@datagrok/bio 2.4.23 → 2.4.25

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.23",
+  "version": "2.4.25",
   "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/demo/bio01a-hierarchical-clustering-and-sequence-space.ts

@@ -27,7 +27,7 @@ export async function demoBio01aUI() {
 
   try {
     const demoScript = new DemoScript(
-      'Demo',
+      'Sequence Space',
       'Exploring sequence space of Macromolecules, comparison with hierarchical clustering results');
     await demoScript
       .step(`Load DNA sequences`, async () => {

package/src/package.ts

@@ -683,6 +683,7 @@ export function bioSubstructureFilter(): BioSubstructureFilter {
 //meta.demoPath: Bioinformatics | Similarity, Diversity
 //description: Sequence similarity tracking and evaluation dataset diversity
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Similarity,%20Diversity
+//meta.isDemoScript: True
 export async function demoBioSimilarityDiversity(): Promise<void> {
   await demoBio01UI();
 }
@@ -692,6 +693,7 @@ export async function demoBioSimilarityDiversity(): Promise<void> {
 //meta.demoPath: Bioinformatics | Sequence Space
 //description: Exploring sequence space of Macromolecules, comparison with hierarchical clustering results
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Sequence%20Space
+//meta.isDemoScript: True
 export async function demoBioSequenceSpace(): Promise<void> {
   await demoBio01aUI();
 }
@@ -701,6 +703,7 @@ export async function demoBioSequenceSpace(): Promise<void> {
 //meta.demoPath: Bioinformatics | Activity Cliffs
 //description: Activity Cliffs analysis on Macromolecules data
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Activity%20Cliffs
+//meta.isDemoScript: True
 export async function demoBioActivityCliffs(): Promise<void> {
   await demoBio01bUI();
 }
@@ -710,6 +713,7 @@ export async function demoBioActivityCliffs(): Promise<void> {
 //meta.demoPath: Bioinformatics | Atomic Level
 //description: Atomic level structure of Macromolecules
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Atomic%20Level
+//meta.isDemoScript: True
 export async function demoBioAtomicLevel(): Promise<void> {
   await demoBio03UI();
 }
@@ -719,6 +723,7 @@ export async function demoBioAtomicLevel(): Promise<void> {
 //meta.demoPath: Bioinformatics | Helm, MSA, Sequence Space
 //description: MSA and composition analysis on Helm data
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Helm,%20MSA,%20Sequence%20Space
+//meta.isDemoScript: True
 export async function demoBioHelmMsaSequenceSpace(): Promise<void> {
   await demoBio05UI();
 }

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

@@ -44,8 +44,8 @@ export async function multipleSequenceAlignmentUI(options: multipleSequenceAlgin
     let performAlignment: (() => Promise<DG.Column<string>>) | undefined;
 
     // TODO: allow only macromolecule colums to be chosen
-    const colInput = ui.columnInput('Sequence', table, seqCol, () => {
-      performAlignment = onColInputChange(
+    const colInput = ui.columnInput('Sequence', table, seqCol, async () => {
+      performAlignment = await onColInputChange(
         colInput.value, table, inputRootStyles, methodInput, clustersColInput, gapOpenInput, gapExtendInput);
     }
     ) as DG.InputBase<DG.Column<string>>;
@@ -55,7 +55,7 @@ export async function multipleSequenceAlignmentUI(options: multipleSequenceAlgin
     colInput.fireChanged();
     //if column is specified (from tests), run alignment and resolve with the result
     if (options.col) {
-      performAlignment = onColInputChange(
+      performAlignment = await onColInputChange(
         options.col, table, inputRootStyles, methodInput, clustersColInput, gapOpenInput, gapExtendInput);
 
       await onDialogOk(colInput, table, performAlignment, resolve, reject);
@@ -105,7 +105,7 @@ async function onDialogOk(
 }
 
 
-function onColInputChange(
+async function onColInputChange(
   col: DG.Column<string>,
   table: DG.DataFrame,
   inputRootStyles: CSSStyleDeclaration[],
@@ -113,7 +113,7 @@ function onColInputChange(
   clustersColInput: DG.InputBase<DG.Column<any> | null>,
   gapOpenInput: DG.InputBase<number | null>,
   gapExtendInput: DG.InputBase<number | null>
-): (() => Promise<DG.Column<string>>) | undefined {
+): Promise<(() => Promise<DG.Column<string>>) | undefined> {
   try {
     if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
       return;
@@ -136,6 +136,19 @@ function onColInputChange(
 
       return async () => await runPepsea(col, unusedName, methodInput.value!,
           gapOpenInput.value!, gapExtendInput.value!, clustersColInput.value);
+        } 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())
+            return;
+          const helmCol = potentialColNC.convert(NOTATION.HELM);
+          for (const inputRootStyle of inputRootStyles)
+            inputRootStyle.removeProperty('display');
+          console.log(helmCol.toList());
+          // convert to helm and assign alignment function to PepSea
+    
+          return async () => await runPepsea(helmCol, unusedName, methodInput.value!,
+            gapOpenInput.value!, gapExtendInput.value!, clustersColInput.value);
     } else {
       for (const inputRootStyle of inputRootStyles)
         inputRootStyle.display = 'none';