@datagrok/bio 2.4.39 → 2.4.41

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.39",
+  "version": "2.4.41",
   "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",
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.32.1",
+    "@datagrok-libraries/bio": "^5.32.2",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.37",
     "@datagrok-libraries/tutorials": "^1.3.2",

package/src/utils/convert.ts

@@ -17,13 +17,12 @@ let convertDialogSubs: Subscription[] = [];
  * @param {DG.column} col Column with 'Macromolecule' semantic type
  */
 export function convert(col?: DG.Column): void {
-
   let tgtCol = col ?? grok.shell.t.columns.bySemType('Macromolecule')!;
   if (!tgtCol)
     throw new Error('No column with Macromolecule semantic type found');
   let converter = new NotationConverter(tgtCol);
   let currentNotation: NOTATION = converter.notation;
-  const dialogHeader =  ui.divText(
+  const dialogHeader = ui.divText(
     'Current notation: ' + currentNotation,
     {
       style: {
@@ -48,9 +47,11 @@ export function convert(col?: DG.Column): void {
     tgtCol = newCol;
     converter = new NotationConverter(tgtCol);
     currentNotation = converter.notation;
+    if (currentNotation === NOTATION.HELM)
+      separatorInput.value = '/'; // helm monomers can have - in the name like D-aThr;
     dialogHeader.textContent = 'Current notation: ' + currentNotation;
     filteredNotations = notations.filter((e) => e !== currentNotation);
-    targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations);
+    targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations, toggleSeparator);
     toggleSeparator();
     convertDialog?.clear();
     convertDialog?.add(ui.div([
@@ -58,14 +59,13 @@ export function convert(col?: DG.Column): void {
       targetColumnInput.root,
       targetNotationInput.root,
       separatorInput.root
-    ]))
+    ]));
   };
 
   const targetColumnInput = ui.columnInput('Column', grok.shell.t, tgtCol, toggleColumn);
 
   const separatorArray = ['-', '.', '/'];
   let filteredNotations = notations.filter((e) => e !== currentNotation);
-  let targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations);
 
   const separatorInput = ui.choiceInput('Separator', separatorArray[0], separatorArray);
 
@@ -76,6 +76,7 @@ export function convert(col?: DG.Column): void {
     else
       $(separatorInput.root).show();
   };
+  let targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations, toggleSeparator);
 
   // set correct visibility on init
   toggleSeparator();

package/src/utils/multiple-sequence-alignment-ui.ts

@@ -11,7 +11,7 @@ import {_package} from '../package';
 import {multipleSequenceAlginmentUIOptions} from './types';
 import {kalignVersion, msaDefaultOptions} from './constants';
 import '../../css/msa.css';
-import { ColumnInputOptions } from '@datagrok-libraries/utils/src/type-declarations';
+import {ColumnInputOptions} from '@datagrok-libraries/utils/src/type-declarations';
 export class MsaWarning extends Error {
   constructor(message: string, options?: ErrorOptions) {
     super(message, options);
@@ -41,7 +41,7 @@ export async function multipleSequenceAlignmentUI(
     methodInput.setTooltip('Alignment method');
 
     // UI for Kalign alignment
-    const terminalGapInput = ui.floatInput('Terminal gap', options?.kalign?.terminalGap ?? msaDefaultOptions.kalign.terminalGap);
+    const terminalGapInput = ui.floatInput('Terminal gap', options?.kalign?.terminalGap ?? null);
     terminalGapInput.setTooltip('Penalty for opening a gap at the beginning or end of the sequence');
     const kalignVersionDiv = ui.p(`Kalign version: ${kalignVersion}`, 'kalign-version');
 
@@ -51,6 +51,13 @@ export async function multipleSequenceAlignmentUI(
     const gapExtendInput = ui.floatInput('Gap extend', options.pepsea.gapExtend);
     gapExtendInput.setTooltip('Gap extension penalty to skip the alignment');
 
+    const msaParamsDiv = ui.inputs([gapOpenInput, gapExtendInput, terminalGapInput]);
+    const msaParamsButton = ui.button('Alignment parameters', () => {
+      msaParamsDiv.hidden = !msaParamsDiv.hidden;
+    }, 'Adjust alignment parameters such as penalties for opening and extending gaps');
+    msaParamsButton.classList.add('msa-params-button');
+    msaParamsDiv.hidden = true;
+    msaParamsButton.prepend(ui.icons.settings(() => null));
     const pepseaInputRootStyles: CSSStyleDeclaration[] = [methodInput.root.style];
     const kalignInputRootStyles: CSSStyleDeclaration[] = [terminalGapInput.root.style, kalignVersionDiv.style];
 
@@ -84,9 +91,8 @@ export async function multipleSequenceAlignmentUI(
       .add(colInput)
       .add(clustersColInput)
       .add(methodInput)
-      .add(gapOpenInput)
-      .add(gapExtendInput)
-      .add(terminalGapInput)
+      .add(msaParamsDiv)
+      .add(msaParamsButton)
       .add(kalignVersionDiv)
       .onOK(async () => { await onDialogOk(colInput, table, performAlignment, resolve, reject); })
       .show();
@@ -142,9 +148,9 @@ async function onColInputChange(
       [NOTATION.FASTA, NOTATION.SEPARATOR], [ALPHABET.DNA, ALPHABET.RNA, ALPHABET.PT], false)
     ) { // Kalign - natural alphabets. if the notation is separator, convert to fasta and then run kalign
       switchDialog(pepseaInputRootStyles, kalignInputRootStyles, 'kalign');
-      gapOpenInput.value ??= msaDefaultOptions.kalign.gapOpen;
-      gapExtendInput.value ??= msaDefaultOptions.kalign.gapExtend;
-      terminalGapInput.value ??= msaDefaultOptions.kalign.terminalGap;
+      gapOpenInput.value = null;
+      gapExtendInput.value = null;
+      terminalGapInput.value = null;
       const potentialColNC = new NotationConverter(col);
       const performCol: DG.Column<string> = potentialColNC.isFasta() ? col :
         potentialColNC.convert(NOTATION.FASTA);
@@ -161,8 +167,10 @@ async function onColInputChange(
     } else if (checkInputColumnUI(col, col.name, [NOTATION.SEPARATOR], [ALPHABET.UN], false)) {
       //if the column is separator with unknown alphabet, it might be helm. check if it can be converted to helm
       const potentialColNC = new NotationConverter(col);
-      if (!await potentialColNC.checkHelmCompatibility())
+      if (!await potentialColNC.checkHelmCompatibility()) {
+        switchDialog(pepseaInputRootStyles, kalignInputRootStyles, 'pepsea');
         return;
+      }
       const helmCol = potentialColNC.convert(NOTATION.HELM);
       switchDialog(pepseaInputRootStyles, kalignInputRootStyles, 'pepsea');
       gapOpenInput.value ??= msaDefaultOptions.pepsea.gapOpen;
@@ -172,6 +180,9 @@ async function onColInputChange(
       return async () => await runPepsea(helmCol, unusedName, methodInput.value!,
             gapOpenInput.value!, gapExtendInput.value!, clustersColInput.value);
     } else {
+      gapOpenInput.value = null;
+      gapExtendInput.value = null;
+      terminalGapInput.value = null;
       switchDialog(pepseaInputRootStyles, kalignInputRootStyles, 'kalign');
       return;
     }