@datagrok/bio 2.4.2 → 2.4.5

package/src/utils/pepsea.ts

@@ -6,18 +6,21 @@ import * as C from './constants';
 
 export const pepseaMethods = ['mafft --auto', 'mafft', 'linsi', 'ginsi', 'einsi', 'fftns', 'fftnsi', 'nwns', 'nwnsi'];
 const alignmentObjectMetaKeys = ['AlignedSeq', 'AlignedSubpeptide', 'HELM', 'ID', 'PolymerID'];
-type PepseaRepsonse = {
+type PepseaResponse = {
   Alignment: {
     PolymerID: string, AlignedSubpeptide: string, HELM: string, ID: string, AlignedSeq: string, [key: string]: string,
   }[],
-  AlignmentScore: {[key: string]: number | null},
+  AlignmentScore: { [key: string]: number | null },
 };
-type PepseaBodyUnit = {ID: string, HELM: string};
+type PepseaBodyUnit = { ID: string, HELM: string };
 
+/** Gets the column containing MSA sequences produced by the 'PepSeA' tool from the {@link srcCol} column.
+ * Does not add the result column to the dataframe of {@link srcCol}.
+ */
 export async function runPepsea(srcCol: DG.Column<string>, unUsedName: string,
   method: typeof pepseaMethods[number] = 'ginsi', gapOpen: number = 1.53, gapExtend: number = 0.0,
   clustersCol: DG.Column<string | number> | null = null,
-  ): Promise<DG.Column<string>> {
+): Promise<DG.Column<string>> {
   const peptideCount = srcCol.length;
   clustersCol ??= DG.Column.int('Clusters', peptideCount).init(0);
   if (clustersCol.type != DG.COLUMN_TYPE.STRING)
@@ -58,13 +61,14 @@ export async function runPepsea(srcCol: DG.Column<string>, unUsedName: string,
   alignedSequencesCol.setTag(bioTAGS.separator, C.PEPSEA.SEPARATOR);
   alignedSequencesCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
   alignedSequencesCol.setTag(bioTAGS.alphabet, ALPHABET.UN);
+  alignedSequencesCol.setTag(bioTAGS.alphabetIsMultichar, 'true');
   alignedSequencesCol.semType = DG.SEMTYPE.MACROMOLECULE;
 
   return alignedSequencesCol;
 }
 
 async function requestAlignedObjects(dockerfileId: string, body: PepseaBodyUnit[], method: string, gapOpen: number,
-  gapExtend: number): Promise<PepseaRepsonse> {
+  gapExtend: number): Promise<PepseaResponse> {
   const params = {
     method: 'POST',
     headers: {'Accept': 'application/json', 'Content-Type': 'application/json'},

package/tsconfig.json

@@ -6,7 +6,7 @@
     // "incremental": true,                         /* Enable incremental compilation */
     "target": "es6",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
     "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
-    "lib": ["es2020", "dom", "ES2021.String"],      /* Specify library files to be included in the compilation. */
+    "lib": ["ES2022", "dom"],      /* Specify library files to be included in the compilation. */
     // "allowJs": true,                             /* Allow javascript files to be compiled. */
     // "checkJs": true,                             /* Report errors in .js files. */
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */