@datagrok/bio 2.16.7 → 2.16.9

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.16.7",
+  "version": "2.16.9",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,12 +37,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.45.5",
+    "@datagrok-libraries/bio": "^5.45.7",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.2",
     "@datagrok-libraries/ml": "^6.7.4",
     "@datagrok-libraries/tutorials": "^1.4.3",
-    "@datagrok-libraries/utils": "^4.3.6",
+    "@datagrok-libraries/utils": "^4.3.7",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -58,8 +58,8 @@
     "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.12",
-    "@datagrok-libraries/js-draw-lite": "^0.0.9",
+    "@datagrok-libraries/helm-web-editor": "^1.1.13",
+    "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/chem": "^1.12.3",
     "@datagrok/dendrogram": "^1.2.33",
     "@datagrok/helm": "^2.5.3",

package/src/package.ts

@@ -102,52 +102,46 @@ let initBioPromise: Promise<void> | null = null;
 
 //tags: init
 export async function initBio(): Promise<void> {
-  if (initBioPromise === null) {
+  if (initBioPromise === null)
     initBioPromise = initBioInt();
-  }
+
   await initBioPromise;
 }
 
 async function initBioInt() {
   const logPrefix = 'Bio: _package.initBio()';
   _package.logger.debug(`${logPrefix}, start`);
-  let monomerLib!: IMonomerLib;
-  let monomerSets!: IMonomerSet;
-  let rdKitModule!: RDModule;
-  let libHelper!: MonomerLibManager;
   const t1: number = window.performance.now();
-  await Promise.all([
-    (async () => {
-      libHelper = await MonomerLibManager.getInstance();
-      // Fix user lib settings for explicit stuck from a terminated test
-      const libSettings = await getUserLibSettings();
-      if (libSettings.explicit) {
-        libSettings.explicit = [];
-        await setUserLibSettings(libSettings);
-      }
-      libHelper.awaitLoaded(Infinity).then(() => {
-        // Do not wait for monomers and sets loaded
-        return Promise.all([libHelper.loadMonomerLib(), libHelper.loadMonomerSets()]);
-      });
-      monomerLib = libHelper.getMonomerLib();
-      monomerSets = libHelper.getMonomerSets();
-    })(),
-    (async () => {
-      const pkgProps = await _package.getProperties();
-      const bioPkgProps = new BioPackageProperties(pkgProps);
-      _package.properties = bioPkgProps;
-    })(),
-    (async () => { rdKitModule = await getRdKitModule(); })(),
-  ]).finally(() => {
-    const t2: number = window.performance.now();
-    _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
+  // very important that loading should happen in correct order!
+  // first make sure chem and rdkit module are loaded
+  const rdKitModule = await getRdKitModule();
+  // then load package settings
+  const pkgProps = await _package.getProperties();
+  const bioPkgProps = new BioPackageProperties(pkgProps);
+  _package.properties = bioPkgProps;
+  // then load monomer lib
+  const libHelper = await MonomerLibManager.getInstance();
+  // Fix user lib settings for explicit stuck from a terminated test
+  const libSettings = await getUserLibSettings();
+  if (libSettings.explicit) {
+    libSettings.explicit = [];
+    await setUserLibSettings(libSettings);
+  }
+  libHelper.awaitLoaded(Infinity).then(() => {
+    // Do not wait for monomers and sets loaded
+    return Promise.all([libHelper.loadMonomerLib(), libHelper.loadMonomerSets()]);
   });
-  const seqHelper = new SeqHelper(libHelper, rdKitModule);
-  _package.completeInit(seqHelper, monomerLib, monomerSets, rdKitModule);
+  const monomerLib = libHelper.getMonomerLib();
+  const monomerSets = libHelper.getMonomerSets();
+  // finally log
+  const t2: number = window.performance.now();
+  _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
 
   const monomers: string[] = [];
   const logPs: number[] = [];
 
+  const seqHelper = new SeqHelper(libHelper, rdKitModule);
+  _package.completeInit(seqHelper, monomerLib, monomerSets, rdKitModule);
   const series = monomerLib!.getMonomerMolsByPolymerType('PEPTIDE')!;
   Object.keys(series).forEach((symbol) => {
     monomers.push(symbol);
@@ -1216,6 +1210,7 @@ export async function detectMacromoleculeProbe(file: DG.FileInfo, colName: strin
 //name: getSeqHelper
 //output: object result
 export async function getSeqHelper(): Promise<ISeqHelper> {
+  await initBio();
   return _package.seqHelper;
 }
 

package/src/tests/seq-handler-get-helm-tests.ts

@@ -81,8 +81,8 @@ category('SeqHandler: getHelm', () => {
     await grok.data.detectSemanticTypes(df);
 
     const sh = seqHelper.getSeqHandler(seqCol);
-    const resMValue = await sh.getValue(0);
-    const resHelm = resMValue.helm;
+    const resSeqValue = await sh.getValue(0);
+    const resHelm = resSeqValue.helm;
     expect(resHelm, tgtHelm);
   }
 });

package/src/utils/cell-renderer.ts

@@ -81,8 +81,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
     const [gridCol, tableCol, temp] = getGridCellColTemp<string, MonomerPlacer>(gridCell);
-    const back = temp.rendererBack;
-    back.onMouseMove(gridCell, e);
+    temp.rendererBack?.onMouseMove(gridCell, e);
   }
 
   override onMouseLeave(gridCell: DG.GridCell, e: MouseEvent) {
@@ -99,7 +98,6 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
    * @param {number} h height of the cell.
    * @param {DG.GridCell} gridCell Grid cell.
    * @param {DG.GridCellStyle} _cellStyle Cell style.
-   * @memberof AlignedSequenceCellRenderer
    */
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,

package/src/utils/seq-helper/seq-handler.ts

@@ -14,7 +14,7 @@ import {GAP_SYMBOL, GapOriginals} from '@datagrok-libraries/bio/src/utils/macrom
 import {CellRendererBackBase, GridCellRendererTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
-import {ISeqHandler, ConvertFunc, JoinerFunc, SeqTemps, MacromoleculeValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {ConvertFunc, ISeqHandler, JoinerFunc, SeqTemps, SeqValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 import {SeqHelper} from './seq-helper';
 
@@ -28,7 +28,7 @@ export class SeqHandler implements ISeqHandler {
   protected readonly _units: string; // units, of the form fasta, separator
   protected readonly _notation: NOTATION; // current notation (without :SEQ:NT, etc.)
   protected readonly _defaultGapOriginal: string;
-  protected readonly notationProvider: INotationProvider | null = null;
+  protected readonly notationProvider!: INotationProvider;
 
   private _splitter: SplitterFunc | null = null;
 
@@ -38,15 +38,25 @@ export class SeqHandler implements ISeqHandler {
     if (col.type !== DG.TYPE.STRING)
       throw new Error(`Unexpected column type '${col.type}', must be '${DG.TYPE.STRING}'.`);
     this._column = col;
-    const units = this._column.meta.units;
-    if (units !== null && units !== undefined)
-      this._units = units;
-    else
+    const units: string | null = this._column.meta.units;
+    if (!units)
       throw new Error('Units are not specified in column');
+    this._units = units!;
+
     this._notation = this.getNotation();
-    this._defaultGapOriginal = (this.isFasta()) ? GapOriginals[NOTATION.FASTA] :
-      (this.isHelm()) ? GapOriginals[NOTATION.HELM] :
-        GapOriginals[NOTATION.SEPARATOR];
+    if (this.isCustom()) {
+      // this.column.temp[SeqTemps.notationProvider] must be set at detector stage
+      this.notationProvider = this.column.temp[SeqTemps.notationProvider] ?? null;
+    }
+
+    const defaultGapOriginal = this.isFasta() ? GapOriginals[NOTATION.FASTA] :
+      this.isSeparator() ? GapOriginals[NOTATION.SEPARATOR] :
+        this.isHelm() ? GapOriginals[NOTATION.HELM] :
+          this.isCustom() ? this.notationProvider.defaultGapOriginal :
+            undefined;
+    if (defaultGapOriginal == undefined)
+      throw new Error(`Unexpected defaultGapOriginal for notation '${this.notation}'`);
+    this._defaultGapOriginal = defaultGapOriginal;
 
     if (!this.column.tags.has(TAGS.aligned) || !this.column.tags.has(TAGS.alphabet) ||
       (!this.column.tags.has(TAGS.alphabetIsMultichar) && !this.isHelm() && this.alphabet === ALPHABET.UN)
@@ -60,6 +70,8 @@ export class SeqHandler implements ISeqHandler {
         this.seqHelper.setUnitsToSeparatorColumn(this, separator);
       } else if (this.isHelm())
         this.seqHelper.setUnitsToHelmColumn(this);
+      else if (this.isCustom())
+        this.notationProvider!.setUnits(this);
       else
         throw new Error(`Unexpected units '${this.column.meta.units}'.`);
     }
@@ -82,10 +94,6 @@ export class SeqHandler implements ISeqHandler {
       }
     }
 
-    if (this.column.meta.units === NOTATION.CUSTOM) {
-      // this.column.temp[SeqTemps.notationProvider] must be set at detector stage
-      this.notationProvider = this.column.temp[SeqTemps.notationProvider] ?? null;
-    }
     this.columnVersion = this.column.version;
   }
 
@@ -241,16 +249,23 @@ export class SeqHandler implements ISeqHandler {
   }
 
   /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
-  public async getValue(rowIdx: number, options?: any): Promise<MacromoleculeValueBase> {
+  public getValue(rowIdx: number, options?: any): SeqValueBase {
     const seq: string = this.column.get(rowIdx);
     let resHelm: string;
-    if (this.notationProvider)
-      resHelm = await this.notationProvider.getHelm(seq, options);
-    else {
-      resHelm = this.convertToHelm(seq);
-    }
-    const resMValue = new MacromoleculeValueBase(resHelm, this, rowIdx);
-    return resMValue;
+    const resSeqValue = new SeqValueBase(rowIdx, this);
+    return resSeqValue;
+  }
+
+  public getHelm(rowIdx: number): string {
+    let resHelm: string;
+    const seq = this.column.get(rowIdx);
+    if (this.notation === NOTATION.HELM)
+      resHelm = seq;
+    else if (this.notation === NOTATION.CUSTOM)
+      resHelm = this.notationProvider!.getHelm(seq, {});
+    else
+      resHelm = this.getConverter(NOTATION.HELM)(seq);
+    return resHelm;
   }
 
   private _stats: SeqColStats | null = null;
@@ -306,6 +321,8 @@ export class SeqHandler implements ISeqHandler {
 
   public isHelm(): boolean { return this.notation === NOTATION.HELM; }
 
+  public isCustom(): boolean { return this.notation === NOTATION.CUSTOM; }
+
   public isRna(): boolean { return this.alphabet === ALPHABET.RNA; }
 
   public isDna(): boolean { return this.alphabet === ALPHABET.DNA; }
@@ -452,6 +469,12 @@ export class SeqHandler implements ISeqHandler {
     return newColumn;
   }
 
+  get splitter(): SplitterFunc {
+    if (this._splitter === null)
+      this._splitter = this.getSplitter();
+    return this._splitter;
+  }
+
   /** Gets function to split seq value to monomers */
   protected getSplitter(limit?: number): SplitterFunc {
     let splitter: SplitterFunc | null = null;
@@ -543,12 +566,6 @@ export class SeqHandler implements ISeqHandler {
 
   // -- Notation Converter --
 
-  protected get splitter(): SplitterFunc {
-    if (this._splitter === null)
-      this._splitter = this.getSplitter();
-    return this._splitter;
-  }
-
   public toFasta(targetNotation: NOTATION): boolean { return targetNotation === NOTATION.FASTA; }
 
   public toSeparator(targetNotation: NOTATION): boolean { return targetNotation === NOTATION.SEPARATOR; }