jbrowse-plugin-msaview 2.5.1 → 2.5.2

package/dist/utils/ncbiDomains.js

@@ -73,7 +73,9 @@ function parseFeature(featureXml) {
             : noteName || quals.site_type || 'site';
         const accession = isDomain ? cddId : `${cddId}:${name}`;
         return {
-            signature: { entry: { name, description: quals.note ?? name, accession } },
+            signature: {
+                entry: { name, description: quals.note ?? name, accession },
+            },
             locations: [span],
         };
     }

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.5.1";
+export declare const version = "2.5.2";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.5.1';
+export const version = '2.5.2';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.5.1",
+  "version": "2.5.2",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -21,37 +21,37 @@
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",
     "react-msaview": "^5.4.1",
-    "swr": "^2.4.1"
+    "swr": "^2.4.2"
   },
   "devDependencies": {
     "@emotion/react": "^11.14.0",
     "@eslint/js": "^10.0.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
     "@jbrowse/core": "^4.3.0",
-    "@jbrowse/mobx-state-tree": "^5.10.8",
+    "@jbrowse/mobx-state-tree": "^5.11.1",
     "@jbrowse/plugin-linear-genome-view": "^4.3.0",
     "@mui/icons-material": "^7.3.11",
     "@mui/material": "^7.3.11",
     "@mui/system": "^7.3.11",
-    "@mui/x-data-grid": "^8.28.7",
-    "@types/node": "^25.9.1",
-    "@types/react": "^19.2.16",
-    "@typescript-eslint/eslint-plugin": "^8.60.1",
-    "@typescript-eslint/parser": "^8.60.1",
-    "esbuild": "^0.28.0",
-    "eslint": "^10.4.1",
-    "eslint-plugin-import-x": "^4.16.2",
+    "@mui/x-data-grid": "^8.29.1",
+    "@types/node": "^25.9.4",
+    "@types/react": "^19.2.17",
+    "@typescript-eslint/eslint-plugin": "^8.62.0",
+    "@typescript-eslint/parser": "^8.62.0",
+    "esbuild": "^0.28.1",
+    "eslint": "^10.5.0",
+    "eslint-plugin-import-x": "^4.17.0",
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.1.1",
     "eslint-plugin-unicorn": "^64.0.0",
-    "mobx": "^6.15.4",
+    "mobx": "^6.16.1",
     "mobx-react": "^9.2.2",
     "msa-parsers": "5.4.1",
     "pixelmatch": "^7.2.0",
     "pngjs": "^7.0.0",
-    "prettier": "^3.8.3",
+    "prettier": "^3.8.4",
     "pretty-bytes": "^7.1.0",
-    "puppeteer": "^25.1.0",
+    "puppeteer": "^25.2.1",
     "react": "^19.2.7",
     "react-dom": "^19.2.7",
     "rimraf": "^6.1.3",
@@ -59,8 +59,8 @@
     "serve": "^14.2.6",
     "tss-react": "^4.9.21",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.60.1",
-    "vitest": "^4.1.8"
+    "typescript-eslint": "^8.62.0",
+    "vitest": "^4.1.9"
   },
   "scripts": {
     "clean": "rimraf dist",

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -282,46 +282,71 @@ export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
   }
 }
 
+/**
+ * Mirror a connected 3D protein view's hovered residue onto the MSA's
+ * highlighted columns. Returns the autorun body and keeps a flag tracking
+ * whether the current highlight was set by THIS sync: when a protein hover ends
+ * we restore the declarative highlightColumns seed (or clear) rather than
+ * blindly wiping it.
+ *
+ * Without the flag this autorun fires once on creation — with the view connected
+ * to a *genome* LGV but no 3D protein structure attached — computes zero columns,
+ * and calls setHighlightedColumns(undefined), clobbering the seed that
+ * MSAModelF.afterCreate just set from the declarative `highlightColumns`. That is
+ * the bug that made the BRAF/TP53 genome-browser links open with no V600/R248
+ * column lit (SRC has no highlightColumns, so nothing was there to wipe).
+ */
 export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
-  const { connectedViewId, transcriptToMsaMap, querySeqName } = self
+  let proteinDriven = false
+  return () => {
+    const { connectedViewId, transcriptToMsaMap, querySeqName } = self
 
-  if (!connectedViewId || !transcriptToMsaMap) {
-    return
-  }
+    if (!connectedViewId || !transcriptToMsaMap) {
+      return
+    }
 
-  const columns = new Set<number>()
+    const columns = new Set<number>()
 
-  for (const view of getProteinViews(getSession(self).views)) {
-    for (const structure of view.structures) {
-      if (structure.connectedViewId !== connectedViewId) {
-        continue
-      }
+    for (const view of getProteinViews(getSession(self).views)) {
+      for (const structure of view.structures) {
+        if (structure.connectedViewId !== connectedViewId) {
+          continue
+        }
 
-      const highlights = structure.hoverGenomeHighlights
-      if (!highlights || highlights.length === 0) {
-        continue
-      }
+        const highlights = structure.hoverGenomeHighlights
+        if (!highlights || highlights.length === 0) {
+          continue
+        }
 
-      const { g2p } = transcriptToMsaMap
-      for (const highlight of highlights) {
-        for (let coord = highlight.start; coord < highlight.end; coord++) {
-          const proteinPos = g2p[coord]
-          if (proteinPos !== undefined) {
-            const col = self.seqPosToGlobalCol(querySeqName, proteinPos)
-            columns.add(col)
+        const { g2p } = transcriptToMsaMap
+        for (const highlight of highlights) {
+          for (let coord = highlight.start; coord < highlight.end; coord++) {
+            const proteinPos = g2p[coord]
+            if (proteinPos !== undefined) {
+              const col = self.seqPosToGlobalCol(querySeqName, proteinPos)
+              columns.add(col)
+            }
           }
         }
       }
     }
-  }
-
-  const visibleColumns = Array.from(columns)
-    .map(col => self.globalColToVisibleCol(col))
-    .filter((col): col is number => col !== undefined)
 
-  self.setHighlightedColumns(
-    visibleColumns.length > 0 ? visibleColumns : undefined,
-  )
+    const visibleColumns = Array.from(columns)
+      .map(col => self.globalColToVisibleCol(col))
+      .filter((col): col is number => col !== undefined)
+
+    if (visibleColumns.length > 0) {
+      self.setHighlightedColumns(visibleColumns)
+      proteinDriven = true
+    } else if (proteinDriven) {
+      // our protein-hover highlight ended — fall back to the declarative seed
+      // instead of wiping a column the URL/user asked to keep lit
+      self.setHighlightedColumns(
+        self.highlightColumns?.length ? self.highlightColumns : undefined,
+      )
+      proteinDriven = false
+    }
+  }
 }
 
 export function runCleanup() {

package/src/MsaViewPanel/model.ts

@@ -471,7 +471,6 @@ export default function stateModelFactory() {
           highlightConnectedStructures,
           autoConnectStructures,
           autoLoadProteinDomains,
-          observeProteinHighlights,
         ]) {
           addDisposer(
             self,
@@ -480,7 +479,10 @@ export default function stateModelFactory() {
             }),
           )
         }
+        // these two keep per-reaction state across runs (a "did I set it?" flag),
+        // so they're factories returning the autorun body rather than plain fns
         addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)))
+        addDisposer(self, autorun(observeProteinHighlights(self)))
       },
     }))
 }

package/src/utils/domainCache.ts

@@ -26,8 +26,7 @@ export async function getCachedDomains(accessions: string[]) {
   const tx = db.transaction(STORE_NAME, 'readonly')
   const results = await Promise.all(
     accessions.map(
-      accession =>
-        tx.store.get(accession) as Promise<CachedDomain | undefined>,
+      accession => tx.store.get(accession) as Promise<CachedDomain | undefined>,
     ),
   )
   await tx.done

package/src/utils/ncbiDomains.ts

@@ -83,7 +83,9 @@ function parseFeature(featureXml: string): DomainMatch | undefined {
       : noteName || quals.site_type || 'site'
     const accession = isDomain ? cddId : `${cddId}:${name}`
     return {
-      signature: { entry: { name, description: quals.note ?? name, accession } },
+      signature: {
+        entry: { name, description: quals.note ?? name, accession },
+      },
       locations: [span],
     }
   }

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.5.1'
+export const version = '2.5.2'