@datagrok/sequence-translator 1.3.13 → 1.3.14

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.3.13",
+  "version": "1.3.14",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
@@ -22,7 +22,7 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.42.11",
+    "@datagrok-libraries/bio": "5.42.12",
     "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/tutorials": "^1.3.13",
     "@datagrok-libraries/utils": "^4.2.29",

package/src/polytool/cyclized.ts

@@ -1,56 +0,0 @@
-import {GAP_SYMBOL, INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc}
-  from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {getSplitterWithSeparator, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
-import {GapOriginals} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-
-export class CyclizedNotationProvider implements INotationProvider {
-  private readonly separatorSplitter: SplitterFunc;
-  public readonly splitter: SplitterFunc;
-
-  constructor(
-    public readonly separator: string
-  ) {
-    this.separatorSplitter = getSplitterWithSeparator(this.separator);
-    this.splitter = this._splitter.bind(this);
-  }
-
-  private _splitter(seq: string): ISeqSplitted {
-    const baseSS: ISeqSplitted = this.separatorSplitter(seq);
-    return new CyclizedSeqSplitted(baseSS.originals, GapOriginals[NOTATION.SEPARATOR]);
-  };
-}
-
-/** Gets canonical monomers for original ones with cyclization marks */
-export class CyclizedSeqSplitted extends StringListSeqSplitted {
-  private readonly seqCList: (string | null)[];
-
-  private _canonicals: string[] | null = null;
-  override get canonicals(): SeqSplittedBase {
-    if (!this._canonicals) {
-      const len = this.length;
-      this._canonicals = new Array<string>(len);
-      for (let posIdx = 0; posIdx < len; ++posIdx)
-        this._canonicals[posIdx] = this.getCanonical(posIdx);
-    }
-    return this._canonicals;
-  }
-
-  override getCanonical(posIdx: number): string {
-    if (this.isGap(posIdx)) return GAP_SYMBOL;
-
-    let cmRes: string | null = this.seqCList[posIdx];
-    if (cmRes === null) {
-      const om = this.getOriginal(posIdx);
-      cmRes = om;
-      if (om[om.length - 1] === ')')
-        cmRes = this.seqCList[posIdx] = om.replace(/\(\d+\)$/, '');
-    }
-    return cmRes;
-  }
-
-  constructor(seqOList: SeqSplittedBase, gapOriginalMonomer: string) {
-    super(seqOList, gapOriginalMonomer);
-    this.seqCList = new Array<string | null>(this.length).fill(null);
-  }
-}