@datagrok-libraries/bio 5.41.5 → 5.41.7

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Files changed (8) hide show
  1. package/CHANGELOG.md +10 -0
  2. package/package.json +1 -1
  3. package/src/utils/cell-renderer-monomer-placer.d.ts +2 -1
  4. package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
  5. package/src/utils/cell-renderer-monomer-placer.js +14 -9
  6. package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
  7. package/src/utils/seq-handler.js +1 -1
  8. package/src/utils/seq-handler.js.map +1 -1
package/CHANGELOG.md CHANGED
@@ -1,5 +1,15 @@
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  # bio changelog
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+ ## 5.41.7 (2024-05-28)
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+
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+ ### Bug fixes
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+
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+ * GROK-15796: Bio: Fix to Helm cell renderer for convert to Helm
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+
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+ ## 5.41.6 (2024-05-20)
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+
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+ Fix monomer placer optimization for column width changed
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+
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  ## 5.41.5 (2024-05-16)
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  Fix separator splitter to ceil splitter limit
package/package.json CHANGED
@@ -8,7 +8,7 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.41.5",
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+ "version": "5.41.7",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.71",
package/src/utils/cell-renderer-monomer-placer.d.ts CHANGED
@@ -13,6 +13,7 @@ type MonomerPlacerProps = {
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  export declare function hitBounds(bounds: number[], x: number): number | null;
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  export declare class MonomerPlacer extends CellRendererBackBase<string> {
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  private readonly propsProvider;
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+ private colWidth;
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  private _monomerLengthList;
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  private separatorWidth;
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  props: MonomerPlacerProps;
@@ -30,7 +31,7 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
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  constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>, logger: ILogger, propsProvider: () => MonomerPlacerProps);
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  protected reset(): void;
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  /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
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- getCellMonomerLengths(rowIdx: number, width: number): [number[], number[]];
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+ getCellMonomerLengths(rowIdx: number, newWidth: number): [number[], number[]];
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  private getCellMonomerLengthsForSeq;
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  private getCellMonomerLengthsForSeqMsa;
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  /** Returns seq position for pointer x */
package/src/utils/cell-renderer-monomer-placer.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"cell-renderer-monomer-placer.d.ts","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AACzC,OAAO,EAAC,kBAAkB,EAAC,MAAM,iBAAiB,CAAC;AAGnD,OAAO,EAAC,oBAAoB,EAAC,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAGjC,KAAK,kBAAkB,GAAG;IACxB,UAAU,EAAE,UAAU,CAAC;IACvB,gBAAgB,EAAE,MAAM,CAAC;IAAC,cAAc,EAAE,MAAM,CAAC;IACjD,cAAc,EAAE,kBAAkB,CAAC;IAAC,kBAAkB,EAAE,MAAM,CAAC;CAChE,CAAC;AAEF,wBAAgB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAoBpE;AAED,qBAAa,aAAc,SAAQ,oBAAoB,CAAC,MAAM,CAAC;IAoB3D,OAAO,CAAC,QAAQ,CAAC,aAAa;IAnBhC,OAAO,CAAC,kBAAkB,CAA2B;IAGrD,OAAO,CAAC,cAAc,CAAK;IACpB,KAAK,EAAE,kBAAkB,CAAC;IACjC,OAAO,CAAC,cAAc,CAAY;IAClC,OAAO,CAAC,6BAA6B,CAAa;IAElD,OAAO,CAAC,QAAQ,CAAkB;IAClC,IAAW,OAAO,IAAI,OAAO,CAA0B;IAEhD,iBAAiB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IACvD,oBAAoB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IAEjE,sEAAsE;gBAEpE,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAC7B,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAC3B,MAAM,EAAE,OAAO,EACE,aAAa,EAAE,MAAM,kBAAkB;cAsBvC,KAAK,IAAI,IAAI;IAQhC,qGAAqG;IAC9F,qBAAqB,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;IAWjF,OAAO,CAAC,2BAA2B;IA8BnC,OAAO,CAAC,8BAA8B;IAmDtC,yCAAyC;IAClC,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IASpE,qBAAqB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAK1C,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAKtC,KAAK,IAAI,OAAO;CAGxB"}
1
+ {"version":3,"file":"cell-renderer-monomer-placer.d.ts","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AACzC,OAAO,EAAC,kBAAkB,EAAC,MAAM,iBAAiB,CAAC;AAEnD,OAAO,EAAC,oBAAoB,EAAC,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAGjC,KAAK,kBAAkB,GAAG;IACxB,UAAU,EAAE,UAAU,CAAC;IACvB,gBAAgB,EAAE,MAAM,CAAC;IAAC,cAAc,EAAE,MAAM,CAAC;IACjD,cAAc,EAAE,kBAAkB,CAAC;IAAC,kBAAkB,EAAE,MAAM,CAAC;CAChE,CAAC;AAEF,wBAAgB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAoBpE;AAED,qBAAa,aAAc,SAAQ,oBAAoB,CAAC,MAAM,CAAC;IAqB3D,OAAO,CAAC,QAAQ,CAAC,aAAa;IApBhC,OAAO,CAAC,QAAQ,CAAa;IAC7B,OAAO,CAAC,kBAAkB,CAA2B;IAGrD,OAAO,CAAC,cAAc,CAAK;IACpB,KAAK,EAAE,kBAAkB,CAAC;IACjC,OAAO,CAAC,cAAc,CAAY;IAClC,OAAO,CAAC,6BAA6B,CAAa;IAElD,OAAO,CAAC,QAAQ,CAAkB;IAClC,IAAW,OAAO,IAAI,OAAO,CAA0B;IAEhD,iBAAiB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IACvD,oBAAoB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IAEjE,sEAAsE;gBAEpE,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAC7B,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAC3B,MAAM,EAAE,OAAO,EACE,aAAa,EAAE,MAAM,kBAAkB;cAsBvC,KAAK,IAAI,IAAI;IAQhC,qGAAqG;IAC9F,qBAAqB,CAAC,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;IAepF,OAAO,CAAC,2BAA2B;IA8BnC,OAAO,CAAC,8BAA8B;IAmDtC,yCAAyC;IAClC,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IASpE,qBAAqB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAK1C,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAKtC,KAAK,IAAI,OAAO;CAGxB"}
package/src/utils/cell-renderer-monomer-placer.js CHANGED
@@ -29,6 +29,7 @@ export class MonomerPlacer extends CellRendererBackBase {
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  constructor(gridCol, tableCol, logger, propsProvider) {
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  super(gridCol, tableCol, logger);
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  this.propsProvider = propsProvider;
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+ this.colWidth = 0;
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  this._monomerLengthList = null;
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  // width of separator symbol
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  this.separatorWidth = 5;
@@ -62,22 +63,26 @@ export class MonomerPlacer extends CellRendererBackBase {
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  this._monomerStructureMap = {};
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  }
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  /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
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- getCellMonomerLengths(rowIdx, width) {
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- const res = this.props.seqHandler.isMsa() ? this.getCellMonomerLengthsForSeqMsa(width) :
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- this.getCellMonomerLengthsForSeq(rowIdx, width);
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+ getCellMonomerLengths(rowIdx, newWidth) {
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+ if (this.colWidth < newWidth) {
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+ this.colWidth = newWidth;
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+ this.reset();
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+ }
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+ const res = this.props.seqHandler.isMsa() ? this.getCellMonomerLengthsForSeqMsa() :
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+ this.getCellMonomerLengthsForSeq(rowIdx);
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  const resSum = new Array(res.length + 1);
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  resSum[0] = 5; // padding
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  for (let pos = 1; pos < resSum.length; pos++)
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  resSum[pos] = resSum[pos - 1] + res[pos - 1];
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  return [res, resSum];
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  }
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- getCellMonomerLengthsForSeq(rowIdx, width) {
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+ getCellMonomerLengthsForSeq(rowIdx) {
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  if (this._monomerLengthList === null) {
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  this._monomerLengthList = new Array(this.tableCol.length).fill(null);
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  this._updated = true;
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  }
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  const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
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- const maxVisibleSeqLength = Math.ceil(width / minMonWidth);
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+ const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
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  const seqMonList = SeqHandler.forColumn(this.tableCol).getSplitted(rowIdx).originals;
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  const visibleSeqLength = Math.min(maxVisibleSeqLength, seqMonList.length);
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  let res = this._monomerLengthList[rowIdx];
@@ -91,14 +96,14 @@ export class MonomerPlacer extends CellRendererBackBase {
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  const seqMonWidth = separatorWidth + shortMon.length * this.props.monomerCharWidth;
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  res[seqMonI] = seqMonWidth;
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  seqWidth += seqMonWidth;
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- if (seqWidth > width)
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+ if (seqWidth > this.colWidth)
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  break;
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  }
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  this._updated = true;
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  }
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  return res;
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  }
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- getCellMonomerLengthsForSeqMsa(width) {
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+ getCellMonomerLengthsForSeqMsa() {
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  var _a;
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  if (this._monomerLengthList === null) {
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  this._monomerLengthList = new Array(1).fill(null);
@@ -125,7 +130,7 @@ export class MonomerPlacer extends CellRendererBackBase {
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  }
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  })();
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  const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
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- const maxVisibleSeqLength = Math.ceil(width / minMonWidth);
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+ const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
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  for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
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  if (this._processedRows.get(seqIdx) && maxVisibleSeqLength <= this._processedMaxVisibleSeqLength)
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  continue;
@@ -141,7 +146,7 @@ export class MonomerPlacer extends CellRendererBackBase {
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  const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.monomerCharWidth;
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  res[seqMonI] = Math.max(res[seqMonI] ?? 0, seqMonWidth);
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  seqWidth += seqMonWidth;
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- if (seqWidth >= width)
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+ if (seqWidth >= this.colWidth)
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  break;
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  }
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  this._updated = true;
package/src/utils/cell-renderer-monomer-placer.js.map CHANGED
@@ -1 +1 @@
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- 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package/src/utils/seq-handler.js CHANGED
@@ -323,7 +323,7 @@ export class SeqHandler {
323
323
  throw new Error(`Notation \'${NOTATION.SEPARATOR}\' requires separator value.`);
324
324
  newColumn.setTag("separator" /* TAGS.separator */, tgtSeparator);
325
325
  }
326
- newColumn.setTag(DG.TAGS.CELL_RENDERER, 'sequence'); // cell.renderer
326
+ newColumn.setTag(DG.TAGS.CELL_RENDERER, tgtNotation === NOTATION.HELM ? 'helm' : 'sequence'); // cell.renderer
327
327
  const srcAligned = col.getTag("aligned" /* TAGS.aligned */);
328
328
  if (srcAligned)
329
329
  newColumn.setTag("aligned" /* TAGS.aligned */, srcAligned);
package/src/utils/seq-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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