",
     "cash-dom": "latest",
     "datagrok-api": "^1.6.7",
@@ -70,11 +70,7 @@
     "Developers"
   ],
   "sources": [
-    "css/helm.css",
-    "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js",
-    "helm/JSDraw/Scilligence.JSDraw2.Lite.js",
-    "helm/JSDraw/Scilligence.JSDraw2.Resources.js",
-    "helm/JSDraw/Pistoia.HELM-uncompressed.js"
+    "css/helm.css"
   ],
   "category": "Bioinformatics"
 }

package/src/package.ts

@@ -37,17 +37,6 @@ import * as C from './utils/constants';
 export async function initBio() {
 }
 
-//name: testManySequencesPerformance
-export function testManySequencesPerformance(): void {
-  performanceTest(generateManySequences, 'Many sequences');
-}
-
-//name: testLongSequencesPerformance
-export function testLongSequencesPerformance(): void {
-  performanceTest(generateLongSequence, 'Long sequences');
-}
-
-
 //name: fastaSequenceCellRenderer
 //tags: cellRenderer
 //meta.cellType: Sequence
@@ -148,7 +137,7 @@ export function vdRegionViewer() {
 //input: dataframe table [Input data table]
 //input: column macroMolecule {semType: Macromolecule}
 //input: column activities
-//input: double similarity = 80 [Similarity cutoff]
+//input: double similarity = 90 [Similarity cutoff]
 //input: string methodName { choices:["UMAP", "t-SNE", "SPE"] }
 export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column, activities: DG.Column,
   similarity: number, methodName: string): Promise<DG.Viewer | undefined> {
@@ -457,7 +446,16 @@ export function splitToMonomers(col: DG.Column<string>): void {
   for (const tempCol of tempDf.columns) {
     const newCol = originalDf.columns.add(tempCol);
     newCol.semType = C.SEM_TYPES.MONOMER;
-    // newCol.setTag(DG.TAGS.CELL_RENDERER, C.SEM_TYPES.MONOMER);
+    newCol.setTag(DG.TAGS.CELL_RENDERER, C.SEM_TYPES.MONOMER);
     newCol.setTag(C.TAGS.ALPHABET, col.getTag(C.TAGS.ALPHABET));
   }
+  (grok.shell.v as DG.TableView)?.grid.invalidate();
 }
+
+//name: Bio: getHelmMonomers
+//input: column col {semType: Macromolecule}
+//output: string[] result
+export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
+  const stats = WebLogo.getStats(seqCol, 5, WebLogo.splitterAsHelm);
+  return Object.keys(stats.freq);
+}

package/src/tests/renderers-test.ts

@@ -6,6 +6,7 @@ import {importFasta, multipleSequenceAlignmentAny} from '../package';
 import {convertDo} from '../utils/convert';
 import {ALPHABET, NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {SEM_TYPES, TAGS} from '../utils/constants';
+import {generateLongSequence, generateManySequences, performanceTest} from './test-sequnces-generators';
 
 category('renderers', () => {
   let tvList: DG.TableView[];
@@ -22,6 +23,14 @@ category('renderers', () => {
     tvList.forEach((tv: DG.TableView) => tv.close());
   });
 
+  test('long sequence performance ', async () => {
+    performanceTest(generateLongSequence, 'Long sequences');
+  });
+
+  test('many sequence performance', async () => {
+    performanceTest(generateManySequences, 'Many sequences');
+  });
+
   test('afterMsa', async () => {
     await _testAfterMsa();
   });

package/src/utils/cell-renderer.ts

@@ -196,7 +196,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 }
 
 export class MonomerCellRenderer extends DG.GridCellRenderer {
-  get name(): string {return 'MonomerCR';}
+  get name(): string {return C.SEM_TYPES.MONOMER;}
 
   get cellType(): string {return C.SEM_TYPES.MONOMER;}
 
@@ -217,21 +217,17 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
    */
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-    cellStyle: DG.GridCellStyle): void {
-    y -= 2;
-    g.save();
-    g.beginPath();
-    g.rect(x, y, w, h);
-    g.clip();
+    _cellStyle: DG.GridCellStyle): void {
     g.font = `12px monospace`;
-    g.textBaseline = 'top';
+    g.textBaseline = 'middle';
+    g.textAlign = 'center';
 
-    const palette = getPaletteByType(gridCell.tableColumn!.tags[C.TAGS.ALPHABET]);
+    const palette = getPaletteByType(gridCell.cell.column.getTag(C.TAGS.ALPHABET));
     const s: string = gridCell.cell.value ? gridCell.cell.value : '-';
     const color = palette.get(s);
 
-    printLeftOrCentered(x, y, w, h, g, s, color, 0, false);
-    g.restore();
+    g.fillStyle = color;
+    g.fillText(s, x + (w / 2), y - (h / 2));
   }
 }
 

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

@@ -4,47 +4,32 @@ import * as ui from 'datagrok-api/ui';
 import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
 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';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
   const stringArray = col.toList();
   const distances = new Array(stringArray.length).fill(0);
-  for (let i = 0; i < stringArray.length; ++i)
-    distances[i] = stringArray[i] ? AvailableMetrics['String']['Levenshtein'](stringArray[i], seq) : null;
+  for (let i = 0; i < stringArray.length; ++i) {
+    const distance = stringArray[i] ? AvailableMetrics['String']['Levenshtein'](stringArray[i], seq) : null;
+    distances[i] = distance ? distance/Math.max((stringArray[i] as string).length, seq.length) : null;
+  }
   return distances;
 }
 
 export async function getSimilaritiesMarix(dim: number, seqCol: DG.Column, df: DG.DataFrame, colName: string, simArr: DG.Column[])
   : Promise<DG.Column[]> {
 
-  function arrayMin(arr: number[]) {
-    return arr.reduce(function (p, v) {
-      return (p < v ? p : v);
-    });
-  }
-
-  function arrayMax(arr: number[]) {
-    return arr.reduce(function (p, v) {
-      return (p > v ? p : v);
-    });
-  }
   const distances = new Array(simArr.length).fill(null);
-  let min = Infinity;
-  let max = -Infinity;
   for (let i = 0; i != dim - 1; ++i) {
-    const seq = seqCol.get(i);
+    const seq: string = seqCol.get(i);  
     df.rows.removeAt(0, 1, false);
     distances[i] = (await getDistances(df.col(colName)!, seq))!;
-    const newMin = arrayMin(distances[i]);
-    const newMax = arrayMax(distances[i]);
-    if (newMin < min)
-      min = newMin;
-    if (newMax > max)
-      max = newMax;
   }
 
   for (let i = 0; i < distances.length; i++) {
     for (let j = 0; j < distances[i].length; j++) {
-      distances[i][j] = getSimilarityFromDistance((distances[i][j] - min)/(max - min));
+      distances[i][j] = getSimilarityFromDistance(distances[i][j]);
     }
     simArr[i] = DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances[i]);
   }

package/{test-Bio-f1ac5a5eade4-a0f7e8c0.html → test-Bio-c5a05867bf79-1b9affa5.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=f1ac5a5eade4. Commit a0f7e8c0.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=c5a05867bf79. Commit 1b9affa5.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   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=f1ac5a5eade4. Commit a0f7e8c0.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-08 10:03:50</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">10.76s</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">0s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Unknown server alias. Please add it to /home/runner/.grok/config.yaml
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=c5a05867bf79. Commit 1b9affa5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-13 11:28:35</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">8.755s</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">0s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Unknown server alias. Please add it to /home/runner/.grok/config.yaml
     at getDevKey (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:48:13)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:57:15)
     at Generator.next (&lt;anonymous&gt;)