@datagrok/sequence-translator 1.10.5 → 1.10.7

package/src/polytool/pt-placeholders-breadth-input.ts

@@ -7,6 +7,15 @@ import {PolyToolBreadthPlaceholder} from './types';
 import {parseMonomerSymbolList} from './pt-placeholders-input';
 import {GridCellRenderArgs} from 'datagrok-api/dg';
 
+/** Callback invoked when user double-clicks a Monomers cell in the breadth grid.
+ * @param start 0-based start position index
+ * @param end 0-based end position index
+ * @param currentMonomers current monomer symbols
+ * @returns new monomer symbols, or null if cancelled */
+export type BreadthMonomerCellEditCallback = (
+  start: number, end: number, currentMonomers: string[],
+) => Promise<string[] | null>;
+
 export class PolyToolPlaceholdersBreadthInput extends DG.JsInputBase<DG.DataFrame> {
   get inputType(): string { return 'Breadth'; }
 
@@ -30,6 +39,9 @@ export class PolyToolPlaceholdersBreadthInput extends DG.JsInputBase<DG.DataFram
     return dfToPlaceholdersBreadth(this.grid.dataFrame);
   }
 
+  /** Set this callback to handle double-click editing of the Monomers column */
+  onMonomerCellEdit: BreadthMonomerCellEditCallback | null = null;
+
   private readonly gridHost: HTMLDivElement;
   public grid: DG.Grid;
 
@@ -91,6 +103,18 @@ export class PolyToolPlaceholdersBreadthInput extends DG.JsInputBase<DG.DataFram
       }
     });
 
+    // Make Monomers column non-editable (editing via double-click dialog)
+    const monomersGridCol = this.grid.columns.byName('Monomers');
+    if (monomersGridCol)
+      monomersGridCol.editable = false;
+
+    // Double-click on Monomers cell opens the monomer selection dialog
+    this.subs.push(this.grid.onCellDoubleClick.subscribe((gc: DG.GridCell) => {
+      if (gc.tableColumn?.name === 'Monomers' &&
+        gc.tableRowIndex != null && gc.tableRowIndex >= 0)
+        this.handleMonomerCellDoubleClick(gc.tableRowIndex);
+    }));
+
     this.updateGridHeight(heightRowCount ?? this.grid.dataFrame.rowCount + 0.7);
     this.subs.push(ui.onSizeChanged(this.grid.root)
       .subscribe(this.gridRootOnSizeChanged.bind(this)));
@@ -140,6 +164,21 @@ export class PolyToolPlaceholdersBreadthInput extends DG.JsInputBase<DG.DataFram
 
   // -- Handle events --
 
+  private async handleMonomerCellDoubleClick(tableRowIdx: number): Promise<void> {
+    if (!this.onMonomerCellEdit)
+      return;
+    const df = this.grid.dataFrame;
+    const start = parseInt(df.get('Start', tableRowIdx)) - 1;
+    const end = parseInt(df.get('End', tableRowIdx)) - 1;
+    if (isNaN(start) || isNaN(end))
+      return;
+    const currentStr: string = df.get('Monomers', tableRowIdx) ?? '';
+    const currentMonomers = parseMonomerSymbolList(currentStr);
+    const result = await this.onMonomerCellEdit(start, end, currentMonomers);
+    if (result !== null)
+      df.set('Monomers', tableRowIdx, result.join(', '));
+  }
+
   private gridRootOnSizeChanged(): void {
     this.grid.columns.byIndex(4)!.width = this.grid.root.clientWidth - this.grid.horzScroll.root.offsetWidth -
       this.grid.columns.byIndex(0)!.width - this.grid.columns.byIndex(1)!.width -

package/src/polytool/pt-placeholders-input.ts

@@ -7,6 +7,12 @@ import {fromEvent, Unsubscribable} from 'rxjs';
 import {PolyToolPlaceholder} from './types';
 import {GridCellRenderArgs} from 'datagrok-api/dg';
 
+/** Callback invoked when user double-clicks a Monomers cell.
+ * @param position 0-based position index
+ * @param currentMonomers current monomer symbols
+ * @returns new monomer symbols, or null if cancelled */
+export type MonomerCellEditCallback = (position: number, currentMonomers: string[]) => Promise<string[] | null>;
+
 export class PolyToolPlaceholdersInput extends DG.JsInputBase<DG.DataFrame> {
   get inputType(): string { return 'Positions'; }
 
@@ -38,6 +44,9 @@ export class PolyToolPlaceholdersInput extends DG.JsInputBase<DG.DataFrame> {
     return dfToPlaceholders(this.grid.dataFrame);
   }
 
+  /** Set this callback to handle double-click editing of the Monomers column */
+  onMonomerCellEdit: MonomerCellEditCallback | null = null;
+
   private readonly gridHost: HTMLDivElement;
   private grid!: DG.Grid;
 
@@ -89,6 +98,17 @@ export class PolyToolPlaceholdersInput extends DG.JsInputBase<DG.DataFrame> {
       }
     });
 
+    // Make Monomers column non-editable (editing is done via double-click dialog)
+    const monomersGridCol = this.grid.columns.byName('Monomers');
+    if (monomersGridCol)
+      monomersGridCol.editable = false;
+
+    // Double-click on Monomers cell opens the monomer selection dialog
+    this.subs.push(this.grid.onCellDoubleClick.subscribe((gc: DG.GridCell) => {
+      if (gc.tableColumn?.name === 'Monomers' && gc.tableRowIndex != null && gc.tableRowIndex >= 0)
+        this.handleMonomerCellDoubleClick(gc.tableRowIndex);
+    }));
+
     this.updateGridHeight(heightRowCount ?? this.grid.dataFrame.rowCount + 0.7);
     this.subs.push(ui.onSizeChanged(this.grid.root)
       .subscribe(this.gridRootOnSizeChanged.bind(this)));
@@ -160,6 +180,20 @@ export class PolyToolPlaceholdersInput extends DG.JsInputBase<DG.DataFrame> {
 
   // -- Handle events --
 
+  private async handleMonomerCellDoubleClick(tableRowIdx: number): Promise<void> {
+    if (!this.onMonomerCellEdit)
+      return;
+    const df = this.grid.dataFrame;
+    const position = parseInt(df.get('Position', tableRowIdx)) - 1;
+    if (isNaN(position))
+      return;
+    const currentMonomersStr: string = df.get('Monomers', tableRowIdx) ?? '';
+    const currentMonomers = parseMonomerSymbolList(currentMonomersStr);
+    const result = await this.onMonomerCellEdit(position, currentMonomers);
+    if (result !== null)
+      df.set('Monomers', tableRowIdx, result.join(', '));
+  }
+
   private gridRootOnSizeChanged(): void {
     this.grid.columns.byIndex(3)!.width = this.grid.root.clientWidth - this.grid.horzScroll.root.offsetWidth -
       this.grid.columns.byIndex(0)!.width - this.grid.columns.byIndex(1)!.width -

package/src/tests/files-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 
 import {getHelm} from './utils';

package/src/tests/formats-support.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {DEFAULT_FORMATS} from '../apps/common/model/const';
 import {getTranslatedSequences} from '../apps/translator/model/conversion-utils';
 import {ITranslationHelper} from '../types';

package/src/tests/formats-to-helm.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {getFormat, getHelm} from './utils';
 import {ITranslationHelper} from '../types';
 

package/src/tests/helm-to-nucleotides.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {getNucleotidesSequence} from '../apps/translator/model/conversion-utils';
 import {ITranslationHelper} from '../types';
 

package/src/tests/polytool-chain-from-notation-tests.ts

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 import {Chain} from '../polytool/conversion/pt-chain';
 import {getRules} from '../polytool/conversion/pt-rules';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';

package/src/tests/polytool-chain-parse-notation-tests.ts

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 import {Chain} from '../polytool/conversion/pt-chain';
 import {getInnerIdx, getOuterIdx} from '../polytool/conversion/pt-misc';
 import {getRules} from '../polytool/conversion/pt-rules';

package/src/tests/polytool-convert-tests.ts

@@ -4,7 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {before, after, category, expect, test, expectArray, testEvent, expectObject}
-  from '@datagrok-libraries/utils/src/test';
+  from '@datagrok-libraries/test/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {

package/src/tests/polytool-detectors-custom-notation-test.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, expect, before} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, before} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper, getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {ALIGNMENT, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {_testNeg, _testPos, DetectorTestData, DfReaderFunc, PosCol} from './utils/detect-macromolecule-utils';

package/src/tests/polytool-enumerate-breadth-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/polytool-enumerate-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/polytool-unrule-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 
 import {doPolyToolUnrule} from '../polytool/pt-unrule';
 import {getRules} from '../polytool/conversion/pt-rules';

package/src/tests/toAtomicLevel-tests.ts

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 import {Monomer, MonomerLibData} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';

package/src/tests/utils/detect-macromolecule-utils.ts

@@ -3,7 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {ALIGNMENT, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {delay, expect} from '@datagrok-libraries/utils/src/test';
+import {delay, expect} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 export type DetectorTestData = { [testName: string]: { csv: string, neg?: string[], pos?: { [colName: string]: PosCol } } };

package/src/utils/cyclized.ts

@@ -6,7 +6,7 @@ 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 {INotationProvider, ISeqSplitted, NotationProviderBase, 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';
@@ -22,16 +22,22 @@ import {CyclizedCellRendererBack} from './cell-renderer-cyclized';
 
 /* eslint-enable max-len */
 
-export class CyclizedNotationProvider implements INotationProvider {
+export class CyclizedNotationProvider extends NotationProviderBase implements INotationProvider {
   private readonly separatorSplitter: SplitterFunc;
   public readonly splitter: SplitterFunc;
 
+  static override get notationName(): string { return 'Harmonized Sequence'; }
+  static override get implementsFromHelm(): boolean { return false; }
+  static override convertFromHelm(helm: string, options: any): string {
+    throw new Error('converting from helm not supported yet');
+  }
   get defaultGapOriginal(): string { return ''; }
 
   constructor(
     public readonly separator: string,
     protected readonly helmHelper: IHelmHelper
   ) {
+    super();
     this.separatorSplitter = getSplitterWithSeparator(this.separator);
     this.splitter = this._splitter.bind(this);
   }