@datagrok/bio 2.0.7 → 2.0.9

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.0.7",
+  "version": "2.0.9",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^4.2.1",
+    "@datagrok-libraries/bio": "^4.4.0",
     "@datagrok-libraries/chem-meta": "1.0.0",
     "@datagrok-libraries/ml": "^6.2.0",
     "@datagrok-libraries/utils": "^1.6.2",

package/src/calculations/monomerLevelMols.ts

@@ -65,7 +65,6 @@ M  V30 BEGIN CTAB
     molV3000 += 'M  V30 END BOND\n';
     molV3000 += 'M  V30 END CTAB\n';
     molV3000 += 'M  END';
-    console.log(molV3000);
     mols[i] = molV3000;
   }
 

package/src/package.ts

@@ -315,9 +315,11 @@ export async function compositionAnalysis(): Promise<void> {
     return;
   } else if (colList.length > 1) {
     const colListNames: string [] = colList.map((col) => col.name);
-    const colInput: DG.InputBase = ui.choiceInput('Column', colListNames[0], colListNames);
+    const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
+    const colInput: DG.InputBase = ui.choiceInput(
+      'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
     ui.dialog({
-      title: 'R-Groups Analysis',
+      title: 'Composition Analysis',
       helpUrl: '/help/domains/bio/macromolecules.md#composition-analysis'
     })
       .add(ui.div([

package/src/tests/Palettes-test.ts

@@ -1,12 +1,31 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
-
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {_testPaletteN, _testPaletteAA} from '@datagrok-libraries/bio/src/tests/palettes.test';
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+
+import {_testPaletteN, _testPaletteAA} from '@datagrok-libraries/bio/src/tests/palettes-tests';
+import {ALPHABET, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
 
 category('Palettes', () => {
   test('testPaletteN', async () => { await _testPaletteN(); });
   test('testPaletteAA', async () => { await _testPaletteAA(); });
+
+  test('testPalettePtMe', async () => {
+    const colorMeNle = AminoacidsPalettes.GrokGroups.get('MeNle');
+    const colorMeA = AminoacidsPalettes.GrokGroups.get('MeA');
+    const colorMeG = AminoacidsPalettes.GrokGroups.get('MeG');
+    const colorMeF = AminoacidsPalettes.GrokGroups.get('MeF');
+
+    const colorL = AminoacidsPalettes.GrokGroups.get('L');
+    const colorA = AminoacidsPalettes.GrokGroups.get('A');
+    const colorG = AminoacidsPalettes.GrokGroups.get('G');
+    const colorF = AminoacidsPalettes.GrokGroups.get('F');
+
+    expect(colorMeNle, colorL);
+    expect(colorMeA, colorA);
+    expect(colorMeG, colorG);
+    expect(colorMeF, colorF);
+  });
 });

package/src/tests/WebLogo-positions-test.ts

@@ -1,4 +1,4 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, test, expect, expectObject, delay} from '@datagrok-libraries/utils/src/test';
 
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
@@ -31,6 +31,7 @@ ATC-G-TTGC--
     tvList.forEach((tv: DG.TableView) => tv.close());
     currentView = grok.shell.tv;
   });
+
   test('allPositions', async () => {
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
     const tv: DG.TableView = grok.shell.addTableView(df);
@@ -71,8 +72,8 @@ ATC-G-TTGC--
         expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
       }
     }
-
   });
+
   test('positions with shrinkEmptyTail option true (filterd)', async () => {
     let csvDf2 = `seq 
     -TC-G-TTGC--
@@ -122,7 +123,6 @@ ATC-G-TTGC--
         expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
       }
     }
-
   });
 
   test('positions with skipEmptyPositions option', async () => {
@@ -163,5 +163,4 @@ ATC-G-TTGC--
       }
     }
   });
-
 });

package/src/tests/detectors-test.ts

@@ -131,8 +131,8 @@ MWRSWY-CKHP
 
   const samples: { [key: string]: string } = {
     'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
-    'fastaFasta': 'System:AppData/Bio/samples/sample_FASTA.fasta',
-    'fastaPtCsv': 'System:AppData/Bio/samples/sample_FASTA_PT.csv',
+    'fastaFasta': 'System:AppData/Bio/data/sample_FASTA.fasta',
+    'fastaPtCsv': 'System:AppData/Bio/data/sample_FASTA_PT.csv',
     'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
     'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
     'peptidesComplex': 'System:AppData/Bio/tests/peptides_complex_msa.csv',