@datagrok/bio 2.27.9 → 2.27.11

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.27.9",
+  "version": "2.27.11",
   "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",

package/src/demo/feature_demos.ts

@@ -95,9 +95,14 @@ export async function sirnaDemo() {
   const df = await _package.files.readCsv('demo-files/SIRNA.csv');
   const layoutTXT = await _package.files.readAsText('demo-files/SIRNA.layout');
   const layout = DG.ViewLayout.fromJson(layoutTXT);
+  df.col('sense_seq')!.setTag('aligned', 'SEQ.MSA');
+  df.col('antisense_seq')!.setTag('aligned', 'SEQ.MSA');
   const tv = grok.shell.addTableView(df);
   await DG.delay(100);
   tv.loadLayout(layout, true);
   await df.meta.detectSemanticTypes();
   grok.shell.info('Hover over the oligo structrues to see modifications to different sugars, linkers and residues.', {timeout: 10});
+  setTimeout(() => {
+    df.currentCell = df.cell(0, 'oligo_helm');
+  }, 300);
 }

package/src/package.g.ts

@@ -746,7 +746,7 @@ export async function demoBioSequenceSpace() : Promise<void> {
 }
 
 //description: Activity Cliffs analysis on Macromolecules data
-//meta.demoPath: Bioinformatics | Activity Cliffs
+//meta.demoPath: Bioinformatics | Sequence Activity Cliffs
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Activity%20Cliffs
 export async function demoBioActivityCliffs() : Promise<void> {
   await PackageFunctions.demoBioActivityCliffs();

package/src/package.ts

@@ -236,6 +236,15 @@ export class PackageFunctions {
 
   @grok.decorators.editor({tags: ['editor']})
   static SequenceSpaceEditor(call: DG.FuncCall) {
+    const df = grok.shell.tv?.dataFrame;
+    if (!df) {
+      grok.shell.error('Sequence Space requires an open table with a Macromolecule column');
+      return;
+    }
+    if (df.columns.bySemType(DG.SEMTYPE.MACROMOLECULE) == null) {
+      grok.shell.error('Current table does not contain a Macromolecule column');
+      return;
+    }
     const funcEditor = new DimReductionBaseEditor({semtype: DG.SEMTYPE.MACROMOLECULE});
     const dialog = ui.dialog({title: 'Sequence Space'})
       .add(funcEditor.getEditor())
@@ -258,6 +267,15 @@ export class PackageFunctions {
 
   @grok.decorators.editor({tags: ['editor']})
   static SeqActivityCliffsEditor(call: DG.FuncCall) {
+    const df = grok.shell.tv?.dataFrame;
+    if (!df) {
+      grok.shell.error('Sequence Activity Cliffs requires an open table with a Macromolecule column');
+      return;
+    }
+    if (df.columns.bySemType(DG.SEMTYPE.MACROMOLECULE) == null) {
+      grok.shell.error('Current table does not contain a Macromolecule column');
+      return;
+    }
     const funcEditor = new ActivityCliffsEditor({semtype: DG.SEMTYPE.MACROMOLECULE});
     const dialog = ui.dialog({title: 'Activity Cliffs'})
       .add(funcEditor.getEditor())
@@ -1539,7 +1557,7 @@ export class PackageFunctions {
 
   @grok.decorators.demo({
     description: 'Activity Cliffs analysis on Macromolecules data',
-    demoPath: 'Bioinformatics | Activity Cliffs',
+    demoPath: 'Bioinformatics | Sequence Activity Cliffs',
     path: '/apps/Tutorials/Demo/Bioinformatics/Activity%20Cliffs',
   })
   static async demoBioActivityCliffs(): Promise<void> {