@datagrok/bio 2.25.7 → 2.25.9

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.25.7",
+  "version": "2.25.9",
   "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",
@@ -44,7 +44,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.61.3",
+    "@datagrok-libraries/bio": "^5.61.4",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.7",

package/src/package.g.ts

@@ -310,7 +310,7 @@ export async function toAtomicLevelPanel(sequence: DG.SemanticValue) : Promise<a
 //name: To Atomic Level Single sequence
 //description: Converts a single sequence to molblock
 //input: string sequence { semType: Macromolecule }
-//output: string result
+//output: string molfile { semType: Molecule }
 export async function toAtomicLevelSingleSeq(sequence: string) : Promise<string> {
   return await PackageFunctions.toAtomicLevelSingleSeq(sequence);
 }

package/src/package.ts

@@ -706,7 +706,8 @@ export class PackageFunctions {
 
   @grok.decorators.func({
     name: 'To Atomic Level Single sequence',
-    description: 'Converts a single sequence to molblock'
+    description: 'Converts a single sequence to molblock',
+    outputs: [{name: 'molfile', type: 'string', options: {semType: 'Molecule'}}]
   })
   static async toAtomicLevelSingleSeq(
     @grok.decorators.param({name: 'sequence', type: 'string', options: {semType: 'Macromolecule'}}) sequence: string,

package/src/widgets/bio-substructure-filter.ts

@@ -62,7 +62,7 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
   set calculating(value: boolean) { this.loader.style.display = value ? 'initial' : 'none'; }
 
   get filterSummary(): string {
-    return this.bioFilter!.filterSummary;
+    return this.bioFilter?.filterSummary ?? '';
   }
 
   get isFiltering(): boolean {
@@ -108,6 +108,9 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
     const superAttach = super.attach.bind(this);
     const logPrefix = `${this.filterToLog()}.attach()`;
     this.filterSyncer.sync(logPrefix, async () => {
+      // make sure semtypes are detected
+      if (dataFrame)
+        await dataFrame.meta.detectSemanticTypes();
       superAttach(dataFrame);
 
       if (!this.column) {
@@ -116,18 +119,18 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
         else
           this.column = dataFrame.columns.bySemType(DG.SEMTYPE.MACROMOLECULE);
       }
-      const sh = this.seqHelper.getSeqHandler(this.column!);
+      const _sh = this.seqHelper.getSeqHandler(this.column!);
       this.columnName ??= this.column?.name;
       this.notation ??= this.column?.meta.units!;
 
       this.bioFilter = this.notation === NOTATION.FASTA ?
         new FastaBioFilter() : this.notation === NOTATION.SEPARATOR ?
           new SeparatorBioFilter(this.column!.getTag(bioTAGS.separator)) : new HelmBioFilter(this.seqHelper);
-      this.root.appendChild(this.bioFilter!.filterPanel);
+      this.root.appendChild(this.bioFilter.filterPanel);
       this.root.appendChild(this.loader);
       await this.bioFilter.attach(); // may await waitForElementInDom
 
-      this.viewSubs.push(DG.debounce(this.bioFilter!.onChanged, this.debounceTime)
+      this.viewSubs.push(DG.debounce(this.bioFilter.onChanged, this.debounceTime)
         .subscribe(this.bioFilterOnChangedDebounced.bind(this)));
       this.viewSubs.push(grok.events.onResetFilterRequest
         .subscribe(this.grokEventsOnResetFilterRequest.bind(this)));
@@ -151,10 +154,10 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
   // -- Sync -
 
   private filterOnSync(state: FilterState): void {
-    if (state.filterId === this.filterId) return;
+    if (state.filterId === this.filterId || !this.bioFilter) return;
     if (state.dataFrameId !== this.dataFrame!.id || state.columnName !== this.columnName) return;
 
-    this.bioFilter!.props = state.props;
+    this.bioFilter.props = state.props;
   }
 
   // -- Layout --
@@ -173,7 +176,8 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
     const logPrefix = `${this.filterToLog()}.saveState()`;
     const state = super.saveState();
     this.logger.debug(`${logPrefix}, super.state = ${JSON.stringify(state)}`);
-    state.props = this.bioFilter!.saveProps();
+    if (this.bioFilter)
+      state.props = this.bioFilter.saveProps();
     return state;
   }
 
@@ -194,10 +198,12 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
     const logPrefix = `${this.filterToLog()}.fireFilterSync()`;
     this.logger.debug(`${logPrefix}, ` +
       `bioFilter = ${!!this.bioFilter ? this.bioFilter.constructor.name : 'null'}` +
-      (!!this.bioFilter ? `, props = ${JSON.stringify(this.bioFilter!.saveProps())}` : ''));
+      (!!this.bioFilter ? `, props = ${JSON.stringify(this.bioFilter.saveProps())}` : ''));
 
+    if (!this.bioFilter)
+      return;
     grok.events.fireCustomEvent(FILTER_SYNC_EVENT, new FilterState(
-      this.bioFilter!.props, this.filterId, this.dataFrame!.id, this.columnName!, this.bitset));
+      this.bioFilter.props, this.filterId, this.dataFrame!.id, this.columnName!, this.bitset));
   }
 
   // -- Handle events
@@ -212,7 +218,7 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
     const logPrefix = `${this.filterToLog()}.bioFilterOnChangedDebounced()`;
     this.logger.debug(`${logPrefix}, start, ` +
       `isFiltering = ${this.isFiltering}, ` +
-      `props = ${JSON.stringify(this.bioFilter!.saveProps())}`);
+      `props = ${this.bioFilter ? JSON.stringify(this.bioFilter?.saveProps()) : 'null'}`);
 
     if (!this.isFiltering) {
       this.bitset = null;

package/src/widgets/sequence-scrolling-widget.ts

@@ -324,7 +324,9 @@ class LazyConservationTrack extends ConservationTrack {
 // ============================================================================
 
 export const MSA_HEADER_INITIALIZED_FLAG = '__msa-scroller-initialized';
-export const MSA_SCROLLER_GRID_SUBSCRIPTION = '__msa-scroller-subscription';
+export const MSA_SCROLLER_GRID_SUBSCRIPTIONS = '__msa-scroller-subscription';
+
+type Unsubscibable = { unsubscribe: () => void };
 
 export function handleSequenceHeaderRendering() {
   const handleGrid = (grid: DG.Grid) => {
@@ -334,19 +336,26 @@ export function handleSequenceHeaderRendering() {
       const df = grid.dataFrame;
       if (!df) return;
 
-      const seqCols = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
+      if (!grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTIONS])
+        grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTIONS] = [] as Unsubscibable[];
+      let headerSubs = grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTIONS] as Unsubscibable[];
+      headerSubs.forEach((s) => s.unsubscribe());
+      grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTIONS] = headerSubs = [];
 
-      grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTION]?.unsubscribe();
-      grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTION] = DG.debounce(rxjs.merge(df.onColumnsAdded, df.onSemanticTypeDetected), 200).subscribe(() => handleGrid(grid));
-      grid.sub(grid.temp[MSA_SCROLLER_GRID_SUBSCRIPTION]);
+      const sub = (s: Unsubscibable) => {
+        headerSubs.push(s);
+      };
+      const seqCols = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
+      sub(DG.debounce(rxjs.merge(df.onColumnsAdded, df.onColumnsRemoved, df.onSemanticTypeDetected, grid.onEvent('d4-data-frame-changed')), 200).subscribe(() => handleGrid(grid)));
 
       for (const seqCol of seqCols) {
         // first check if the column was already processed
         const gCol = grid.col(seqCol.name);
         if (!gCol) continue;
 
-        if (gCol.temp[MSA_HEADER_INITIALIZED_FLAG])
-          continue;
+        // if (gCol.temp[MSA_HEADER_INITIALIZED_FLAG])
+        //   continue;
+        const wasInitialized = gCol.temp[MSA_HEADER_INITIALIZED_FLAG] === true;
         gCol.temp[MSA_HEADER_INITIALIZED_FLAG] = true;
 
 
@@ -428,7 +437,7 @@ export function handleSequenceHeaderRendering() {
           }, 50);
         });
 
-        grid.sub(filterChangeSub);
+        sub(filterChangeSub);
 
         const initializeHeaders = (monomerLib: IMonomerLib) => {
           const tracks: { id: string, track: MSAHeaderTrack, priority: number }[] = [];
@@ -501,7 +510,7 @@ export function handleSequenceHeaderRendering() {
 
           scroller.setSelectionData(df, seqCol, sh);
 
-          if (maxSeqLen > 50) {
+          if (maxSeqLen > 50 && !wasInitialized) {
             grid.props.colHeaderHeight = initialHeaderHeight;
 
             // Set column width
@@ -511,10 +520,12 @@ export function handleSequenceHeaderRendering() {
             }, 300);
           }
 
+          sub({unsubscribe: () => scroller.detach()}); // Ensure proper cleanup
           // Handle cell rendering for MSA
-          grid.sub(grid.onCellRender.subscribe((e) => {
+          const tableCol = gCol.column;
+          sub(grid.onCellRender.subscribe((e) => {
             const cell = e.cell;
-            if (!cell || !cell.isColHeader || cell?.gridColumn?.name !== gCol?.name)
+            if (!cell || !cell.isColHeader || cell?.tableColumn?.dart !== tableCol?.dart)
               return;
 
             const cellBounds = e.bounds;