@datagrok/sequence-translator 1.2.0 → 1.2.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.2.0",
+  "version": "1.2.1",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"

package/src/plugins/mermade.ts

@@ -6,7 +6,7 @@ import * as DG from 'datagrok-api/dg';
 import {ExternalPluginUI} from '../view/app-ui';
 import {ColoredTextInput} from '../view/utils/colored-input/colored-text-input';
 import {highlightInvalidSubsequence} from '../view/utils/colored-input/input-painters';
-import {codesToHelmDictionary} from '../model/data-loading-utils/json-loader';
+import {codesToSymbolsDictionary} from '../model/data-loading-utils/json-loader';
 import {MERMADE} from './const';
 
 export async function getExternalAppViewFactories(): Promise<{[name: string]: () => DG.View} | undefined> {
@@ -43,6 +43,6 @@ function getMerMadeParameters(): {[name: string]: any} {
 
   return {
     coloredInput: input,
-    codes: codesToHelmDictionary
+    codes: codesToSymbolsDictionary
   }
 }

package/src/tests/formats-support.ts

@@ -5,7 +5,6 @@ import * as DG from 'datagrok-api/dg';
 
 import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 import {DEFAULT_FORMATS} from '../model/const';
-import {FormatConverter} from '../model/format-translation/format-converter';
 import {getJsonData} from '../model/data-loading-utils/json-loader';
 import {formatsToHelm} from './const';
 import {SequenceValidator} from '../model/parsing-validation/sequence-validator';
@@ -34,7 +33,7 @@ category('Formats support', () => {
       const result = Object.keys(output).length;
       // +1 due to nucleotides
       const expected = Object.keys(formatsToHelm).length + 1;
-      expect(result, expected);
+      expect(true, expected <= result);
     });
   });
 });

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

@@ -4,8 +4,6 @@ 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 {DEFAULT_FORMATS} from '../model/const';
-import {FormatConverter} from '../model/format-translation/format-converter';
 import {getNucleotidesSequence} from '../model/format-translation/conversion-utils';
 import {getJsonData} from '../model/data-loading-utils/json-loader';
 import {helmToNucleotides} from './const';

package/src/view/apps/oligo-structure.ts

@@ -9,7 +9,6 @@ import $ from 'cash-dom';
 
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
-// import {drawMolecule} from '../../utils/structures-works/draw-molecule';
 import {highlightInvalidSubsequence} from '../utils/colored-input/input-painters';
 import {getLinkedMolfile, saveSdf} from '../../model/sequence-to-structure-utils/sdf-tab';
 import {ColoredTextInput} from '../utils/colored-input/colored-text-input';
@@ -176,7 +175,8 @@ export class StructureLayoutHandler {
     let molfile = '';
     try {
       const strandData = this.getStrandData();
-      molfile = this.getMolfile(strandData.ss, strandData.as, strandData.as2);
+      if (Object.values(strandData).some((data) => data.strand !== ''))
+        molfile = this.getMolfile(strandData.ss, strandData.as, strandData.as2);
     } catch (err) {
       const errStr = errorToConsole(err);
       console.error(errStr);

package/src/view/utils/molecule-img.ts

@@ -21,6 +21,11 @@ export class MoleculeImage {
   get molblock(): string { return this._validMolBlock; }
 
   set molblock(value: string) {
+    if (value === '') {
+      this._validMolBlock = value;
+      return;
+    }
+
     try {
       this.validateMolBlock(value);
     } catch (error) {