@datagrok/bio 2.15.13 → 2.16.2

package/src/utils/cyclized.ts

@@ -1,89 +0,0 @@
-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';
-
-import {INotationProvider, ISeqSplitted, SeqSplittedBase, SplitterFunc}
-  from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {getSplitterWithSeparator, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {CellRendererBackBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
-import {GAP_SYMBOL, GapOriginals} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
-import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-
-import {monomerToShortFunction} from './cell-renderer';
-
-import {_package} from '../package';
-
-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(
-      wu.count(0).take(baseSS.length).map((p) => baseSS.getOriginal(p)).toArray(),
-      GapOriginals[NOTATION.SEPARATOR]);
-  }
-
-  public async getHelm(seqCol: DG.Column<string>, options?: any): Promise<DG.Column<string>> {
-    const polyToolPackageName: string = 'SequenceTranslator';
-
-    const funcList = DG.Func.find({package: polyToolPackageName, name: 'polyToolConvert2'});
-    if (funcList.length == 0)
-      throw new Error(`Package '${polyToolPackageName}' must be installed for Cyclized notation provider.`);
-    const func = funcList[0];
-
-    const ptConvertCall = await func.prepare({table: seqCol.dataFrame, seqCol: seqCol, ...options});
-
-    const editorFunc = DG.Func.find({package: polyToolPackageName, name: 'getPolyToolConvertEditor'})[0];
-    const resHelmCol = (await editorFunc.prepare({call: ptConvertCall}).call()).getOutputParamValue() as DG.Column<string>;
-    return resHelmCol;
-  }
-
-  public createCellRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string> {
-    let maxLengthOfMonomer: number = (_package.properties ? _package.properties.maxMonomerLength : 4) ?? 50;
-    return new MonomerPlacer(gridCol, tableCol, _package.logger, maxLengthOfMonomer,
-      () => {
-        const sh = SeqHandler.forColumn(tableCol);
-        return {
-          seqHandler: sh,
-          monomerCharWidth: 7,
-          separatorWidth: 11,
-          monomerToShort: monomerToShortFunction,
-        };
-      });
-  }
-}
-
-/** 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

@@ -1,10 +0,0 @@
-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 {
-
-}