@datagrok/bio 2.26.5 → 2.26.7

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.26.5",
+  "version": "2.26.7",
   "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": "^5.63.5",
+    "@datagrok-libraries/bio": "^5.63.6",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.11",

package/src/package-api.ts

@@ -121,6 +121,10 @@ export namespace funcs {
     return await grok.functions.call('Bio:CompositionAnalysisWidget', { sequence });
   }
 
+  export async function monomerInfoPanel(monomerSv: any ): Promise<any> {
+    return await grok.functions.call('Bio:MonomerInfoPanel', { monomerSv });
+  }
+
   export async function macromoleculeDifferenceCellRenderer(): Promise<any> {
     return await grok.functions.call('Bio:MacromoleculeDifferenceCellRenderer', {});
   }
@@ -380,8 +384,8 @@ export namespace funcs {
     return await grok.functions.call('Bio:ManageMonomersView', {});
   }
 
-  export async function manageMonomerLibrariesView(): Promise<DG.View> {
-    return await grok.functions.call('Bio:ManageMonomerLibrariesView', {});
+  export async function manageMonomerLibrariesView(path?: string ): Promise<DG.View> {
+    return await grok.functions.call('Bio:ManageMonomerLibrariesView', { path });
   }
 
   export async function manageMonomerLibrariesViewTreeBrowser(treeNode: any ): Promise<void> {

package/src/package.g.ts

@@ -160,6 +160,16 @@ export function compositionAnalysisWidget(sequence: DG.SemanticValue) : any {
   return PackageFunctions.compositionAnalysisWidget(sequence);
 }
 
+//name: Monomer
+//tags: bio, panel
+//input: semantic_value monomerSv { semType: Monomer }
+//output: widget result
+//meta.domain: bio
+//meta.role: panel
+export function monomerInfoPanel(monomerSv: DG.SemanticValue) : any {
+  return PackageFunctions.monomerInfoPanel(monomerSv);
+}
+
 //name: MacromoleculeDifferenceCellRenderer
 //tags: cellRenderer
 //output: grid_cell_renderer result
@@ -599,12 +609,13 @@ export async function manageMonomersView() : Promise<void> {
 
 //name: Manage Monomer Libraries
 //tags: app
+//input: string path { meta.url: true; optional: true }
 //output: view result
 //meta.role: app
 //meta.browsePath: Peptides
 //meta.icon: files/icons/monomers.png
-export async function manageMonomerLibrariesView() : Promise<any> {
-  return await PackageFunctions.manageMonomerLibrariesView();
+export async function manageMonomerLibrariesView(path?: string) : Promise<any> {
+  return await PackageFunctions.manageMonomerLibrariesView(path);
 }
 
 //name: Monomer Manager Tree Browser

package/src/package.ts

@@ -44,10 +44,12 @@ import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
 import {invalidateMols, MONOMERIC_COL_TAGS, SubstructureSearchDialog} from './substructure-search/substructure-search';
 import {convert} from './utils/convert';
 import {getMacromoleculeColumnPropertyPanel} from './widgets/representations';
+import {getMonomerInfoWidget} from './widgets/monomer-info-widget';
 import {saveAsFastaUI} from './utils/save-as-fasta';
 import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
 import {WebLogoViewer} from './viewers/web-logo-viewer';
 import {MonomerLibManager} from './utils/monomer-lib/lib-manager';
+import {MonomerCollectionHandler} from './utils/monomer-lib/monomer-collection-handler';
 import {getMonomerLibraryManagerLink, showManageLibrariesDialog, showManageLibrariesView} from './utils/monomer-lib/library-file-manager/ui';
 import {demoBioSimDiv} from './demo/bio01-similarity-diversity';
 import {demoSeqSpace} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
@@ -382,6 +384,15 @@ export class PackageFunctions {
     return getCompositionAnalysisWidget(sequence, _package.monomerLib, _package.seqHelper);
   }
 
+  @grok.decorators.panel({name: 'Monomer',
+    tags: ['bio', 'panel'],
+    meta: {domain: 'bio'},
+  })
+  static monomerInfoPanel(
+    @grok.decorators.param({options: {semType: 'Monomer'}}) monomerSv: DG.SemanticValue): DG.Widget {
+    return getMonomerInfoWidget(monomerSv.value as string, _package.monomerLib);
+  }
+
   @grok.decorators.func({
     name: 'MacromoleculeDifferenceCellRenderer',
     tags: ['cellRenderer'],
@@ -1309,8 +1320,12 @@ export class PackageFunctions {
     browsePath: 'Peptides',
     icon: 'files/icons/monomers.png',
   })
-  static async manageMonomerLibrariesView(): Promise<DG.View> {
-    return await showManageLibrariesView(false);
+  static async manageMonomerLibrariesView(
+    @grok.decorators.param({options: {metaUrl: true, optional: true}}) path?: string
+  ): Promise<DG.View> {
+    const res = await showManageLibrariesView(false);
+    res.parentCall = grok.functions.getCurrentCall();
+    return res;
   }
 
   // @grok.decorators.func({tags: ['monomer-lib-provider'], result: {type: 'object', name: 'result'}})
@@ -1327,7 +1342,8 @@ export class PackageFunctions {
       // eslint-disable-next-line rxjs/no-ignored-subscription, rxjs/no-async-subscribe
       libNode.onSelected.subscribe(async () => {
         const monomerManager = await MonomerManager.getInstance();
-        await monomerManager.getViewRoot(libName, true);
+        const res = await monomerManager.getViewRoot(libName, true);
+        res.parentCall = grok.functions.getCurrentCall();
         monomerManager.resetCurrentRowFollowing();
       });
     });
@@ -1667,6 +1683,9 @@ async function initBioInt() {
 
   // hydrophobPalette = new SeqPaletteCustom(palette);
 
+  // Register object handlers
+  DG.ObjectHandler.register(new MonomerCollectionHandler());
+
   _package.logger.debug(`${logPrefix}, end`);
   handleSequenceHeaderRendering();
 }

package/src/tests/projects-tests.ts

@@ -195,8 +195,4 @@ category('projects', () => {
     await setUserLibSettings(userLibSettings);
     await monomerLibHelper.loadMonomerLib(true);
   }, {timeout: 60000});
-
-  after(async () => {
-    grok.shell.closeAll();
-  });
 });

package/src/utils/monomer-cell-renderer.ts

@@ -14,11 +14,8 @@ import {undefinedColor} from '@datagrok-libraries/bio/src/utils/cell-renderer-mo
 import {HelmType, HelmTypes, PolymerType, PolymerTypes} from '@datagrok-libraries/js-draw-lite/src/types/org';
 import {polymerTypeToHelmType} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 
-const Tags = new class {
-  tooltipHandlerTemp = 'tooltip-handler.Monomer';
-}();
-
 const DASH_GAP_SYMBOL = '-';
+const MONOMER_MARGIN = 2;
 
 export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase {
   constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column) {
@@ -68,6 +65,8 @@ export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase
       g.font = `12px monospace`;
       g.textBaseline = 'middle';
       g.textAlign = 'left';
+      const mMet = g.measureText('M');
+      const lineHeight = mMet.actualBoundingBoxAscent + mMet.actualBoundingBoxDescent + MONOMER_MARGIN * 4;
 
       let value: string = gridCell.cell.value;
       // render original value
@@ -80,10 +79,11 @@ export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase
       //cell width of monomer should dictate how many characters can be displayed
       // for width 40, 6 characters can be displayed (0.15 is 6 / 40)
       const shortSymbols = symbols.map((s) => monomerToShort(s, Math.max(2, Math.floor(w * 0.15 / symbols.length))));
-      const symbolWidths = shortSymbols.map((s) => g.measureText(s).width);
+      const symbolWidths = shortSymbols.map((s) => g.measureText(s).width + MONOMER_MARGIN * 2);
+      // symbolWidths[symbolWidths.length - 1] -= MONOMER_MARGIN;
       const totalWidth = symbolWidths.reduce((a, b) => a + b, 0);
       const xOffset = (w - totalWidth) / 2;
-      let xPos = x + xOffset;
+      let xPos = x + xOffset + MONOMER_MARGIN;
       const alphabet = this.tableCol.getTag(bioTAGS.alphabet);
       const biotype = alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
       for (let i = 0; i < shortSymbols.length; i++) {
@@ -100,9 +100,15 @@ export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase
           } else
             textcolor = this.monomerLib.getMonomerTextColor(actBioType, symbol);
         }
-        if (applyToBackground && symbols.length == 1) {
+        if (applyToBackground) {
           g.fillStyle = backgroundcolor;
-          g.fillRect(x, y, w, h);
+          if (w < 30 || h < 30)
+            g.fillRect(x + i * w / shortSymbols.length, y, w / shortSymbols.length, h);
+          else {
+            const radius = MONOMER_MARGIN;
+            g.roundRect(xPos - MONOMER_MARGIN, y + (h / 2) - lineHeight / 2, symbolWidths[i], lineHeight, radius);
+            g.fill();
+          }
         }
         g.fillStyle = textcolor;
         g.fillText(shortSymbols[i], xPos, y + (h / 2), w);

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -83,7 +83,8 @@ class MonomerLibraryManagerWidget {
 
   private async getWidgetContent(): Promise<HTMLElement> {
     const libControlsForm = await LibraryControlsManager.createControlsForm();
-    $(libControlsForm).addClass('monomer-lib-controls-form');
+    $(libControlsForm).addClass('monomer-lib-controls-form')
+    .addClass('d4-dialog-contents');
     setTimeout(() => {
       libControlsForm && $(libControlsForm) && $(libControlsForm).removeClass('ui-form-condensed');
     }, 200);
@@ -174,7 +175,7 @@ class LibraryControlsManager {
   private async _createControlsForm(): Promise<HTMLElement> {
     const libraryControls = await this.createLibraryControls();
     const inputsForm = ui.wideForm(libraryControls, undefined);
-    $(inputsForm).addClass('monomer-lib-controls-form');
+    $(inputsForm).addClass('monomer-lib-controls-form').addClass('d4-dialog-contents');
 
     return inputsForm;
   }

package/src/utils/monomer-lib/monomer-collection-handler.ts

@@ -0,0 +1,359 @@
+/* eslint-disable max-len */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {MonomerCollection, IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';
+import {HelmType, PolymerType} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
+import {MonomerSelectionWidget} from '@datagrok-libraries/bio/src/utils/monomer-selection-dialog';
+
+import {MonomerLibManager} from './lib-manager';
+import {SEM_TYPES} from '../constants';
+import {_package} from '../../package';
+
+/** Wrapper that pairs a collection name with its loaded data. */
+export interface MonomerCollectionInfo {
+  name: string; // file name (with .json)
+  displayName: string; // name without .json
+  data: MonomerCollection;
+}
+
+const HANDLER_TYPE = 'MonomerCollection';
+
+/**
+ * ObjectHandler for one or more monomer collections.
+ * When a single collection is selected it renders details in the context panel.
+ * When multiple collections are selected it renders merge / bulk-delete actions.
+ */
+export class MonomerCollectionHandler extends DG.ObjectHandler<MonomerCollectionInfo | MonomerCollectionInfo[]> {
+  get type() { return HANDLER_TYPE; }
+  get name() { return 'Monomer Collection'; }
+
+  isApplicable(x: any): boolean {
+    if (Array.isArray(x))
+      return x.length > 0 && x.every((item: any) => this.isSingleCollection(item));
+    return this.isSingleCollection(x);
+  }
+
+  private isSingleCollection(x: any): boolean {
+    return x != null && typeof x === 'object' && 'name' in x && 'displayName' in x && 'data' in x &&
+      typeof (x as MonomerCollectionInfo).data?.monomerSymbols !== 'undefined';
+  }
+
+  getCaption(x: MonomerCollectionInfo | MonomerCollectionInfo[]): string {
+    if (Array.isArray(x))
+      return `${x.length} collections`;
+    return x.displayName;
+  }
+
+  renderProperties(x: MonomerCollectionInfo | MonomerCollectionInfo[], context: any = null): HTMLElement {
+    if (Array.isArray(x))
+      return this.renderMultiProperties(x);
+    return this.renderSingleProperties(x);
+  }
+
+  // -- Single collection panel --
+
+  private renderSingleProperties(info: MonomerCollectionInfo): HTMLElement {
+    const acc = ui.accordion('Monomer Collection');
+    const currentUser = DG.User.current().login;
+    const isOwner = info.data.updatedBy === currentUser;
+
+    // Details pane
+    acc.addPane('Details', () => {
+      const map: {[key: string]: any} = {
+        'Name': info.displayName,
+      };
+      if (info.data.description)
+        map['Description'] = info.data.description;
+      if (info.data.tags && info.data.tags.length > 0)
+        map['Tags'] = info.data.tags.join(', ');
+      map['Monomers'] = `${info.data.monomerSymbols.length}`;
+      if (info.data.updatedBy)
+        map['Updated by'] = info.data.updatedBy;
+      if (info.data.updatedOn) {
+        try { map['Updated on'] = new Date(info.data.updatedOn).toLocaleString(); } catch { /* ignore */ }
+      }
+      return ui.tableFromMap(map);
+    }, true);
+
+    // Monomers pane
+    acc.addPane('Monomers', () => {
+      const container = ui.div([], {style: {display: 'flex', flexWrap: 'wrap', gap: '4px'}});
+      const monomerLib = this.getMonomerLib();
+      for (const symbol of info.data.monomerSymbols) {
+        const tag = ui.div([symbol], {
+          style: {
+            display: 'inline-block', padding: '2px 8px', borderRadius: '4px',
+            background: 'var(--grey-1)', border: '1px solid var(--grey-2)',
+            fontSize: '11px', color: 'var(--grey-5)', cursor: 'pointer',
+          },
+        });
+        tag.addEventListener('mouseenter', () => {
+          if (monomerLib) {
+            const tooltipEl = MonomerCollectionHandler.getMonomerTooltipSafe(monomerLib, symbol);
+            if (tooltipEl) {
+              const rect = tag.getBoundingClientRect();
+              ui.tooltip.show(tooltipEl, rect.left, rect.bottom + 4);
+            }
+          }
+        });
+        tag.addEventListener('mouseleave', () => ui.tooltip.hide());
+        tag.addEventListener('click', () => {
+          grok.shell.o = DG.SemanticValue.fromValueType(symbol, SEM_TYPES.MONOMER);
+        });
+        container.appendChild(tag);
+      }
+      return container;
+    }, true);
+
+    // Actions pane
+    acc.addPane('Actions', () => {
+      const actions: HTMLElement[] = [];
+
+      const editBtn = ui.button('Edit', async () => {
+        if (isOwner) await this.editCollection(info);
+      }, isOwner ? 'Edit this collection' : 'Only the author can edit');
+      if (!isOwner) MonomerCollectionHandler.disableButton(editBtn);
+      actions.push(editBtn);
+
+      const deleteBtn = ui.button('Delete', async () => {
+        if (isOwner) await this.deleteCollection(info);
+      }, isOwner ? 'Delete this collection' : 'Only the author can delete');
+      if (!isOwner) MonomerCollectionHandler.disableButton(deleteBtn);
+      actions.push(deleteBtn);
+
+      actions.push(ui.button('Duplicate', async () => {
+        await this.duplicateCollection(info);
+      }, 'Create a copy of this collection'));
+
+      return ui.divH(actions);
+    }, true);
+
+    return acc.root;
+  }
+
+  // -- Multi-collection panel --
+
+  private renderMultiProperties(items: MonomerCollectionInfo[]): HTMLElement {
+    const acc = ui.accordion('Monomer Collections');
+    const currentUser = DG.User.current().login;
+    const allOwned = items.every((c) => c.data.updatedBy === currentUser);
+
+    // Summary pane
+    acc.addPane('Selection', () => {
+      const list = ui.list(items.map((c) => c.displayName));
+      return ui.divV([
+        ui.divText(`${items.length} collections selected`),
+        list,
+      ]);
+    }, true);
+
+    // Actions pane
+    acc.addPane('Actions', () => {
+      const actions: HTMLElement[] = [];
+
+      actions.push(ui.button('Merge', async () => {
+        await this.mergeCollections(items);
+      }, 'Merge selected collections into one'));
+
+      const deleteAllBtn = ui.button('Delete All', async () => {
+        if (allOwned) await this.deleteMultipleCollections(items);
+      }, allOwned ? 'Delete all selected collections' : 'Only the author can delete (you must be author of all)');
+      if (!allOwned) MonomerCollectionHandler.disableButton(deleteAllBtn);
+      actions.push(deleteAllBtn);
+
+      return ui.divH(actions);
+    }, true);
+
+    return acc.root;
+  }
+
+  // -- Actions --
+
+  private async editCollection(info: MonomerCollectionInfo): Promise<void> {
+    // Find existing view and trigger edit
+    const view = Array.from(grok.shell.views).find((v) => v.name === 'Monomer Collections');
+    if (view && (view as any)._mcView) {
+      const mcView = (view as any)._mcView as import('./monomer-collections-view').MonomerCollectionsView;
+      mcView.editCollectionPublic(info.name, info.data);
+    } else {
+      // Fallback: open the edit dialog directly
+      const libHelper = await MonomerLibManager.getInstance();
+      await libHelper.awaitLoaded();
+      const monomerLib = libHelper.getMonomerLib();
+      this.showEditDialog(info, libHelper, monomerLib!);
+    }
+  }
+
+  private showEditDialog(info: MonomerCollectionInfo, libHelper: MonomerLibManager, monomerLib: IMonomerLib): void {
+    const polymerTypes: PolymerType[] = ['PEPTIDE', 'RNA', 'CHEM'];
+    const nameInput = ui.input.string('Name', {value: info.displayName, nullable: false});
+    const descInput = ui.input.string('Description', {value: info.data.description ?? '', nullable: true});
+    const tagsInput = ui.input.string('Tags', {value: (info.data.tags ?? []).join(', '), nullable: true, placeholder: 'Comma-separated tags'});
+    const polymerTypeInput = ui.input.choice('Polymer Type', {items: [...polymerTypes], value: 'PEPTIDE', nullable: false});
+    const monomerWidget = new MonomerSelectionWidget(monomerLib, polymerTypeInput.value as PolymerType, [...(info.data.monomerSymbols ?? [])], libHelper);
+
+    // eslint-disable-next-line rxjs/no-ignored-subscription
+    polymerTypeInput.onChanged.subscribe(() => monomerWidget.setPolymerType(polymerTypeInput.value as PolymerType));
+
+    const dlg = ui.dialog({title: `Edit Collection: ${info.displayName}`})
+      .add(ui.divV([nameInput, descInput, tagsInput, polymerTypeInput, ui.element('hr'), monomerWidget.root]))
+      .onOK(async () => {
+        const name = nameInput.value?.trim();
+        if (!name) { grok.shell.warning('Collection name is required'); return; }
+        const selectedMonomers = monomerWidget.getSelectedMonomers();
+        if (selectedMonomers.length === 0) { grok.shell.warning('Please select at least one monomer'); return; }
+        const tags = this.parseTags(tagsInput.value);
+        try {
+          if (name !== info.displayName)
+            await libHelper.deleteMonomerCollection(info.name);
+          await libHelper.addOrUpdateMonomerCollection(name, selectedMonomers, descInput.value ?? undefined, tags.length > 0 ? tags : undefined);
+          grok.shell.info(`Collection "${name}" saved successfully`);
+          await this.refreshView();
+        } catch (err: any) {
+          grok.shell.error('Error saving collection');
+        }
+      })
+      .show({resizable: true});
+    dlg.root.style.width = '550px';
+    monomerWidget.focus();
+  }
+
+  private async deleteCollection(info: MonomerCollectionInfo): Promise<void> {
+    ui.dialog({title: 'Delete Collection'})
+      .add(ui.divText(`Are you sure you want to delete "${info.displayName}"?`))
+      .onOK(async () => {
+        try {
+          const libHelper = await MonomerLibManager.getInstance();
+          await libHelper.deleteMonomerCollection(info.name);
+          grok.shell.info(`Collection "${info.displayName}" deleted`);
+          await this.refreshView();
+        } catch (err: any) {
+          grok.shell.error('Error deleting collection');
+        }
+      })
+      .show();
+  }
+
+  private async duplicateCollection(info: MonomerCollectionInfo): Promise<void> {
+    const nameInput = ui.input.string('New Name', {value: `${info.displayName} (copy)`, nullable: false});
+    ui.dialog({title: 'Duplicate Collection'})
+      .add(nameInput)
+      .onOK(async () => {
+        const name = nameInput.value?.trim();
+        if (!name) { grok.shell.warning('Name is required'); return; }
+        try {
+          const libHelper = await MonomerLibManager.getInstance();
+          await libHelper.addOrUpdateMonomerCollection(name, [...info.data.monomerSymbols], info.data.description, info.data.tags ? [...info.data.tags] : undefined);
+          grok.shell.info(`Collection "${name}" created`);
+          await this.refreshView();
+        } catch (err: any) {
+          grok.shell.error('Error duplicating collection');
+        }
+      })
+      .show();
+  }
+
+  private async mergeCollections(items: MonomerCollectionInfo[]): Promise<void> {
+    const nameInput = ui.input.string('Merged Name', {value: 'Merged Collection', nullable: false});
+    const descInput = ui.input.string('Description', {nullable: true, placeholder: 'Optional description'});
+    ui.dialog({title: `Merge ${items.length} Collections`})
+      .add(ui.divV([
+        ui.divText(`Merging: ${items.map((c) => c.displayName).join(', ')}`),
+        nameInput,
+        descInput,
+      ]))
+      .onOK(async () => {
+        const name = nameInput.value?.trim();
+        if (!name) { grok.shell.warning('Name is required'); return; }
+        try {
+          const allSymbols = [...new Set(items.flatMap((c) => c.data.monomerSymbols))];
+          const allTags = [...new Set(items.flatMap((c) => c.data.tags ?? []))];
+          const libHelper = await MonomerLibManager.getInstance();
+          await libHelper.addOrUpdateMonomerCollection(name, allSymbols, descInput.value ?? undefined, allTags.length > 0 ? allTags : undefined);
+          grok.shell.info(`Merged collection "${name}" created with ${allSymbols.length} monomers`);
+          await this.refreshView();
+        } catch (err: any) {
+          grok.shell.error('Error merging collections');
+        }
+      })
+      .show();
+  }
+
+  private async deleteMultipleCollections(items: MonomerCollectionInfo[]): Promise<void> {
+    ui.dialog({title: 'Delete Collections'})
+      .add(ui.divText(`Are you sure you want to delete ${items.length} collections?\n${items.map((c) => c.displayName).join(', ')}`))
+      .onOK(async () => {
+        try {
+          const libHelper = await MonomerLibManager.getInstance();
+          for (const item of items)
+            await libHelper.deleteMonomerCollection(item.name);
+          grok.shell.info(`${items.length} collections deleted`);
+          await this.refreshView();
+        } catch (err: any) {
+          grok.shell.error('Error deleting collections');
+        }
+      })
+      .show();
+  }
+
+  private async refreshView(): Promise<void> {
+    const view = Array.from(grok.shell.views).find((v) => v.name === 'Monomer Collections');
+    if (view && (view as any)._mcView) {
+      const mcView = (view as any)._mcView as import('./monomer-collections-view').MonomerCollectionsView;
+      await mcView.refresh();
+    }
+  }
+
+  private parseTags(input: string | null): string[] {
+    if (!input) return [];
+    return input.split(',').map((t) => t.trim()).filter((t) => t.length > 0);
+  }
+
+  /** Gets the current monomer lib (synchronous, returns null if not loaded). */
+  private getMonomerLib(): IMonomerLib | null {
+    return _package.monomerLib ?? null;
+  }
+
+  /** Gets a monomer tooltip element, searching across all HELM types. */
+  private static getMonomerTooltipSafe(monomerLib: IMonomerLib, symbol: string): HTMLElement | null {
+    const helmTypes: HelmType[] = [HelmTypes.AA, HelmTypes.NUCLEOTIDE, HelmTypes.CHEM, HelmTypes.BLOB];
+    for (const ht of helmTypes) {
+      try {
+        const wem = monomerLib.getWebEditorMonomer(ht, symbol);
+        if (wem) return monomerLib.getTooltip(ht, symbol);
+      } catch { /* skip */ }
+    }
+    return null;
+  }
+
+  /** Applies custom disabled styling to a button (greyed out, not clickable). */
+  private static disableButton(btn: HTMLElement): void {
+    btn.style.opacity = '0.4';
+    btn.style.cursor = 'default';
+  }
+
+  /** Builds a context menu for a single collection. */
+  static buildContextMenu(menu: DG.Menu, info: MonomerCollectionInfo, handler: MonomerCollectionHandler): void {
+    const currentUser = DG.User.current().login;
+    const isOwner = info.data.updatedBy === currentUser;
+
+    menu.item('Edit', () => { if (isOwner) handler.editCollection(info); }, null,
+      {isEnabled: () => isOwner ? null : 'Only the author can edit'});
+    menu.item('Delete', () => { if (isOwner) handler.deleteCollection(info); }, null,
+      {isEnabled: () => isOwner ? null : 'Only the author can delete'});
+    menu.item('Duplicate', () => handler.duplicateCollection(info));
+  }
+
+  /** Builds a context menu for multiple collections. */
+  static buildMultiContextMenu(menu: DG.Menu, items: MonomerCollectionInfo[], handler: MonomerCollectionHandler): void {
+    const currentUser = DG.User.current().login;
+    const allOwned = items.every((c) => c.data.updatedBy === currentUser);
+
+    menu.item('Merge', () => handler.mergeCollections(items));
+    menu.item('Delete All', () => { if (allOwned) handler.deleteMultipleCollections(items); }, null,
+      {isEnabled: () => allOwned ? null : 'Only the author can delete (you must be author of all)'});
+  }
+}