@datagrok/bio 2.4.28 → 2.4.29

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.28",
+  "version": "2.4.29",
   "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",

package/src/analysis/sequence-space.ts

@@ -8,6 +8,9 @@ import {ISequenceSpaceParams} from '@datagrok-libraries/ml/src/viewers/activity-
 import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import * as grok from 'datagrok-api/grok';
+import { NotationConverter } from '@datagrok-libraries/bio/src/utils/notation-converter';
+import { ALPHABET, NOTATION } from '@datagrok-libraries/bio/src/utils/macromolecule';
+import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
 export interface ISequenceSpaceResult {
   distance: Matrix;
@@ -55,15 +58,24 @@ export async function sequenceSpaceByFingerprints(spaceParams: ISequenceSpacePar
 }
 
 export async function getSequenceSpace(spaceParams: ISequenceSpaceParams): Promise<ISequenceSpaceResult> {
-  const uh = new UnitsHandler(spaceParams.seqCol);
-  if (uh.isFasta()) {
-    const distanceFName = uh.getDistanceFunctionName();
+  const nc = new NotationConverter(spaceParams.seqCol);
+  if (nc.isFasta() || (nc.isSeparator() && nc.alphabet && nc.alphabet !== ALPHABET.UN)) {
+    let distanceFName = MmDistanceFunctionsNames.LEVENSHTEIN;
+    let seqList = spaceParams.seqCol.toList();
+    if (nc.isSeparator()) {
+      const fastaCol = nc.convert(NOTATION.FASTA);
+      seqList = fastaCol.toList();
+      const uh = new UnitsHandler(fastaCol);
+      distanceFName = uh.getDistanceFunctionName();
+    }
+    else {
+      distanceFName = nc.getDistanceFunctionName();
+    }
     const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
-      spaceParams.seqCol.toList(),
+      seqList,
       spaceParams.methodName,
       distanceFName,
       spaceParams.options);
-    console.log(sequenceSpaceResult);
     const cols: DG.Column[] = spaceParams.embedAxesNames.map(
       (name: string, index: number) => DG.Column.fromFloat32Array(name, sequenceSpaceResult.embedding[index]));
     return {distance: sequenceSpaceResult.distance, coordinates: new DG.ColumnList(cols)};

package/src/package.ts

@@ -32,7 +32,7 @@ import {substructureSearchDialog} from './substructure-search/substructure-searc
 import {saveAsFastaUI} from './utils/save-as-fasta';
 import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
 import {delay} from '@datagrok-libraries/utils/src/test';
-import {getStats, splitterAsHelm, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {getStats, splitterAsHelm, TAGS as bioTAGS, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
@@ -53,6 +53,7 @@ import {demoBio03UI} from './demo/bio03-atomic-level';
 import {demoBio05UI} from './demo/bio05-helm-msa-sequence-space';
 import {checkInputColumnUI} from './utils/check-input-column';
 import {multipleSequenceAlignmentUI} from './utils/multiple-sequence-alignment-ui';
+import { NotationConverter } from '@datagrok-libraries/bio/src/utils/notation-converter';
 
 export const _package = new DG.Package();
 
@@ -290,13 +291,22 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
     'separator': macroMolecule.getTag(bioTAGS.separator),
     'alphabet': macroMolecule.getTag(bioTAGS.alphabet),
   };
-  const uh = new UnitsHandler(macroMolecule);
+  const nc = new NotationConverter(macroMolecule);
   let columnDistanceMetric = 'Tanimoto';
-  if (uh.isFasta())
-    columnDistanceMetric = uh.getDistanceFunctionName();
+  let seqCol = macroMolecule;
+  if (nc.isFasta() || (nc.isSeparator() && nc.alphabet && nc.alphabet !== ALPHABET.UN)){
+    if (nc.isFasta()){
+      columnDistanceMetric = nc.getDistanceFunctionName();
+    } else {
+      seqCol = nc.convert(NOTATION.FASTA);
+      const uh = new UnitsHandler(seqCol);
+      columnDistanceMetric = uh.getDistanceFunctionName();
+      tags.units = NOTATION.FASTA;
+    }
+  }
   const sp = await getActivityCliffs(
     df,
-    macroMolecule,
+    seqCol,
     null,
     axesNames,
     'Activity cliffs', //scatterTitle