@datagrok/bio 2.15.5 → 2.15.6

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

@@ -11,22 +11,18 @@ import {
   HelmType, HelmAtom,
   MonomerSetType, MonomerType, PolymerType, IWebEditorMonomer,
 } from '@datagrok-libraries/bio/src/helm/types';
-import {HelmTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
-import {IMonomerLib, IMonomerSet, Monomer, MonomerLibSummaryType, RGroup} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLibBase, IMonomerLib, IMonomerSet, Monomer, MonomerLibData, MonomerLibSummaryType, RGroup} from '@datagrok-libraries/bio/src/types';
 import {HELM_OPTIONAL_FIELDS as OPT, HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP} from '@datagrok-libraries/bio/src/utils/const';
 import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
-import {getUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {GapOriginals} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
 import {MonomerLibBase, MonomerLibDataType} from './monomer-lib-base';
 
-import '../../../css/cell-renderer.css';
-
 import {_package} from '../../package';
 
+import '../../../css/cell-renderer.css';
 
 /** Wrapper for monomers obtained from different sources. For managing monomere
  * libraries, use MolfileHandler class instead */
@@ -83,7 +79,7 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
       }
     } else {
       const dict = this._monomers[polymerType];
-      res = dict ? dict[monomerSymbol] : null;
+      res = dict?.[monomerSymbol] ?? null;
     }
     return res;
   }
@@ -287,4 +283,29 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     }
     return res;
   }
+
+  override(data: MonomerLibData): IMonomerLibBase {
+    return new OverriddenMonomerLib(data, this);
+  }
+}
+
+class OverriddenMonomerLib extends MonomerLibBase {
+  constructor(
+    private readonly data: MonomerLibData,
+    private readonly base: MonomerLibBase
+  ) {
+    super(data);
+  }
+
+  get onChanged(): Observable<any> { return this.base.onChanged; }
+
+  addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer {
+    return this.base.addMissingMonomer(polymerType, monomerSymbol);
+  }
+
+  getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null {
+    const dataMonomer = this.data[polymerType as string]?.[monomerSymbol];
+    const resMonomer = dataMonomer ?? this.base.getMonomer(polymerType, monomerSymbol);
+    return resMonomer;
+  }
 }

package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts

@@ -8,12 +8,12 @@ import * as DG from 'datagrok-api/dg';
 import {IMonomerManager, INewMonomerForm} from '@datagrok-libraries/bio/src/utils/monomer-ui';
 import {IMonomerLib, Monomer, RGroup} from '@datagrok-libraries/bio/src/types';
 import {DUMMY_MONOMER, HELM_RGROUP_FIELDS} from '@datagrok-libraries/bio/src/utils/const';
-import {LIB_PATH} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {ItemsGrid} from '@datagrok-libraries/utils/src/items-grid';
 import {mostSimilarNaturalAnalog} from '@datagrok-libraries/bio/src/utils/macromolecule/monomers';
 import {PolymerType, MonomerType} from '@datagrok-libraries/bio/src/helm/types';
 
 import {MonomerLibManager} from '../lib-manager';
+import {LIB_PATH} from '../consts';
 
 import '../../../../css/monomer-manager.css';
 

package/src/utils/pepsea.ts

@@ -80,7 +80,7 @@ export async function runPepsea(srcCol: DG.Column<string>, unUsedName: string,
 
   const alignedSequences: string[] = new Array(peptideCount);
   for (const body of bodies) { // getting aligned sequences for each cluster
-    const alignedObject = await fetchWrapper(() => requestAlignedObjects(pepseaContainer.id, body, method, gapOpen, gapExtend, logger));
+    const alignedObject = await requestAlignedObjects(pepseaContainer.id, body, method, gapOpen, gapExtend, logger);
     const alignments = alignedObject.Alignment;
 
     for (const alignment of alignments) { // filling alignedSequencesCol

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

@@ -1 +0,0 @@
-export const HELM_JSON_SCHEMA_PATH = 'System:AppData/Bio/tests/libraries/HELMmonomerSchema.json';