@datagrok/bio 2.11.11 → 2.11.13

package/files/tests/to-atomic-level-pt-fasta-2.mol

@@ -30,7 +30,7 @@ M  V30 3 1 2 4
 M  V30 4 2 4 5
 M  V30 5 1 4 14
 M  V30 6 1 6 7
-M  V30 7 2 7 8 CFG=3
+M  V30 7 2 7 8
 M  V30 8 1 7 9
 M  V30 9 1 9 10
 M  V30 10 1 10 11

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.11",
+  "version": "2.11.13",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -34,11 +34,11 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.6",
-    "@datagrok-libraries/chem-meta": "^1.0.1",
-    "@datagrok-libraries/ml": "^6.3.55",
-    "@datagrok-libraries/tutorials": "^1.3.6",
-    "@datagrok-libraries/utils": "^4.0.17",
+    "@datagrok-libraries/bio": "^5.39.9",
+    "@datagrok-libraries/chem-meta": "^1.2.1",
+    "@datagrok-libraries/ml": "^6.3.56",
+    "@datagrok-libraries/tutorials": "^1.3.11",
+    "@datagrok-libraries/utils": "^4.1.28",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
     "datagrok-api": "^1.16.0",
@@ -64,8 +64,8 @@
     "webpack": "^5.76.3",
     "webpack-bundle-analyzer": "latest",
     "webpack-cli": "^4.9.1",
-    "@datagrok/chem": "^1.8.4",
-    "@datagrok/helm": "^2.1.21",
+    "@datagrok/chem": "^1.8.6",
+    "@datagrok/helm": "^2.1.22",
     "@datagrok/dendrogram": "^1.2.21"
   },
   "scripts": {

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

@@ -81,7 +81,7 @@ ATC-G-TTGC--
     });
     df.filter.fireChanged();
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo',
-      {'shrinkEmptyTail': true})) as WebLogoViewer;
+      {'shrinkEmptyTail': true})) as unknown as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
     }, 500);
@@ -119,7 +119,7 @@ ATC-G-TTGC--
     seqCol.setTag(bioTAGS.aligned, 'SEQ.MSA');
 
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo',
-      {'skipEmptyPositions': true})) as WebLogoViewer;
+      {'skipEmptyPositions': true})) as unknown as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
     }, 500);
@@ -155,7 +155,7 @@ ATC-G-TTGC--
       startPositionName: '3',
       endPositionName: '7',
       skipEmptyPositions: true,
-    })) as WebLogoViewer;
+    })) as unknown as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
     }, 500);

package/src/tests/mm-distance-tests.ts

@@ -76,13 +76,13 @@ ATCGAATCGA`;
   // Note that here the result is actually an inverted value of alignment score, which is coorelated with distance
   // tests using default BLOSUM62 matrix are in agreement with the results of the online tool
   test('needleman-blosum62', async () => {
-    const df = mmDistanceFunctions[MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH]();
-    _testDistance(prot1, prot2, df, 0.205);
+    const df = mmDistanceFunctions[MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH]({gapOpen: 8, gapExtend: 2});
+    _testDistance(prot1, prot2, df, -6);
   });
 
   test('needleman-blosum62-del', async () => {
-    const df = mmDistanceFunctions[MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH]();
-    _testDistance(prot3, prot4, df, 0.65);
+    const df = mmDistanceFunctions[MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH]({gapOpen: 8, gapExtend: 2});
+    _testDistance(prot3, prot4, df, -1.8);
   });
 
   test('needleman-custom-sub', async () => {

package/src/tests/splitters-test.ts

@@ -21,9 +21,6 @@ import {
   NOTATION
 } from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {splitToMonomersUI} from '../utils/split-to-monomers';
-import {SEMTYPE} from 'datagrok-api/dg';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {TAGS} from '../utils/constants';
 
 
 category('splitters', async () => {

package/src/tests/to-atomic-level-tests.ts

@@ -22,9 +22,9 @@ const appPath = 'System:AppData/Bio';
 const fileSource = new DG.FileSource(appPath);
 
 const testNames: { [k: string]: string } = {
-  PT: 'peptides fasta',
-  DNA: 'dna fasta',
-  MSA: 'msa separator',
+  PT: 'peptides-fasta',
+  DNA: 'dna-fasta',
+  MSA: 'msa-separator',
 };
 
 const inputPath: { [k: string]: string } = {

package/src/viewers/vd-regions-viewer.ts

@@ -328,7 +328,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
             positionWidth: this.positionWidth,
             positionHeight: this.positionHeight,
             filterSource: this.filterSource,
-          }) as WebLogoViewer;
+          }) as unknown as WebLogoViewer;
           wl.onSizeChanged.subscribe(() => { this.calcSize(); });
           return [orderI, chain, wl];
         })());