@datagrok/sequence-translator 1.4.4 → 1.4.6

package/src/utils/cyclized.ts

@@ -0,0 +1,88 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import wu from 'wu';
+
+/* eslint-disable max-len */
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {getSplitterWithSeparator} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {GAP_SYMBOL, GapOriginals, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {CellRendererBackBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
+import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
+import {monomerToShort, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+
+import {Chain} from '../polytool/pt-conversion';
+
+import {_package} from '../package';
+
+/* eslint-enable max-len */
+
+export class CyclizedNotationProvider implements INotationProvider {
+  private readonly separatorSplitter: SplitterFunc;
+  public readonly splitter: SplitterFunc;
+
+  constructor(
+    public readonly separator: string,
+    protected readonly seqHelper: ISeqHelper
+  ) {
+    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(
+      wu.count(0).take(baseSS.length).map((p) => baseSS.getOriginal(p)).toArray(),
+      GapOriginals[NOTATION.SEPARATOR]);
+  }
+
+  public async getHelm(seq: string, options?: any): Promise<string> {
+    const helmHelper = await getHelmHelper();
+    const seqChain = await Chain.parseNotation(seq, helmHelper);
+    const resPseudoHelm = seqChain.getNotationHelm();
+    return resPseudoHelm;
+  }
+
+  public createCellRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string> {
+    let maxLengthOfMonomer: number = 4; // (_package.bioProperties ? _package.bioProperties.maxMonomerLength : 4) ?? 50;
+    const back = new MonomerPlacer(gridCol, tableCol, _package.logger, maxLengthOfMonomer,
+      () => {
+        const sh = this.seqHelper.getSeqHandler(tableCol);
+        return {
+          seqHandler: sh,
+          monomerCharWidth: 7,
+          separatorWidth: 11,
+          monomerToShort: monomerToShort,
+        };
+      });
+    back.init().then(() => {});
+    return back;
+  }
+}
+
+/** Gets canonical monomers for original ones with cyclization marks */
+export class CyclizedSeqSplitted extends StringListSeqSplitted {
+  private readonly seqCList: (string | null)[];
+
+  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);
+  }
+}

package/src/utils/dimerized.ts

@@ -0,0 +1,10 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {CyclizedNotationProvider} from './cyclized';
+
+
+export class DimerizedNotationProvider extends CyclizedNotationProvider {
+
+}