@datagrok-libraries/bio - npm Package Compare versions

Comparing version 5.42.11 to 5.42.12

CHANGELOG.md

 # bio changelog
 
+## 5.42.12 (2024-08-30)
+
+Add getHelm to SeqHandler and INotationProvider
+
 ## 5.42.11 (2024-08-24)
@@ -4,0 +8,0 @@

package.json

@@ -11,3 +11,3 @@ {
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.11",
+  "version": "5.42.12",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
@@ -31,4 +31,4 @@ "dependencies": {
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.9",
-    "@datagrok-libraries/js-draw-lite": "^0.0.7",
+    "@datagrok-libraries/helm-web-editor": "^1.1.11",
+    "@datagrok-libraries/js-draw-lite": "^0.0.8",
     "@types/signals": "1.0.1",
@@ -35,0 +35,0 @@ "@types/three": "^0.159.0",

src/utils/macromolecule/types.d.ts

@@ -0,1 +1,2 @@
+import * as DG from 'datagrok-api/dg';
 /** Canonical gap symbol */
@@ -16,2 +17,3 @@ export declare const GAP_SYMBOL: string;
     get splitter(): SplitterFunc;
+    getHelm(seqCol: DG.Column<string>): Promise<DG.Column<string>>;
 }
@@ -18,0 +20,0 @@ export type SeqColStats = {

src/utils/seq-handler.d.ts

 import * as DG from 'datagrok-api/dg';
 import { NOTATION } from './macromolecule';
-import { ISeqSplitted, SeqColStats, SplitterFunc, INotationProvider } from './macromolecule/types';
+import { INotationProvider, ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
@@ -48,2 +48,4 @@ import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
     getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
+    /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
+    getHelm(rowIdx: number): Promise<string>;
     private _stats;
@@ -50,0 +52,0 @@ get stats(): SeqColStats;

src/utils/seq-handler.js

 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { TAGS, ALPHABET, NOTATION, candidateAlphabets, positionSeparator, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, } from './macromolecule';
+import { ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS } from './macromolecule';
 import { GAP_SYMBOL, } from './macromolecule/types';
@@ -226,2 +226,12 @@ import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
     }
+    /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
+    async getHelm(rowIdx) {
+        const seq = this.column.get(rowIdx);
+        if (this.notationProvider) {
+            const helmCol = await this.notationProvider.getHelm(this.column);
+            return helmCol.get(rowIdx);
+        }
+        else
+            return this.convertToHelm(seq);
+    }
     get stats() {
@@ -228,0 +238,0 @@ if (this._stats === null) {

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